Syngistix 2.2 For ICP MS Software Guide

Syngistix™ Software for ICP-MS v.2.
2
Software Reference Guide
April 2017
Release History
Release Publication Date
Syngistix for ICP-MS software release April 2014
Syngistix for ICP-MS software Enhanced Security March 2015

release
Syngistix for ICP-MS software 2.0 October 2016
Syngistix for ICP-MS software 2.1 to support 2000 HW January 2017
Syngistix for ICP-MS software 2.2 to support April 2017

ES and Win10 content
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Shelton, CT 06484-4794
U.S.A.
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Shelton, CT 06484 USA
is ISO 9001 registered.
© 2017 edition PerkinElmer, Inc. PKI.
Documentation produced in Canada.
Software release date: April 2017
Syngistix for ICP-MS Software Reference Guide compiled April 11, 2017: DPS
Table of Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Using this Software Reference Guide . . . . . . . . . . . . . . . . . . . . . . . .15
Additional Assistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Using the Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Contents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
To perform a search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Favorites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Chapter 1 Introduction to the Software . . . . . . . . . . . . . . . . . . . . .19

Supported Instrument Configurations. . . . . . . . . . . . . . . . . . . . . . . . .19
NexION® 2000 Series . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
NexION® 2000B Base UCT Instrument. . . . . . . . . . . . . . . . . . . . . .20
NexION® 2000C Core UCT Instrument . . . . . . . . . . . . . . . . . . . . . .20
NexION® 2000P Productivity UCT Instrument . . . . . . . . . . . . . . . .21
NexION® 2000S SEMI UCT Instrument . . . . . . . . . . . . . . . . . . . . .21
NexION® 300/350 Series . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
NexION® 300/350Q Basic Quadrupole Instruments . . . . . . . . . . . .22
NexION® 300/350X UCT Instruments . . . . . . . . . . . . . . . . . . . . . . .22
NexION® 300/350D UCT Instruments . . . . . . . . . . . . . . . . . . . . . . .22
NexION® 300/350S UCT Instruments . . . . . . . . . . . . . . . . . . . . . . .22
Software Layout and Organization . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Screen Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Navigating the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
File Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
The Elemental Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Multiple Software Sessions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Understanding Acquisition Profiles. . . . . . . . . . . . . . . . . . . . . . . . . . .31
Acquisition order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Flexible profile and parameter configuration. . . . . . . . . . . . . . . . . . . . . . 32
Sample Acquisition Profile tileset . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Syngistix Options System Configuration . . . . . . . . . . . . . . . . . . . . . .34
Syngistix Options Dialog Box Tabs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Configuration tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Items on the Configuration tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Acquisition Profiles tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Items on the Acquisition Profiles tab . . . . . . . . . . . . . . . . . . . . . . . .38
New Profile Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Peristaltic Pump Defaults tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Default Peristaltic Pump parameters . . . . . . . . . . . . . . . . . . . . . . . .40
Performance Check Defaults tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Performance Check Benchmarks — Default Factory Values . . . . .42
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Startup and Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
Starting the Software and Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3
To start the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

To start the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
To start the instrument after an extended shutdown . . . . . . . . . . . 45
Ignition Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Argon Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Cooling System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Torch and Sample Introduction System . . . . . . . . . . . . . . . . . . . . . 47
Organic Solvents and Vapors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Shutting Down the Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
To shut down the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
To exit the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Task Scheduler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Scheduler Panel Software Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Items on the Scheduler panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Review Files Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Review Files Dialog Box Software Reference. . . . . . . . . . . . . . . . . . . . 50
Items on the Review Files dialog box . . . . . . . . . . . . . . . . . . . . . . . 51
Chapter 2 Instrument and Device Control . . . . . . . . . . . . . . . . . . . 53

System Performance Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Control screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
System View panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Items on the System View panel . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Diagnostics Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Items in the Diagnostics table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Maintenance Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Items on the Maintenance tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Items on the Add Maintenance Reminder dialog box . . . . . . . . . . . 58
Torch Position tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Items on the Torch Position tab . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Device and Instrument Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
Devices Panel Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
ICP-MS Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Items on the ICP-MS Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Pump Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Items on the Pump Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Autosampler Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Items on the Autosampler Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
FIAS Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
PC3 Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
System Status panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Instrument Diagnostics Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Items on the Instrument Diagnostics panel. . . . . . . . . . . . . . . . . . . 69
Getter Regeneration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Chapter 3 Enhanced Security™ Software Administration . . . . . . 73
Introduction to the Syngistix™ for ICP-MS
Enhanced Security™ software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Key features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Security. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Traceability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Integrity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
4 Document controlled under U.S. Export Administration regulations. Unauthorized copy, disclosure, or use prohibited.
Table of Contents
Getting Started — Administrator’s guide . . . . . . . . . . . . . . . . . . . . . .75

Windows tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
ES software tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Logging in for the first time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
To log into Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
To log into Syngistix™ ES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Running as an Administrator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
To run the software and utilities as an administrator . . . . . . . . . . . .77
Overview of the ES Setup Utility. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
To log into the ES Setup utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Selecting Enhanced Security features . . . . . . . . . . . . . . . . . . . . . . . . . . 78
To select your ES features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Setting up and managing users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
To set up a new Enhanced Security user . . . . . . . . . . . . . . . . . . . .80
To edit a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
To delete a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
To unlock a user. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
To set up a new Enhanced Security user in Windows . . . . . . . . . . .84
Setting up and managing groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
To add a group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
To assign users to groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
To edit a group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
To delete a group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
Creating and managing project folders. . . . . . . . . . . . . . . . . . . . . . . . . . 88
To add a project folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
To assign project folders to users . . . . . . . . . . . . . . . . . . . . . . . . . .89
To reassign project folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
To delete a project folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
To enable the auditing of file deletion inside project folders . . . . . .90
Viewing a summary of your security settings . . . . . . . . . . . . . . . . . . . . . 91
To view a summary of your security settings . . . . . . . . . . . . . . . . . .91
Managing password settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
To specify password settings for users . . . . . . . . . . . . . . . . . . . . . .92
Defining signature points and challenge reasons . . . . . . . . . . . . . . . . . . 94
To define signature points and challenge reasons for user operations
94
Understanding challenge dialog boxes. . . . . . . . . . . . . . . . . . . . . . . . . . 96
Overview of the ES Tools Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
To open the ES Tools window . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Running ES Tools as an Administrator. . . . . . . . . . . . . . . . . . . . . . . . . . 99
To run ES Tools as an administrator . . . . . . . . . . . . . . . . . . . . . . . .99
Managing audit trails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100
Managing the Syngistix™ Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . 100
To view and refine Syngistix ES software user workflow events . .100
Managing the security audit trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
To view ES system login events . . . . . . . . . . . . . . . . . . . . . . . . . .103
To view ES system administrative events . . . . . . . . . . . . . . . . . . .104
Managing the file history. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
To view the File History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
To perform review and version control functions in the File History. . .
107
Understanding the Review, Approve, and Reject functions . . . . . . . . . 107
To show differences between two versions of a file . . . . . . . . . . . .109
Document controlled under U.S. Export Administration regulations. Unauthorized copy, disclosure, or use prohibited. 5
Repairing and compacting the databases. . . . . . . . . . . . . . . . . . . . . . 109

To repair and compact the databases . . . . . . . . . . . . . . . . . . . . . 110
Archiving system data and audit files . . . . . . . . . . . . . . . . . . . . . . . . . 110
To archive system data and audit files . . . . . . . . . . . . . . . . . . . . . 111
Restoring archived data and audit files . . . . . . . . . . . . . . . . . . . . . . . . 112
To restore archived data and audit files . . . . . . . . . . . . . . . . . . . . 112
Chapter 4 Optimization Processes . . . . . . . . . . . . . . . . . . . . . . . . 115

Optimizing and Calibrating the Instrument . . . . . . . . . . . . . . . . . . . .115
The SmartTune™ Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .115
The SmartTune™ Express Optimization Tool. . . . . . . . . . . . . . . . . . . 116
The Syngistix Options Performance Check Defaults tab . . . . . . . 116
The SmartTune™ Manual Optimization Tool . . . . . . . . . . . . . . . . . . . 117
The SmartTune™ Manual Pre-defined Files. . . . . . . . . . . . . . . . . . . . 117
Daily Optimization Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Monthly Optimization Process . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Full Optimization Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
SmartTune™ Manual Optimization Procedures . . . . . . . . . . . . . . . . . 117
When to Perform SmartTune™ Manual Optimization Procedures . . . 123
SmartTune™ Software Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
SmartTune™ Setup Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
SmartTune Common Optimization controls . . . . . . . . . . . . . . . . . 128
SmartTune Manual Common Procedure parameters. . . . . . . . . . 131
SmartTune™ Results Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
SmartTune Results panel controls . . . . . . . . . . . . . . . . . . . . . . . . 132
Conditions screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132
QID Tabs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Items on the QID Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Dual Detector Calibration Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Items on the Dual Detector Calibration Tab . . . . . . . . . . . . . . . . . 135
Manual Adjust Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Items on the Manual Adjust Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Parameters in the Manual Adjust Table . . . . . . . . . . . . . . . . . . . 138
Advanced Optimize Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Items on the Advanced Optimize Tab. . . . . . . . . . . . . . . . . . . . . . 139
Cell Parameters Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Items on the Cell Parameters Tab . . . . . . . . . . . . . . . . . . . . . . . . 141
Custom Mass Calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143
Mass Calibration Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
DAC Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Calibration Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Mass Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Resolution Check or Adjustment . . . . . . . . . . . . . . . . . . . . . . . . . 144
Deadtime Corrections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Deadtime Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Mass Calibration panel Software Reference. . . . . . . . . . . . . . . . . . . . 145
Items on the Mass Calibration panel . . . . . . . . . . . . . . . . . . . . . . 145
LogBook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147
LogBook screen Software Reference . . . . . . . . . . . . . . . . . . . . . . . . . 148
Main LogBook panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Items on the Syngistix LogBook panel . . . . . . . . . . . . . . . . . . . . . 149
Instrument Parameters panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Table of Contents
Items on the Instrument Parameters panel Conditions tab . . . . . .150

Parameters in the MassCal table . . . . . . . . . . . . . . . . . . . . . . . . . .150
Items on the Instrument Parameters panel Diagnostics tab . . . . .151
Statistics panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Chapter 5 Method Development . . . . . . . . . . . . . . . . . . . . . . . . . .153

Modes of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .153
Standard Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
KED Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
DRC™ Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Mode Application Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Analytical Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .155
Quantitative Analysis Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
TotalQuant™ III Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Isotope Dilution Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Autodilution Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .157
Autodilution Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .157
Isotope Ratio Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Data Only Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Fundamentals of Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . .159
Mass Discrimination and Spectral Scanning . . . . . . . . . . . . . . . . . . . . 160
Peak Hop Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Scanning: Data Acquisition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Signal Profile and Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Transient Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .164
Spectral Peak Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Signal Profile Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Fundamentals of Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .168
Calibration in Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
External Standardization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169
Standard Addition Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . .169
Addition Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .171
Calibration in TotalQuant™ Methods . . . . . . . . . . . . . . . . . . . . . . . . . . 171
External Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .171
Sample Addition Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .173
Internal Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Method Panel Software Reference . . . . . . . . . . . . . . . . . . . . . . . . .175
Method Panel Tabs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Timing Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Items on the Timing Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .176
Periodic Table Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .182
Processing Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Items on the Processing Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183
Equation Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Items on the Equation Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .186
Calibration Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Items on the Calibration Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . .188
Parameters in the Calibration Table. . . . . . . . . . . . . . . . . . . . . . . .189
Sampling Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Items on the Sampling Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
Parameters in the Sampling Table . . . . . . . . . . . . . . . . . . . . . . . . .194
Report Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Items on the Report Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Notes Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Chapter 6 Interference Correction . . . . . . . . . . . . . . . . . . . . . . . . 197

Interferences in ICP-MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .197
Matrix Interferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Spectral Interferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Isobaric Overlaps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Plasma-Induced Polyatomic Ions . . . . . . . . . . . . . . . . . . . . . . . . . 198
Matrix Solvent-Induced Polyatomic Ions. . . . . . . . . . . . . . . . . . . . 199
Matrix-Induced Polyatomic Ions . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Dissolved Solids Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Interference Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .200
Interference Correction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .200
Operating Modes and Interference Correction . . . . . . . . . . . . . . . . . . 200
Corrections in Quantitative Analysis, Isotope Ratio, and Isotope Dilution
Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Corrections in TotalQuant™ Analyses . . . . . . . . . . . . . . . . . . . . . 201
Interference Correction: Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Correcting for Spectral Overlap (Quantitative) . . . . . . . . . . . . . . . 202
Detector Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Corrections for Polyatomic Species (Quantitative) . . . . . . . . . . . . 203
Corrections for Spectral Overlap and Polyatomic Interferences
(Quantitative) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Isotope Selection (TotalQuant™ Methods). . . . . . . . . . . . . . . . . . 204
Spectral Overlap (TotalQuant™ Analyses) Corrections . . . . . . . . 204
Chapter 7 Sampling Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

FIAS™ Sampling Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .207
FIAS™ Program Example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Method Panel Devices FIAS Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Items on the Devices FIAS Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Control screen Devices panel FIAS tab . . . . . . . . . . . . . . . . . . . . . . . 210
Chapter 8 Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

Quality Control Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .213
Quality Control Workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Basic QC parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
QC Software Conventions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Quality Control Software Reference. . . . . . . . . . . . . . . . . . . . . . . . .216
Common Information and Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Calibration Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Items on the Calibration Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
QC Standards Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
Items on the QC Standards Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 223
QC Measurement Frequency Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Items on the QC Measurement Frequency Tab . . . . . . . . . . . . . . 225
QC Std Internal Standards Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Items on the QC Standard Internal Standards Tab . . . . . . . . . . . 227
Calibration Standards Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Items on the QC Calibration Standards Tab. . . . . . . . . . . . . . . . . 228
Table of Contents
Sample Internal Standards Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

Items on the Sample Internal Standards Tab. . . . . . . . . . . . . . . . .228
Sample Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Items on the Sample Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .230
Spike Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Items on the Spike Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .231
Dilution Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Items on the Dilution Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .233
Duplicate Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
Items on the Duplicate Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .234
Spike Tables Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Items on the Spike Tables Tab . . . . . . . . . . . . . . . . . . . . . . . . . . .235
QC Action Controls Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Items on the QC Action Controls Tab . . . . . . . . . . . . . . . . . . . . . .236
Autosampler Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
Items on the Autosampler Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . .238
Chapter 9 Sample Preparation and Analysis . . . . . . . . . . . . . . . .239

Sample Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .239
Files Required During an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
Analysis Order for UCT™ Instruments . . . . . . . . . . . . . . . . . . . . . . . . . 241
Sample Files Created using a Text Editor . . . . . . . . . . . . . . . . . . . .241
Sample file format. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Sample Text File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Sample Panel Software Reference . . . . . . . . . . . . . . . . . . . . . . . . .244
Sample Panel Manual Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Items on the Sample Panel Manual Tab . . . . . . . . . . . . . . . . . . . .244
Sample Panel Batch Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Items on the Sample Panel Batch Tab. . . . . . . . . . . . . . . . . . . . . .245
Items in the Batch Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .246
Items in the Run List Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . .248
Measurement Status Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Items in the Measurement Status Dialog Box . . . . . . . . . . . . . . . .250
Chapter 10 Data Reprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . .253

Previously Acquired Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253
Dataset File Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Data Reprocessing Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Data and Parameter Considerations During Reprocessing . . . . . . . . . 255
Files Required for Reprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Dataset and Reprocessing Software . . . . . . . . . . . . . . . . . . . . . . . .257
Colors Used in the Dataset Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Items in the Dataset Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Chapter 11 Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .261

Reporter™ Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .261
Report Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .262
Raw and Net intensities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Reported Shutdown Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Current Sample tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Current Sample Report Example . . . . . . . . . . . . . . . . . . . . . . . . . .265
Raw Intensities tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
Net Intensities tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Concentrations tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Unfactored Concentrations tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Internal Standards tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Blanks and normalization factors . . . . . . . . . . . . . . . . . . . . . . . . . 272
QC tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Enhanced Security Report View functions . . . . . . . . . . . . . . . . . . . . . 275
Report View common controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
Advanced Report View Display Options dialog box . . . . . . . . . . . . . . 278
Advanced dialog box controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
Calibration Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Calibration panel controls and indicators . . . . . . . . . . . . . . . . . . . . . . 281
Report Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .282
Report Options Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Report Appearance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Report Options Template Example . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Report Options Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Report Options for Sections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Report Options for Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Selected Fields for Isotope Ratio Methods . . . . . . . . . . . . . . . . . . 284
Summary Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287
Summary Report after a Realtime Batch Analysis . . . . . . . . . . . . . . . 287
Summary Report after Reprocessing a Batch Analysis . . . . . . . . . . . 287
Intensity versus Time Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287
Exporting Current Sample Reports . . . . . . . . . . . . . . . . . . . . . . . . .288
Chapter 12 Graphic Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Graphic Displays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .289
Graphics Display Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Realtime Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Items in the Realtime Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Realtime Graphics Options Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . 292
Items in the Realtime Options Dialog Boxes . . . . . . . . . . . . . . . . 293
Analyte Display Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 294
Interactive Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Items in the Interactive Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Interactive Graphics Options Dialog Boxes. . . . . . . . . . . . . . . . . . . . . 298
Items in the Interactive Graphics Options Dialog Boxes. . . . . . . . 299
Composite Signal and Spectral Options . . . . . . . . . . . . . . . . . . . . . . . 301
Items in the Composite Signal and Spectral Graphics Options Dialog
Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
Cell Parameter Optimize Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
Calibration View Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303
Items on the Calibration View panel . . . . . . . . . . . . . . . . . . . . . . . 304
Appendix A Diagnostics Message Reference . . . . . . . . . . . . . . . 305

Diagnostics Fault and Status Code Reference . . . . . . . . . . . . . . . .305
Complete Diagnostics Parameter Reference . . . . . . . . . . . . . . . . . .324
Appendix B Nano Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
Nano Application for Syngistix™ ICP-MS Software . . . . . . . . . . . . .345
Table of Contents
Understanding Nanoparticle Analyses . . . . . . . . . . . . . . . . . . . . . . . . . 345

Nano App Software Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . .346
Analysis Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
Sample Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . .348
Items on the Sample Tab Acquisition Panel . . . . . . . . . . . . . . . . .348
TE Tab Acquisition Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .349
Items on the TE Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . .349
Batch Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . .351
Items on the Batch Tab Acquisition Panel . . . . . . . . . . . . . . . . . . .351
Advanced Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . .352
Items on the Advanced Options Dialog Box. . . . . . . . . . . . . . . . . .352
Method Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
Items on the Method Panel Parameters Tab . . . . . . . . . . . . . . . . .353
Items on the Method Panel Calibration Tab . . . . . . . . . . . . . . . . . .355
Items on the Method Panel Pump Settings Tab. . . . . . . . . . . . . . .356
Calibration Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
Items on the Calibration Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . .357
Realtime Signal Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Realtime Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360
Items on the Realtime Histogram Panel. . . . . . . . . . . . . . . . . . . . .360
Results Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
File Options Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
Items on the File Options Panel . . . . . . . . . . . . . . . . . . . . . . . . . . .362
Parameters Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363
Items on the Parameters Panel . . . . . . . . . . . . . . . . . . . . . . . . . . .363
Calibrations Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
Items on the Calibrations Panel . . . . . . . . . . . . . . . . . . . . . . . . . . .364
Results Table Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
Items on the Results Table Panel . . . . . . . . . . . . . . . . . . . . . . . . .365
Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366
Items on the Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . .366
Appendix C Single Cell Application . . . . . . . . . . . . . . . . . . . . . . .369

Single Cell Application for Syngistix™ ICP-MS Software. . . . . . . . .369
Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Optimizing the System for Cell Survival . . . . . . . . . . . . . . . . . . . . . . . . 370
Understanding Transport Efficiency . . . . . . . . . . . . . . . . . . . . . . . .370
Running Single Cell Analyses in DRC mode . . . . . . . . . . . . . . . . . . . . 370
Single Cell App Software Reference . . . . . . . . . . . . . . . . . . . . . . . .371
Analysis Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
Sample Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . .372
Items on the Sample Tab Acquisition Panel . . . . . . . . . . . . . . . . .372
TE Tab Acquisition Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .373
Items on the TE Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . .373
Batch Tab Acquisition Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . .375
Items on the Batch Tab Acquisition Panel . . . . . . . . . . . . . . . . . . .375
Advanced Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . .376
Items on the Advanced Options Dialog Box. . . . . . . . . . . . . . . . . .376
Method Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377
Items on the Method Panel Parameters Tab . . . . . . . . . . . . . . . . .377
Items on the Method Panel Calibration Tab . . . . . . . . . . . . . . . . . .379
Items on the Method Panel Pump Settings Tab . . . . . . . . . . . . . . 380

Calibration Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Items on the Calibration Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Realtime Signal Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Realtime Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Items on the Realtime Histogram Panel . . . . . . . . . . . . . . . . . . . . 383
Results Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
File Options Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
Items on the File Options Panel . . . . . . . . . . . . . . . . . . . . . . . . . . 386
Parameters Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Items on the Parameters Panel . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Calibrations Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
Items on the Calibrations Panel . . . . . . . . . . . . . . . . . . . . . . . . . . 388
Results Table Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
Items on the Results Table Panel. . . . . . . . . . . . . . . . . . . . . . . . . 389
Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390
Items on the Histogram Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . 390
Appendix D Calculations & Algorithms . . . . . . . . . . . . . . . . . . . . 393

Slope, Intercept, Standard Deviation and Correlation Coefficient
algorithms for software calibration regressions . . . . . . . . . . . . . . . .393
Simple Linear Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
The slope and intercept are calculated as follows . . . . . . . . . . . . 394
The standard deviation of the slope and intercept are calculated as
follows: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
The correlation coefficient is calculated as follows: . . . . . . . . . . . 394
Linear Through Zero Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395
The slope is calculated as follows: . . . . . . . . . . . . . . . . . . . . . . . . 395
The standard deviation of the slope is calculated as follows: . . . . 395
Weighted Linear Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395
The slope and intercept are calculated as follows: . . . . . . . . . . . . 395
The standard deviation of the slope and intercept are calculated as
follows: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395
Isotope Ratio Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .396
Correction Factor Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396
Isotope Ratio Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396
Precision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Standard Deviation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Standard Addition Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . .398
Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
Case 1: Blank subtracted before internal standard. . . . . . . . . . . . 398
Case 2: Blank subtracted after internal standard . . . . . . . . . . . . . 398
Case 3: No internal standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
Concentration and Standard deviation calculation in Standard Addition .
398
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
Preface
This Software Reference Guide contains in-depth conceptual information about
the use of the application software, as well as software reference information
regarding screen components. This guide includes information for multiple
configurations of the NexION® ICP-MS instrument. Except where otherwise
specified, all functions are available for use on all instruments.
Using this Software Reference Guide

The sections in this guide are structured to provide the information needed to
understand the overall operation of the instrument. This includes:
• Procedures for starting and shutting down the instrument and software
• Development of analytical methods
• Calibration, tuning, and optimization
• Information about performing analyses and interpreting results
• Reference information regarding the main software screens and panels,
and their controls
Additional Assistance
The system includes the following documentation and help materials:
• Installation Instructions containing comprehensive installation instructions.
This guide is available in PDF format in the installed program directory.
• A Help System providing task-level information for all software procedures.
This is available from the Syngistix ball menu Help submenu.
• A Maintenance Guide containing a detailed description of the instrument
hardware system, and instructions for installation, maintenance, and
troubleshooting.
• A Consumables and Supplies Reference Guide providing a list of the
cones, solutions, and other consumable items used by the system. This is
available from the Syngistix ball menu Help submenu.
• A Safety Manual providing important notices and warnings to guide you
through the safe operation and maintenance of the instrument.
• A Maintenance Log containing maintenance spreadsheets in PDF format.
15
Using the Help System

Use the help system to access basic and procedural information while you are
working in the software.
On any screen, click the button in the upper right-hand corner of the display,
or, on the Syngistix ball menu, click Help > Syngistix Help to access the full
help system. When working in the software, you can also press F1 at any time to
open a help topic specific to the panel or dialog box in which you are working.
At the top of the Help window is a toolbar for common tasks, such as printing and
going back to the previous page. The tabbed pane on the left provides several
navigational aids to help you find the information you need. The main pane on the
right is where the help topics are displayed.
Contents
The Contents tab arranges help topics by subject, just like the Table of Contents in
a book. Click a book icon to display an overview of the topics in that section. Click
a topic icon to display a particular topic.
Index
Use the Index tab to search the help index for a word. Type the word you want to
look up in the text box and click Display, or click the topic in the alphabetical list.
The chosen topic is displayed.
Search
Use the Search tab to locate a word, phrase, or set of words. The help system
uses boolean, wildcard and nested expressions to refine a search. With the AND,
OR, NOT, and NEAR operators you can precisely define your search by creating a
Preface
relationship between search terms. If no operator is specified, AND is used. For

example, the query “spacing border printing” is equivalent to “spacing AND border
AND printing.”
To search for Use Example Results

More than one term AND baseline AND Topics that contain
in the same topic correction both the words
“baseline” and
“correction”
Either of two terms OR spectrum OR Topics containing
spectra either the word
“spectrum” or the
word “spectra” or
both
The first term NOT peak NOT table Topics containing the
without the second word “peak” but not
term the word “table”
Both terms in the NEAR samples NEAR Topics containing the
same topic, close high word “samples”
together within eight words of
the word “high”
Note: The |, &, and ! characters do not work as boolean operators — you must use OR,
AND, and NOT.
To perform a search
1. Type the words or phrase you want to search for in the text box and click
List Topics. The topics containing the word or phrase are displayed,
including a Rank to help you choose the topic you want to view first.
2. Select a topic from the list and click Display. The topic you have chosen is
displayed in the main panel.
Favorites
Use the Favorites tab to quickly find frequently used help topics. You can store the
current help topic in a Favorites list by clicking Add at the bottom of the Favorites
tab, then return to the topic anytime by double-clicking the title on the tab.
Chapter 1
Introduction to the Software

This section provides a brief overview of the Syngistix™ ICP-MS instrument
control software. It introduces the software layout and configuration, and
describes how to start and stop the system.
Topics in this section include:
• Supported Instrument Configurations on page 19
• Software Layout and Organization on page 23
• Navigating the Software on page 29
• Multiple Software Sessions on page 31
• Syngistix Options System Configuration on page 34
• Startup and Shutdown on page 44
• Task Scheduler on page 48
• Review Files Function on page 50
Supported Instrument Configurations

The NexION instrument is an inductively coupled plasma mass spectrometer that
performs elemental analysis of varied samples. The system consists of a bench-
top ICP-MS instrument, roughing pump, recirculator, cooler, and data acquisition
and analysis software. Instruments equipped with Universal Cell Technology™
(UCT™) functionality may be operated in Dynamic Reaction Cell™ (DRC™)
mode for ultimately low detection limits, or in easy-to-use Kinetic Energy
Discrimination (KED) mode for rapid analysis.
This guide includes information for multiple configurations or variations of the
NexION ICP-MS instrument in both the new 2000 series and the classic 300 &
350 series, so whether you are upgrading from an older version of the software on
an existing instrument, or running a brand new instrument, you can access the
new features in this version of the Syngistix software.
Except where otherwise specified, all functions described in this guide are
available on all instruments:
NexION® 2000 Series

Equipped with Universal Cell Technology™ (UCT™) functionality, all NexION
2000 series instruments may be operated in Standard mode for routine analyses;
Dynamic Reaction Cell™ (DRC™) mode for ultimately low detection limits; or in
easy-to-use Kinetic Energy Discrimination (KED) mode for rapid analysis.
• NexION 2000B instrument—three gas inlets; glass sample introduction
system; nickel cones; SPETEC pump
• NexION 2000C instrument—three gas inlets; glass sample introduction
system; nickel cones; SPETEC pump; PC3 Peltier Cooler; AMS matrix
suppression; broad temperature spray chamber
• NexION 2000P instrument—three gas inlets; glass sample Introduction
system; nickel cones; PC3 Peltier Cooler; AMS matrix suppression; PFA
19
nebulizer; ESI FastValve; ESI micropump; broad temperature spray

chamber
• NexION 2000S instrument—three gas inlets; fixed-torch quartz sample
introduction system; platinum cones; SPETEC pump; PC3 Peltier Cooler;
PFA nebulizer; broad temperature spray chamber; tubular lens
The following table outlines the standard and optional components for the different
available 2000 series models of instrument:
2000B 2000C 2000P 2000S

Base Core Productivity SEMI
Torch cassette Blue Green Black White
Torch Fixed Fixed Demountable Fixed
Injector size 2.0mm 2.5mm 2.0mm 2.0mm
Torch/injector Quartz Quartz Quartz UHP quartz
Nebulizer Glass Glass PFA PFA
Spray chamber Glass Glass with Glass with UHP quartz
matrix port matrix port
PC3 Peltier cooler No Yes Yes Yes
Peristaltic pump PKI PKI ESI with PKI
7 port valve
AMS gas flow No Yes Yes No
NexION® 2000B Base UCT Instrument

The 2000B Base instrument is a robust, high-performance, entry-level system that
performs typical ICP-MS analyses of samples using any of three modes: Standard
(for samples with no significant spectral interferences); KED (for samples with
simple polyatomic interferences); and DRC™ mode (for high-sensitivity elemental
analyses involving complex spectral interferences). The instrument provides
outstanding stability, signal sensitivity, and precision, producing low levels of
oxides and doubly charged ions, and minimal background interference.
The 2000B instrument simplifies ICP-MS by providing an easy-to-use, easy-to-
maintain tool for ultratrace elemental analysis. The 2000B instrument is ideal for
environmental, biomonitoring, geochemical and general testing laboratories with
moderate to heavy loads of samples comprising a wide range of concentrations.
The 2000B instrument incorporates three gas channels—one with a getter purifier
to enable use with ammonia as a reaction cell gas. This facilitates higher
sensitivity and a greater range of interferences corrections using the DRC system.
NexION® 2000C Core UCT Instrument
The 2000C Core instrument is a workhorse system that provides everything in the
Base model and more. For improved matrix suppression and a far-ranging
application profile, the 2000C ICP-MS features a PC3 Peltier Cooler, and an AMS
all-matrix solution and broad temperature spray chamber assembly.
NexION® 2000P Productivity UCT Instrument

For high-throughput labs, the 2000P Productivity model is a superior UCT system
that builds on the functionality of the Core instrument. A PFA nebulizer improves
sensitivity, while an ESI FastValve sample system and micropump lowers the
sample load required and speeds analysis.
NexION® 2000S SEMI UCT Instrument
The 2000S instrument is a UCT ICP-MS manufactured to SEMI conductor
hardware certification standards. It provides the highest precision and sensitivity
for ICP-MS analyses in any of three modes: Standard, KED, and DRC mode.
Using a process called chemical resolution, the 2000S instrument eliminates
plasma-based polyatomic interferences before they reach the quadrupole mass
spectrometer, achieving effective resolution that exceeds what is possible with
other high-resolution designs. As with all the NexION 2000 series instruments, the
2000S system employs Axial Field™ Technology to apply a linearly accelerating
axial field to the DRC system. This technology decreases matrix effects, improves
stability and increases the speed of the DRC system, making the 2000S
instrument the choice for applications requiring high performance in challenging
matrices.
NexION® 300/350 Series

• NexION 300/350Q instrument — Basic quadrupole instrument, glass
sample introduction system, nickel cones
• NexION 300/350X instrument — UCT functionality, single gas inlet, glass
sample introduction system, nickel cones (also available with an optional
second cell gas channel)
• NexION 300/350D instrument — UCT functionality, dual cell gas
channels, getter purifier, glass sample Introduction system, nickel cones
• NexION 300/350S instrument — UCT functionality, dual cell gas
channels, getter purifier, quartz sample introduction system, platinum
cones
NexION® 300/350Q Basic Quadrupole Instruments
The 300/350Q instrument is a robust, single-mode, quadrupole system that
performs typical ICP-MS analyses of samples. The instrument provides
outstanding stability, signal sensitivity, and precision, producing low levels of
oxides and doubly charged ions, and minimal background interference.
The 300/350Q instrument simplifies ICP-MS by providing an easy-to-use, easy-to-
maintain tool for ultratrace elemental analysis. The 300/350Q instrument is ideal
for environmental, biomonitoring, geochemical and general testing laboratories
with moderate to heavy loads of samples comprising a wide range of
concentrations.
NexION® 300/350X UCT Instruments
The 300/350X instrument is an entry-level UCT instrument that performs ICP-MS
analyses using any of three modes: Standard (for samples with no significant
spectral interferences); KED (for samples with simple polyatomic interferences);
and DRC™ mode (for high-sensitivity elemental analyses involving complex
spectral interferences). An optional second cell gas channel may be added.
NexION® 300/350D UCT Instruments
The 300/350D instrument is a superior UCT system that performs ICP-MS
analyses in any of three modes: Standard, KED, and DRC mode.
The 300d/350D instrument builds on the 300/350X system, incorporating two gas
channels — one with a getter purifier to enable use with ammonia as a reaction
cell gas. This facilitates higher sensitivity and a greater range of interferences
corrections using the DRC system.
NexION® 300/350S UCT Instruments
The 300/350S instrument is a UCT ICP-MS manufactured to SEMI conductor
hardware certification standards. It provides the highest precision and sensitivity
for ICP-MS analyses in any of three modes: Standard, KED, and DRC mode.
Using a process called chemical resolution, the 300/350S instrument eliminates
plasma-based polyatomic interferences before they reach the quadrupole mass
spectrometer, achieving effective resolution that exceeds what is possible with
other high-resolution designs. As with all NexION UCT instruments, the 300/350S
system employs Axial Field™ Technology to apply a linearly accelerating axial
field to the DRC system. This technology decreases matrix effects, improves
stability and increases the speed of the DRC system, making the 300/350S
instrument the choice for applications requiring high performance in challenging
matrices.
Software Layout and Organization

Inductively coupled plasma mass spectrometry (ICP-MS) is a multi-element
technique used to accurately measure the concentration of over eighty elements
in a variety of sample matrices. The Syngistix™ ICP-MS software helps you to
optimize system performance and simplify operations while performing complex
ICP-MS determinations.
Most of the operations you perform when working with the instrument are carried
out through the software system. The software controls the primary hardware
components of the NexION® ICP mass spectrometer and the sampling
accessories attached to the system. It also manages the data acquisition process
and performs all analytical calculations.
Screen Components
• Syngistix ball menu: Accessed via the Syngistix ball icon in the upper left
corner of the screen, the Syngistix ball menu provides access to all your
Syngistix software administrative, configuration, and file management
commands. Functions include Workspace management; Event History
access; Service Mode access; Systems Tools; Help, Documentation, and
Video tutorial access; Print functions; and access to the Options
configuration dialog box. Not all functions are available all the time; some
are unavailable during particular processes.
If you are using the Enhanced SecurityTM software, the Set Current Project
Folder command is also available here.
• Measurement Status dialog box: The Measurement Status dialog box
appears onscreen whenever an analysis is in progress. It provides real
time updates on the progress of each individual measurement in the
analysis. See the Measurement Status Dialog Box on page 250.
• Status bar: The status bar displays information such as running mode
(working or service mode), plasma and ignition status, faults, and more.
If you are using the Enhanced SecurityM software, the status bar also
displays, in the bottom right corner, the full name of the user currently
logged into the system.
For UCT instruments, the status bar also displays the profile and analytic
state or mode in which the instrument is operating — Standard, KED, or
DRC mode. When the instrument is in the process of changing mode, the
status bar displays a message describing the change in progress, together
with the time remaining. Operations that cause delays, such as cell gate
changes or cell gas flow changes, also cause status messages to appear.
• Workspaces: In the Syngistix software, a Workspace is a discrete set of
working files and configurations saved together for a particular purpose.
The fileset for a given workspace can be reviewed in the Review dialog
box (see Review Files Dialog Box Software Reference on page 50) and
can include the following files and specifications:
 Method file (.mth)
 Dataset location
 Sample (.sam)
 Report Template (.rop)
 Mass Calibration tuning file (.tun)

 Conditions file (.dac)
 Calibration file (.cal)
 SmartTune optimization file (.swz)
 Polyatomic file (.ply)
• Ribbon menu: The ribbon is located permanently at the top of the screen, and has icons
organized into functional groups placed in an intuitive workflow for performing your daily
analyses. Move your cursor over each option to see a screentip describing its functionality.
Syngistix tab
Instrument group
Icon Function
The Control icon accesses the Control screen, where you start, stop, and
monitor the instrument. This screen also contains the system device controls,
where you manage the manual operations of externally connected sampling
devices; and a subset of the system diagnostics
The Diagnostics icon accesses the Instrument Diagnostics screen, which
displays a more comprehensive Diagnostics view, as well as Sample and Realtime
panels for complete diagnostics and troubleshooting
Optimize group
Icon Function
The SmartTune icon accesses the SmartTune screen, where you optimize
instrument parameters using the SmartTune Express and SmartTune Manual
tools. This view includes SmartTune setup and Results panels, and a Realtime
panel where you can monitor your results
The Conditions icon accesses the Conditions screen, where you view and
adjust optimization information
The arrow submenu provides access to a Mass Calibration view, which displays
MassCal and Realtime panels for controlling the automated spectrometer
hardware tuning process used to adjust mass calibration and resolution
The LogBook icon accesses the LogBook screen, where you can review
performance check data to track or troubleshoot issues or trends in your system
Analyze group
Icon Function
The Method icon accesses the Method screen, where you develop analytical
methods for performing determinations, and set up and manage QC (Quality
Control) parameters. This view includes the Method and Periodic Table panels
The arrow submenu provides controls for managing your method:
Sort — Click to define the order of the analyte entries on the Method panel
Timing tab. When you click this command, a list of sort options appears. To use
this command, click Sort, and then click a sort option
Define Group — Click to define an internal standard group in a quantitative
analysis method. To use this command, select the rows containing the analytes
you want to put into an internal standard group, and click Define Group. A
bracket appears in the Int Std column to indicate that the selected analytes are
now part of an internal standard group. This option is available only for the
Method panel Timing and Calibration tabs
Remove Group — Click to remove an internal standard group from a quantitative
analysis method. To use this command, click any analyte belonging to the group
you want to delete, and click Remove Group. The internal standard group is
deleted and the bracket in the Int Std column is removed. This option is available
only for the Method panel Timing and Calibration tabs
Set Internal Std — Click to specify the analyte that will serve as the internal
standard in an internal standard group. To use this command, you must first
specify an internal standard group using the Define Group command. With an
internal standard group defined, click the analyte that is the internal standard,
then click Set Internal Std. An arrowhead appears in the Int Std column to
indicate that the selected analyte is now designated as an internal standard. This
option is available only for the Method panel Timing and Calibration tabs, for
quantitative analysis methods
The Sample icon accesses the Samples screen, where you enter sample
information and control manual and batch determinations. The Sample screen
contains the Sample panel, as well as instances of the Report View and Realtime
panels, allowing you to monitor your results in graphic and tabular
form as they are run
The Dataset icon accesses the Dataset screen, where determination results are
stored, including method information and operating conditions
Results group
Icon Function
The Reporter icon accesses the Report View screen, where you view detailed
determination results for the current sample, and scrolling data for each sample
in your batch
The arrow submenu provides access to the Report Options screen, where you

define summary report contents and layout
The arrow submenu also provides controls for managing QC (Quality Control)
functions. The following commands are available:
Restart QC ‐‐ Click to restart a quality control analysis that has stopped due to a
QC action
Clear QC Reagent Blank — Click to clear reagent blank data that is stored as part
of a QC analysis
Clear QC Logging Data — Click to clear all QC logging data that is stored with the
dataset
The Realtime icon accesses the Realtime graphics screen, where you can view
the raw data from an acquisition in real time
The Interactive icon accesses the Interactive graphics screen, where you can
view and analyze acquired data
The CalibView icon accesses the Calibration View screen, where you analyze

calibration results
The arrow submenu provides controls for managing calibration functions. The
following commands are available:
Clear Calibration — Click to erase any calibration information that is active in the
Calibration View panel and which will be used in any determinations or
reprocessing calculations
Clear Blank — Click to clear any signal data that is stored for the sample blank
Clear Calibration and Blank — Click to clear both calibration information and
blank reading data that would be used in completing a determination or
performing reprocessing
Workflow group
Icon Function
The Scheduler icon accesses the Scheduler screen, where you manage and
run routine tasks. Use the scheduler function to set up an automated run list of
daily tasks
The Review icon accesses the Review Files dialog box, where you load and

save all of the basic files required to support your analyses
Click to review all the active files to be used in an analysis. The Review Files
dialog box lists all the files related to the active or most recently active
workspace
Applications tab
Icon Function
The Nano App icon opens the Nano App software. Available only if the Nano
App is installed, and the instrument is not in a reprocessing session
The Nano App ICP‐MS nano analysis tool allows for the characterization of single
nanoparticles using the Syngistix software system. It is purchased separately
from the Syngistix for ICP‐MS base software, and must be installed on a
computer where the base software is already installed
The Single Cell icon opens the Single Cell App software. Available only if the
Single Cell App is installed, and the instrument is not in a reprocessing session
The Single Cell App performs ultra‐rapid, continuous analysis of discrete pulses to
foster the complete ionization of individual cells in a plasma in order to
determine the levels of metal particulate or dissolved metals within a given
sample
The Spotfire icon opens the Spotfire® data visualization module. Available
only if the Spotfire software is installed, and the instrument is not in a
reprocessing session
TIBCO Spotfire data visualization software is a dynamic, collaborative interface
that assimilates data from multiple sources — chemical structures, text,
numbers, images, chemical properties, biological assays, and more — and
empowers the user to perform complex analyses and create intuitive and
informative visual dashboards
Nano App ribbon
Icon Function
The Analysis icon accesses the Nano Analysis screen, which provides all the
controls needed to set up and run nanoparticle calibrations and sample
determinations, with realtime results panels for parsing your data on the fly
The Results icon accesses the Nano Results screen, where you can review in
detail the calculated histograms and related statistics calculated for each nano
sample or analysis. Here you can also reprocess your data by modifying the
variables used for these calculations
The Exit Nano icon returns you to the main Syngistix interface.
Single Cell App ribbon
Icon Function
The Analysis icon accesses the Single Cell Analysis screen, which provides all the
controls needed to set up and run calibrations and sample determinations, with
results panels for parsing your data in real time
The Results icon accesses the Single Cell Results screen, where you can review in
detail the calculated histograms and related statistics calculated for each single
cell sample or analysis. Here you can also reprocess your data by modifying the
variables used for these calculations
The Exit Single Cell icon returns you to the main Syngistix interface.
Navigating the Software

The main interface of the Syngistix software is built around a Ribbon menu, with screen access icons
organized into functional groups placed in an intuitive workflow for performing your daily analyses.
The Ribbon has two tabbed sections — the Syngistix tab, which contains all the basic functions to
operate the software, and the Applications tab, which contains links to a variety of programs related
to the core software, such as the Nano and Single Cell applications. Each icon provides access to a
main screen containing one or more functional panels to further organize the tools you need for any
given task. Some panels — such as the Realtime graphics panel — appear on multiple screens, to
minimize the amount of time spent clicking between windows. Several icons on the Ribbon provide
additional views or functions via drop-down submenus, accessed via a small arrow below the icon.
Note: This example shows the software for the 2000S instrument, which contains some advanced
functionality, but the software components largely look and function the same across all models.
Syngistix ball menu Ribbon menu
Quick Access toolbar panels Help button
status bar click to expand Measurement Status

the panel dialog box
Figure 1-1 Syngistix for ICP-MS software controls — sample screen
Each icon on the Ribbon provides access to a main screen containing one or more functional panels
to further organize the tools you need for any given task. Some panels — such as the Realtime
graphics panel — appear on multiple screens, to minimize the amount of time spent clicking between
windows. Several icons on the Ribbon also provide additional views or functions via drop-down
menus, accessed via a small arrow below the icon.
File Locations
The software file management features include a specific folder setup for data,
with several subfolders unique to the software. These subfolders are:
• Autosampler: This subfolder contains the files for the different types of
autosampler that can be used with the instrument, including the ESI series
of autosamplers and prepFAST autodiluter; the PerkinElmer AS-XX series;
and the ASX-500 and ADX-500 systems.
• Conditions: This subfolder contains conditions .tun files. The information
contained in these files is used to perform the fine-tuning adjustments for
the hardware subsystems in the torch/quadrupole assembly of the
instrument.
• Dataset: This subfolder comes with a set of default data folders, wherein
files containing the data from your analyses are collected. You can also
create a new Dataset folder elsewhere on your computer if there is a more
convenient place for you to store your analytic data.
• MassCal: This subfolder contains all pre-defined and custom .tun mass
calibration files.
• Method: This subfolder contains any method .mth files developed for
analyses. It also contains a Service subfolder for service-representative-
specific information.
• Nano: This folder contains a variety of additional subfolders for all data
and setup files relevant to the Nano App ICP-MS nano analysis tool. This
folder exists only if the Nano App has been purchased and installed.
• ReportOptions: This subfolder contains the report options .rop templates
used to create a hardcopy or file reports. You can modify a report template
for your needs, name it, and save it to this folder for future use.
• ReportOutput: This subfolder is the destination for report files if no path is
specified in the method.
• Sample: This subfolder contains the sample .sam files for sample
analysis. These files identify the samples, control the order in which
samples are measured and initiate the measurements. In the software,
you fill in the Sample panel and save a file, with a name you select, to this
subfolder.
• Single Cell: This folder contains a variety of additional subfolders for all
data and setup files relevant to the Single Cell App cellular analysis tool.
This folder exists only if the Single Cell App has been purchased and
installed.
• System: This subfolder contains the calibration files and TotalQuant™
response files.
• Wizard: This subfolder contains all pre-defined and custom SmartTune™
.swz files. It also contains a Service subfolder for service-representative-
specific information.
• Workspace: This subfolder contains all pre-defined and custom .wrk
workspace files. It also contains a Service subfolder for service-
representative-specific information.
The Elemental Library

The elemental library contains information on isotopic abundances and
polyatomic species. This library applies to all applications except the TotalQuant
software, which has its own read-only elemental library. The main elemental
library is contained in the Elemental Library.xml file, located in your Syngistix
software root folder.
Multiple Software Sessions

You can launch a second session of the software to analyze or reprocess data
while the instrument gathers data in the initial session. The first software session
is called the Instrument Control session; the second session is called the
Edit/Reprocess session. The Edit/Reprocess session can perform the following
tasks while the Instrument Control session gathers data and controls the
autosampler:
• Reprocess previously acquired data with different compatible methods
• Create new or modify existing file types for Method, Sample,
Calibration/Response, and Report Option files
• Review autosampler parameters in the Control screen Devices panel to
validate autosampler locations for Methods and Batches
• View reprocessed results in the Interactive panel
• Print reports to printer or file
• Print graphics
• View and reprocess information on the Nano or Single Cell App Results
screens, if either application is installed
• Run the Spotfire software, if installed
There is no communication between the two sessions. If an error occurs in one
session, the other session is not impacted by the error.
Note: You cannot modify files in the Instrument Control session. These files are available
on a read-only basis to ensure that files shared between concurrent sessions are not
corrupted.
During an Edit/Reprocess session, there is no access to the functions on the

following panels and tabs:
• System View panel and tabs
• Devices panel (all tabs except the Autosampler and ESI controls)
• Scheduler panel
• Mass Calibration panel
• Realtime panel
• Nano and Single Cell App Analysis screens
Understanding Acquisition Profiles

(UCT instruments only) Acquisition profiles allow you to link each of the cell gases
you use with the desired analytic mode and physical gas channel. You can
maintain up to nine profiles in the system at any one time, and assign these to
your instrument’s physical gas channels (you will have between one and three
channels available, depending on your model and configuration of instrument).
You can create multiple profiles that use the same gas; they will be assigned to
the same channel. If you create more than three profiles for any one mode, not all
profiles will be displayed at once; rather, a scroll bar will appear, which you can
use to scroll up and down through the profiles. Note that only those that are active
(that is, that have been assigned to an available physical gas channel) can be
used to run optimizations and analyses.
Note: The numbers entered for each profile set the base cell gas flow and rejection
parameter values for any new methods created using those profiles. At least one KED
mode profile and one DRC mode profile must have a cell gas flow set to a value greater
than zero.
A number of default profiles are shipped with the software. You can alter the
settings for these profiles, but you cannot delete them from the system. Custom
profiles that you create yourself may be deleted from the system by right-clicking
the relevant profile tile and then clicking Remove Profile.
The pre-defined Standard profile, Ammonia DRC profile (assigned by default to
cell gas channel A), and Helium KED profile (assigned by default to cell gas
channel B) are all required to run SmartTune Express optimizations; they must all
be present and actively assigned to their default channels in order to use this
feature, regardless of which mode you are optimizing for.
Acquisition order
When the system runs an analysis, analytes are processed in a particular order,
as determined by the mode of each, its RF Power setting, and its position on the
Acquisition Profile tab. The order is determined as follows:
• If the RF Power setting changes within a sample, this order is run for the
first RF group, and then repeated for each subsequent RF group.
• Profiles are processed from the top-down and left-to-right as the tiles
appear on the Acquisition Profile tab, so that Analytes linked to KED mode
profiles are processed first, followed by those using DRC mode, and then
Standard mode.
• The acquisition order with each mode is left to right. You can drag and
drop tiles to reorder them within each mode grouping, with the exception of
the pre-defined DRC Ammonia profile, which is always placed last within
the DRC group, and cannot be moved forward. (Remember that if you
exceed three profiles in any one mode grouping, the additional tiles will be
visible only by using the scroll bar that appears to the right of the group.)
Flexible profile and parameter configuration

To extend the capabilities of the Syngistix software system, the acquisition profile
function also allows you to create custom QID configurations and uncouple
otherwise linked parameters (including the ICP-RF Power, Neb Gas, Aux Gas,
Plasma Gas, Oxygen Gas, Makeup Gas, and Deflector Voltage settings) in order
to run different conditions on an analyte-by-analyte basis. Originally conceived for
Cold Plasma (low power ionization) analyses, this flexibility allows other possible
applications, such lowering nebulizer gas settings to facilitate high-oxide rare
earth scans.
Acquisition profiles created with custom QIDs or unlinked .DAC parameters are
displayed with colored tile borders, and the screentip for each indicates which
options the profile uses:
• Custom QID option (turquoise)
• Unlinked DAC parameter option (blue)

• Both options (purple)
• Neither option (no color)
Sample Acquisition Profile tileset
In the following example, the Acquisition Profiles tab for a 2000S instrument with
numerous custom profiles is displayed. While this model shows all possible
functionality, all of the models share a similar layout.
Screentip
1 2 3
4 5 6
7 8
Figure 1-2 Acquisition Profiles

In this example, eight acquisition profiles have been defined and are represented
here by eight tiles. They have been numbered here in the order in which related
analytes would be processed during an analysis. There are the four pre-defined
tiles that come with the system:
• Helium KED — This is assigned to channel B by default.
• Oxygen DRC — This is assigned to channel C by default.
• Ammonia DRC — This is assigned to channel A by default. Channel A is
connected to the hardware Getter for the removal of impurities in the gas.
• Standard — Predefined profile present on all UCT systems.
...and four custom tiles created by the user:
• Helium KED Custom QID — Custom QID profile with a turquoise border.
• Xenon KED unlinked — Profile that is both Unlinked and has a Custom
QID; purple border denotes that both options were selected.
• Oxygen DRC Custom QID— Custom QID profile with a turquoise border.
• Standard unlinked — Unlinked profile with a blue border. (Note that you
cannot create a custom QID in Standard mode.)
Syngistix Options System Configuration

When you first set up your system, you will use the Syngistix Options dialog box to
define basic system parameters and default values.
Syngistix Options Dialog Box Tabs

The Syngistix Options dialog box is comprised of four tabs, containing system
configuration settings, acquisition environment profiles, and default parameters:
• Configuration: Displays and defines basic system parameters.
• Acquisition Profiles: (UCT instruments only) Define profiles linking cell
gases with analytic modes and physical gas channels.
• Peristaltic Pump Defaults: Define default peristaltic pump parameters for
the Scheduler and SmartTune™ functions, and new methods.
• Performance Check Defaults: Displays benchmarks against which
SmartTune Express and SmartTune Manual Performance Check
optimizations are performed.
Configuration tab
Use the Configuration tab to define basic system parameters such as deadtime
corrections, gas flow controls, and notification sounds.
Figure 1-3 Syngistix Options dialog box Configuration tab
Items on the Configuration tab

• Instrument Type: Displays the model of spectrometer to which the
software is connected.
• Mass Flow Control: (MFC) These fields indicate what sample
introduction gas controllers are enabled (installed and activated) or
disabled (not installed, or deactivated). Not all options are available on all
models:
 AMS/O2: 2000 instruments only For the installed AMS (All Matrix
Solution) flow controller, a drop-down list allows you to select Argon or
Oxygen, as required.
Note: If you choose Oxygen here, the related parameters on the

Conditions, SmartTune, and Diagnostics panels are labeled Oxygen; if
you choose Argon here, all related parameters are labeled AMS.
 Plasma/Auxiliary Gas
 Oxygen Gas: 2000 instruments with optional MFC installed and all
300/350 instruments
 Makeup Gas: 300/350 instruments only
 Cell Gas B: 300/350X instruments only
• Deadtime: Displays the system Deadtime. In the Deadtime group, click
Set to access the Deadtime dialog box. Type a new deadtime as required;
the default system value is 35 ns.
• Gas Flow Correction: (300/350 instruments only) Displays the altitude of
your location. In the Gas Flow Correction section, click Set to access the
Elevation dialog box. Type a new altitude as required. Accepted values are
between 0 and 2 000 meters.
• QPS RF Voltage Calibration: Displays the current system QPS RF
voltage calibration factor.
In Service mode, you can adjust this parameter so that the peaks being
scanned move into a DAC range where they can be properly resolved.
Click Set to open the Calibration Factor dialog box and change the value.
Acceptable values are between 700 000 and 900 000 ppm.
• Audible Notifications: Select or clear the check boxes as required:
 Enable Log Event Sound: When selected, the computer beeps
whenever a message is written to the event log.
 Enable Fault Alarm: When selected, the computer beeps every five
seconds whenever a fault condition occurs. The beeping continues
until the fault is corrected.
 Enable End of Analysis Sound: When selected, the computer beeps
whenever the computer finishes an analysis.
• Diagnostics Tab — Service Only: (Service mode only) Displays the
Diagnostics Refresh Rate. In the Refresh Rate field, type the frequency, in
seconds, at which the Instrument panel Diagnostics tab should refresh the
displayed information.
• Vacuum Subsystem: Displays the vacuum manifold type currently
installed on the instrument: the available options are (Version 1)
pneumatic and (Version 2) motorized. Read only — the system

automatically detects the installed equipment type and populates this field.
Acquisition Profiles tab

(UCT instruments only) Acquisition profiles allow you to link each of the cell gases
you use with the desired analytic mode and physical gas channel, and to
configure default flow rates, delays, and related settings for methods using each
profile.
Figure 1-4 Syngistix Options dialog box Acquisition Profiles tab

The numbers entered for each profile set the base cell gas flow and rejection
parameter values for any new methods created using those profiles. At least one
KED mode profile and one DRC mode profile must have a cell gas flow set to a
value greater than zero.
Items on the Acquisition Profiles tab
• Delay settings: These fields indicate the pauses that occur when the
system changes mode or cell gas flow rate. Changing any of these
parameters can affect performance in any mode; always check instrument
performance after changing the gas flow delays:
 Pressurize Delay: This is the delay applied while the instrument
changes from Standard to KED or DRC mode. Type a delay of 10 to
600 seconds. The default value is 60 seconds.
 Exhaust Delay: This is the delay applied while the instrument changes
from KED or DRC mode to Standard mode. Type a delay of 5 to 600
seconds. The default value is 60 seconds.
 Channel Delay: This is the delay applied before data acquisition can
start, when the system switches from one cell gas channel to another.
The indicated value includes exhaust time. Type a delay of 15 to 600
seconds.
• Profile tile parameters:
 Gas Channel: (UCT modes only) Select a physical gas channel on
which to run the gas specified for this profile. Depending on your
instrument, 1 to 3 physical gas channels may be available. If no
channel is selected, the profile is saved but not activated (that is, it
cannot be used to run an analysis or optimization).
 Gas Flow: (UCT modes only) Indicates the default gas flow in
mL/minute for methods using this acquisition profile. Type a value
between 0.1 and 7.288 (or zero).
 Flow Delay: (UCT modes only) This is the delay applied while the
instrument changes from one cell gas flow to another on the same gas
channel. Type a delay of 1 to 600 seconds. The default value is 15
seconds.
 RPa: Indicates the default RPa value in volts to be used for methods
using this acquisition profile. Type a value between 0 and 0.24. The
default value is 0.
 RPq: Indicates the default RPq value in volts to be used for methods
using this acquisition profile. Type a value between 0.05 and 0.9. The
default value is 0.25 for STD and KED mode profiles, and 0.45 for
DRC mode profiles.
 Settling Delay: (Unlinked profiles only) Type a new delay in seconds.
This is the amount of time the instrument waits to allow for potential
parameter value changes before making the analyte measurement.
This delay lets the analyte signal stabilize. The default value is 30. If
the gas flow delays are longer than the settling delay, the settling delay
is not run.
• Add Profile: Click to create and define a new acquisition profile. You can
maintain up to nine profiles in the system, and assign up to three to your
instrument’s physical gas channels (depending on your model and

configuration of instrument). If you create more than three profiles for any
one mode, not all profiles will be displayed at once; rather, a scroll bar will
appear, which you can use to scroll up and down through the profiles.
• Close: Click to close the Syngistix Options dialog box and save your
settings.
New Profile Dialog Box
Use this dialog box to create new acquisition profiles.
Figure 1-5 New Profile dialog box

Items in the New Profile dialog box
• Mode: In the drop-down list, select the analytic mode in which you want
this profile to operate: STD, KED, or DRC mode.
• Gas Name: In the drop-down list, select the gas you want to use with this
profile. A selection of pre-defined gases are available, or you may type
another gas name as required.
• Custom QID: Select this check box to define custom QID (Quadrupole Ion
Deflector) settings for this profile. This adds a new tab to the Conditions
panel for this purpose.
• Remove DAC parameter links: Select this check box to uncouple select
dependent parameters on the Conditions panel Manual Adjust tab for this
profile. This allows you to fine-tune the settings for this configuration.
• Profile Name: Type a unique and meaningful name for this acquisition
profile. The system automatically populates this field with the selected
mode and gas, but you can add to or modify the name as desired.
Note: Keep in mind that the profile name will be used elsewhere in the
system, and that a short, meaningful name will be easier to read and
understand in these cases.
Peristaltic Pump Defaults tab

The values entered on the Peristaltic Pump tab set the base peristaltic pump
parameters for the Scheduler and SmartTune™ functions. They also
automatically populate the Peristaltic Pump group on the Method panel Sampling
tab when you create a new method.
Note: If you leave the wash override parameters in the method empty, the software uses
the wash value specified during acquisition. If you set a wash override value, it overrides
that specified in the method. This lets you specify longer washes to prevent residue when
running high-concentration samples.
Figure 1-6 Syngistix Options dialog box Peristaltic Pump Defaults tab
Default Peristaltic Pump parameters
Sample Sample Read delay Delay and Wash
Wash (sec)
flush (sec) flush speed (sec) analysis speed speed
2000 series instruments
35 -42 15 -35 45 -42
300/350 series instruments
35 -24 15 -20 45 -24
Performance Check Defaults tab

The values entered on the Performance Check Defaults tab set the benchmarks
against which SmartTune Express and SmartTune Manual Performance Check
optimizations are performed. These values are also used in the SmartTune
default .swz files: SmartTune Daily, SmartTune Monthly, and SmartTune Full.
Note: In this release, only some of the available options are editable.
Figure 1-7 Syngistix Options dialog box Performance Checks Defaults tab
Performance Check Benchmarks — Default Factory Values
2000 Instruments
Std mode KED mode
Sensitivity (2000S instruments) Sensitivity
Be > 6 000 cps/1 ppb Co high > 25 000 cps/10 ppb
In > 110 000 cps/1 ppb Background
U > 80 000 cps/1 ppb Ar278 high < 30 cps
Sensitivity (2000C, B, & P) Kr83 high < 300 cps*
Be > 4 500 cps/1 ppb
In > 80 000 cps/1 ppb Oxides
U > 60 000 cps/1 ppb ClO‐high/Co‐high < 0.5%
Background ClO‐low/Co‐low < 2%
< 3 cps @mass 220
Doubly Charged Ions and Oxides
Ce++/Ce < 3% *If 83Kr > 300cps, the argon gas supply
contains high levels of Krypton gas. This
CeO/Ce < 2.5% amount of Krypton is sufficient to degrade
detection limits enough that you will not meet
DRC mode the 78Se detection limit specification and
<20cps @ mass 78 target background. As and
Sensitivity (2000S instruments) Se are performed with low flow conditions and
Fe > 60 000 cps/1 ppb V is performed with high flow conditions.
Sensitivity (2000C, B, & P)
Fe > 50 000 cps/1 ppb
300/350 UCT Instruments
Std mode KED mode
Sensitivity (300/350S instruments) Sensitivity (all UCT instruments)
Be > 4 000 cps/1 ppb Co high > 25 000 cps/10 ppb
In > 55 000 cps/1 ppb
Background
U > 35 000 cps/1 ppb
Ar278 high < 30 cps
Sensitivity Kr83 high < 300 cps*
(300/350X & D instruments)
Oxides
ClO‐high/Co‐high < 0.5%
In > 40 000 cps/1 ppb
ClO‐low/Co‐low < 2%
U > 30 000 cps/1 ppb
CeO‐high/Ce‐high < 1%
Background
< 1 cps @mass 220
Doubly Charged Ions and Oxides *The Kr‐high criterion is for information
CeO/Ce < 2.5% purposes only, and has no pass or fail status
attached to it. If Kr83 > 300 cps, the Argon
Ce++/Ce < 3% contains enough Krypton to affect the Se78
DRC mode detection limit.
Sensitivity (300/350S instruments)
Fe > 40 000 cps/1 ppb
Sensitivity (300/350D instruments)
Fe > 25 000 cps/1 ppb
300/350Q Basic Quadrupole Instruments
Sensitivity
In > 40 000 cps/1 ppb
U > 30 000 cps/1 ppb
Background
< 5 cps @mass 220
Doubly Charged Ions and Oxides
CeO/Ce < 2.5%
Ce++/Ce < 3%
Startup and Shutdown

This section contains instructions for starting up the instrument for routine
operation, and verifying the correct operation of your system before starting an
analysis. It also describes the correct sequence of events for shutting down the
instrument after you have finished your determinations.
Starting the Software and Instrument

The software is your main interface to the instrument. It must be running for full
instrument functionality.
To start the software
1. Turn on the computer, monitor, and printer.
2. On the Windows Start menu, locate and select PerkinElmer Syngistix for
ICP-MS > Syngistix for ICP-MS.
Note: If multiple users have been set up on the instrument and they do not share
project folders, files such as default.tun and default.dac are not shared between
users and the system administrator.
To start the instrument

This section summarizes the basic steps required to start the instrument,
computer system, and peripheral devices. Use this procedure when the
instrument has been shut down for less than three weeks. For further information,
see the Maintenance Guide.
1. Check the condition of the sample introduction system:
 Check the cones for any evidence of blockage, deposits, or erosion of
the edges. Unless the condition of the cones seems severely
degraded, do not remove them. If you are unable to obtain satisfactory
results when you perform system optimization, you may need to clean
or replace the cones.
 Check the ICP torch. If there are deposits clogging it, you must clean
the torch. If severe wear has occurred, you should replace the torch.
 Check that the Pine Cone load coil (2000 instruments) or RF load coil
(300/350 instruments) is clean; this prevents arcing across the coils. If
the humidity in your lab is high, ensure that the coil is dry. If necessary,
use a soft cloth to dry it.
2. Check that the sample tubing and drain tubing leading from the peristaltic
pump to the spray chamber are correctly connected and in good working
condition.
3. If the pump tubing is new, gently stretch it. Attach the clips on the tubing to
the tubing stops. If the pump tubing has been used previously, check its
condition. Replace the tubing if it is discolored, brittle, crushed, or clogged.
Replace the tubing regularly, after every eight hours of use, or as needed.
If you routinely use organic solvents, you will require special tubing, as the
standard tubing is attacked and degraded by solvents. See the
Maintenance Guide for instructions on replacing peristaltic pump tubing.
4. Check that the pump rollers are clean and move freely. Replace the tubing
clamps for each channel and swing the cam levers over to apply tension to
the clamps.
5. Place the capillary tubing into a container of deionized water.
6. Check that the green system ready LED on the instrument control panel is
lit and steady.
If not, there may be a fault in the system and the plasma cannot be ignited.
If this occurs, check the diagnostic display to find which system
component is causing a fault.
7. On the Control screen Devices panel ICP-MS tab, click the Plasma Start
button to ignite the plasma.
The instrument initiates the ignition process — the progress of the ignition
sequence appears in the status bar. If the plasma does not ignite, wait 15
seconds and click the Plasma Start button again.
8. After the plasma ignites, let the instrument warm up for 45 minutes.
To start the instrument after an extended shutdown
This section presents additional information for restarting the instrument after a
period of more than two or three weeks. When the power and vacuum pumps are
off, the system requires additional time to initialize and pump down. For more
information about turning the instrument power on and off, see the Maintenance
Guide.
1. Plug the instrument and roughing pump into the power source, and turn on
the installed gases and the cooling water supply, chiller, or cooler.
2. 2000S SEMI instruments If the instrument is equipped with the optional
red Emergency Off (EMO) button, ensure that the EMO button is pulled out,
and then reset the circuit breakers. Then press the green Power On
button located on the left side of the instrument.
3. Ensure that the software is running.
4. Turn on the Instrument circuit breaker.
5. In the software, access the Control screen System View panel.
A stylized system layout provides a graphic display of the major operating
elements of your instrument, indicating the status of the plasma, argon
flow, cooling system, and interlocks.
6. On the Devices panel ICP-MS tab, click the Vacuum start button.
When a satisfactory vacuum is achieved, the vacuum status bar turns
green and the related status reads Ready, indicating that all the system
hardware is operating properly and that the plasma can be ignited. If the
indicator reads Not Ready, check the schematic diagram to find out which
system is not prepared for operation.
7. Check the base vacuum pressure. For successful operation of the
instrument, the pressure should be in the 1x10-7 to 5x10-7 Torr range.
8. Turn on the RFG (RF Generator) circuit breaker.
9. Record the instrument readings in the appropriate section of the
instrument Maintenance Logs.
10. Turn on any peripheral devices connected to the instrument, such as
alternate sampling systems (flow injection, laser ablation, and so on).
Note: To guarantee that all standards have been met before the system is
turned on, refer to the manuals provided with each peripheral device.
11. Ensure that the green System Ready LED on the instrument is steady.
The instrument is ready for use.
Ignition Problems
The system indicates the progress of the ignition sequence on the Control screen.
If the plasma fails to ignite due to a component failure, an error message appears
together with a diagnostic display indicating which system component is causing
the failure. The following system interlocks must be satisfied before the plasma
can be ignited:
• The torch gas pressure must be achieved
• The vacuum chamber must be locked in the sampling position
• The operating vacuum must be achieved
• The ICP generator must be ready
Additional information is located on the System View panel Diagnostics tab, which
lists operating conditions for the component selected in the system graphic. The
following are a series of checks to assist in correcting failure conditions.
Argon Supply
Check the argon supply pressure and record the pressure on the Maintenance
Log sheet. Ensure that you have enough argon for the amount of time you plan to
use the instrument. For information about argon gas requirements, see the
Maintenance Guide.
• Check that the argon supply valve is open and the regulator is set at the
correct pressure.
• Check for leaks throughout the gas connections.
Cooling System
The cooling system must meet the required specifications and be installed
according to the information in the Maintenance Guide.
• Check that the cooling system is connected at the appropriate points on
the instrument.
• Check that all electrical connections have been made, and check the
external pressure.
• Check that the coolant supply is on and is being properly filtered.

• Check for any leaks in the plumbing connections.
Torch and Sample Introduction System
Verify that all gas fittings to the torch are finger-tight. Leakage of air into any part
of the torch, nebulizer, or spray chamber may cause ignition problems. Therefore,
be sure to regularly check the following items:
• When using the spray chamber, check that the nebulizer end cap is tightly
secured to the spray chamber.
• When using the spray chamber, check that the sample capillary tubing is
attached to the nebulizer sample inlet. The tubing should be clean and in
good condition.
• When using the spray chamber, check that the drain fitting is secured on
the spray chamber drain. A loose-fitting drain can cause pressure leaks
and consequent plasma instability.
• When using dry aerosol sample introduction, check that the transfer tubing
connection to the base of the torch is tight.
• Check that the drain fitting on the spray chamber drain is secure. Ensure
that the pump is properly draining the spray chamber and that the drain
liquid is not backing up into the spray chamber. Check that the spray
chamber drain leads to the drain bottle. Empty the drain bottle, if
necessary. Dispose of waste properly.
• Check that the capillary tubing is attached securely to the nebulizer.
Organic Solvents and Vapors
If you are analyzing organic solvents and cannot ignite the plasma, run the
nebulizer argon for a couple of minutes with the peristaltic pump off to purge the
spray chamber. If organic vapors remain in the torch from an earlier analysis, they
can sometimes cause ignition problems. If you suspect this, purge the sample
introduction system with argon for several minutes.
Shutting Down the Instrument

To maintain your instrument in proper working condition, you must shut down the
different systems and peripherals in the correct order. If you abruptly cut power to
the instrument and peripheral devices, system damage may occur over time.
To shut down the instrument
1. With the plasma on, flush the sample introduction subsystem for five
minutes, using one of the following: deionized water, 2% nitric acid, or a
solvent (for organic samples).
2. Access the Control screen Devices panel ICP-MS tab.
3. Click the Plasma stop button to extinguish the plasma.
Note: For 2000S SEMI instruments with EMO options kits only In an emergency,
you can extinguish the plasma by pressing the red override button on the
instrument.
4. Remove the sample capillary from the deionized water.
WARNING! Always remove the sample capillary or autosampler probe

from the solution when you are finished using the pump; otherwise, the
solution can pour into and flood the spray chamber.
5. Release the compression cams that secure the drain and sample tubing.
Loosen the drain and sample tubing. This increases the usable life of the
tubing.
Note: If you use your instrument on a daily basis, leave the system on with the
vacuum pumping. This permits quick startup the next time you want to run
analyses. When shutting down the instrument for more than two weeks, refer to
the disconnection procedures in the Maintenance Guide.
To exit the software

1. Click File > Exit. You are prompted to save any new or modified files.
2. Click Yes to save the files. When all open files have been saved, the
software closes.
Task Scheduler
Use the Scheduler function to set up an automated run list of daily tasks. You can
automatically start and stop the plasma, and run optimizations and analyses
unattended. You can add multiples of any task type to your Scheduler list. The
following tasks are available:
• AutoStart: Use to start the plasma. Note that if the plasma is not on and
the AutoStart™ option is not selected, and the Scheduler is started, the
software alerts you with a Failed status.
• Warm-up: Use to prepare the instrument for analyses following plasma
ignition.
• SmartTune / SmartTune Express: Use to run performance checks and
optimizations. Ensure that all SmartTune files are correctly configured and
saved before adding them to the task list.
• Wait: Use this option to insert a pause into your run; for example, you
might add a Wait function after a SmartTune optimization, so that you can
check to see that the optimization passed all criteria before proceeding to
run your analyses. The wait function pauses your Scheduler workflow until
you start it again. You can specify a peristaltic Pump Speed for the
duration of the wait period.
• Analyze Samples: Use to add one or more sample or batch runs to the
task list. Ensure that all methods, samples, and sample batch files are
correctly configured and saved before adding them to the task list.
Note: When running a batch through the Scheduler function, it can take a
long time for the Measurement Status dialog box to appear. Click outside
of the Run List to reassert focus and hasten the process.
• Wash: Use to clean the system after an optimization or between sample
batches to prevent contamination.
• AutoStop: Use to shut down the plasma after all samples have been run.
Note: You can leave the Scheduler screen while it is running — the Scheduler status bar
provides task progress.
Scheduler Panel Software Reference

Double-click any task row to access and edit the details for that task. To re-order
the tasks, you can drag them up or down the task list, or click Edit List to
reconfigure the task list.
Figure 1-8 Scheduler panel

Items on the Scheduler panel
• Check boxes: Select the check boxes beside each task you want to
include in the current run. Select the top check box (check all) to include all
tasks.
• Task: Lists all the tasks in the current scheduler run list. Double-click any
task row to access, configure, or edit the details for that task. To re-order
the tasks, you can drag them up or down on the task list, or click Edit List
to reconfigure the task list. The software prevents you from dragging items
above the running or last completed task. When started, the Scheduler
runs tasks in order from top to bottom.
• Details: Provides additional information about each task. Double-click any
task row to access and edit the details for that task.
• Status: Provides information regarding what tasks have run, what the
current status is, and validation faults (for example, Invalid file).
• Start/Stop: Click to start or stop the active Scheduler task run.
• Skip: Click to skip the task in progress, (except the AutoStart function).
• Reset: Click to refresh the Status column, so you can start a new
Scheduler instance or list.
• Edit List: Click to access the Scheduler Edit List. Use this dialog box to
add and order tasks for your Scheduler list. Here you can select the tasks
you want the instrument to perform, and use the Move Up and Move Down
buttons to put them in the appropriate order.
Review Files Function

Use the Review Files function to review all the active files to be used in an
analysis. This dialog box lists all the currently active (or most recently active) files.
Each file type used by the software is listed. If the file is located in a folder other
than the pre-defined factory location, the file name is shown with the full path to its
location. A check box to the right of the file name indicates whether the file has
been modified since it was last saved. If the file has been modified, an x appears
in the check box. You can also open a different file for any of the available options,
or save an edited file.
The set of files here also represents any open workspace, wherein a complete set
of files is saved as a .wrk workspace file (the default.wrk file is loaded and
maintained by default, but you can save or load your own workspaces, using the
Workspace submenu on the Syngistix ball menu).
For Dataset files, you can open an existing dataset using the Load button or
create a new dataset using the New button. The Save button is not available for
datasets, because they are saved automatically when acquired and cannot be
resaved after that time.
Review Files Dialog Box Software Reference
Figure 1-9 Review Files dialog box
Items on the Review Files dialog box

• Method: Indicates the .mth format Method file currently loaded.
• Dataset: Indicates the current folder location to which datasets are saved.
Click the New button to select a different folder location in which to save
datasets.
• Sample: Indicates the .sam format Sample file currently loaded.
• Report Template: Indicates the .rop format Report Template file currently
loaded. These files define the appearance of current sample reports.
• MassCal: Indicates the .tun format Mass Calibration file currently loaded.
• Conditions: Indicates the .dac format Conditions file currently loaded.
• Calibration: Indicates the .cal format Calibration file currently loaded.
• SmartTune: Indicates the .swz format SmartTune Manual optimization file
currently loaded, or indicates if the SmartTune Express option is currently
selected.
• Polyatomic: Indicates the .ply format Polyatomic file currently loaded.
• Modified: These check boxes Indicate when the related file has been
modified.
• Load: Click any Load button to load a different file of the relevant type.
• Save: Click any Save button to save the related file.
Chapter 3
Instrument and Device Control

This section describes the Control screen, which contains the System View,
Devices, and System Status panels, and provides monitoring and overall control
of the mass spectrometer and external devices, such as the peristaltic pump and
autosamplers.
• System Performance Monitoring on page 53
• Device and Instrument Control on page 59
• Getter Regeneration on page 71
System Performance Monitoring

Control screen
The Control screen provides a central point from which you can control and
monitor the main components of your ICP-MS system. Use the Devices panel to
start and stop the ICP-MS, and to configure and control peripheral devices, such
as autosamplers and autodiluters, FIAS systems, and coolers. The System View
and System Status panels work in concert to display current instrument
information in both graphic and message form.
Figure 2-1 Control screen

The Control screen contains the following panels:
53
• System View panel: Contains an interactive instrument schematic that

models instrument activity, and a series of related tab for configuring and
tracking settings.
• System Status panel: Displays critical system status messages, fault
warnings, and maintenance reminders.
• Devices panel: Contains a series of vertical tabbed displays containing the
controls for the main ICP-MS instrument functions, as well as externally
attached peripheral devices.
System View panel

A System View panel contains an interactive instrument schematic that models
instrument activity and displays system issues in red. When you click on a
schematic component, the related diagnostic parameters are displayed in the
tabbed section at the bottom of the panel. An accompanying System Status panel
displays critical system status messages, fault warnings, and maintenance
reminders.
Figure 2-2 Control screen System View panel

The System View panel contains the following tabs:
• Diagnostics Tab: Displays the active status and operating conditions for
the main instrument hardware subsystems, including the cooling, vacuum,
gas, and plasma systems.
A dedicated and comprehensive Instrument Diagnostics screen is also

available via the Ribbon Diagnostics icon; here Sample and Realtime
panels are also provided, so that you can make changes and monitor your
results while adjusting or troubleshooting the system.
• Maintenance Tab: Used to create, view, define, and edit maintenance

reminders. Use these reminders to ensure regular maintenance and
servicing of system components is performed.
• Torch Position tab: Used to view, define, and edit the torch X, Y, and Z
parameters.
Items on the System View panel
• Vacuum Pressure: When the system is running, the vacuum pressure is
displayed in Torr above the System View graphic, and updated
continuously in real time.
• System View graphic: This graphic provides a visual representation of
the instrument and the flow of samples through the system, with major
subsystems delineated either in the main graphic or in the large icons
located below it. When a component is displayed in red, it indicates a fault
in that part of the system (a related message will also appear on the
System Status panel).
Mouse over any component or icon to see a descriptive screentip

identifying it. When you click on a component or an icon, the related
diagnostics parameters are displayed in the Diagnostics tab at the bottom
of the panel.
The XY plot and Z-depth torch graphic components are live; they can be
controlled via the Torch Position tab below, and reflect changes made via
the software optimization functions.
Diagnostics Tab
Use the Diagnostics tab to view the status and operating conditions for
checkpoints in the cooling, vacuum, gas, and plasma systems. Click on a section
of the instrument graphic, or one of the subsystem icons located below the
graphic, to view the diagnostics parameters for that component or subsystem.
Double-click any component to view its details.
Note: A dedicated Instrument Diagnostics Panel is also available via the Ribbon
Diagnostics icon to provide comprehensive diagnostics information for in-depth
troubleshooting.
Figure 2-3 Control screen System View panel Diagnostics tab

Items in the Diagnostics table
 System: Indicates the system where this component resides.
 Subsystem: Indicates the subsystem where this component resides.
 Component: Indicates the component being monitored.
 Status: Indicates the current status or value of a given component.
 Override: (Service mode only) When you click a diagnostics
component row, a check box appears if the option to override this
parameter exists. When you override a value, a check mark appears in
the row.
 Value: Use the Value arrow controls to modify the current value.
Maintenance Tab
Use this tab to track usage and basic maintenance of key instrument components.
The system provides warnings and alerts to let you know when it is time to
inspect, clean, or replace a component. These reminders are configured here and
displayed in the System Status panel. Click any component to view or configure
settings; enable or disable an alert; or to view component statistics (available for
the ICP Power Tube (300/350 instruments only), Vacuum Gauge, and Detector
only). You can also create custom maintenance reminders to your system to track
component life for tasks important to your lab.
Figure 2-4 Control screen System View panel Maintenance tab

Items on the Maintenance tab
• System: This column indicates the system component tracked.
• Criteria: This column indicates the unit of measurement (time, charge,
voltage, and so forth) by which component usage will be tracked.
• Usage: This column displays a visual status of the component vis a vis
criteria set and amount remaining. The colors displayed indicate the
following:
 Yellow: Component is approaching the alert point.
 Red: Component is past the alert point.
• Remaining: This column indicates how much of the designated criteria
(time, charge, voltage, and so forth) remains before an alert is scheduled
to be triggered.
• Settings box: Displays a description of the maintenance item, plus a
selection of configurable settings:
 Depending on the component type, a days, % threshold charge, or
volts field appears to indicate the number of days (or % of the
maximum threshold, or number of volts reached) after which an alert
should appear to remind you to perform maintenance on this
component.
 The related days before alert field (or % before alert, or volts before
alert), indicates the number of days (or % before threshold, or number
of volts below) prior to the actual alert point at which a warning should
appear to let you know that required maintenance is imminent.
 Alert Enabled check box: Select to turn the maintenance reminder for
this component On (deselect the check box to turn this reminder Off).
 Get Defaults: Click to reset the Alert and Warning fields to their pre-
defined settings.
• Statistics box: For certain components (the ICP Power Tube, Vacuum
Gauge, and Detector), the software displays a Statistics section to give
you additional information about the component, such as Ion Counts for
the Detector and Initial vs. Readback Volts for the Vacuum Gauge.
Right-click anywhere in the maintenance table and click Add to create a custom
reminder. Note that Calendar Time (the number of days) is the only available
criteria for custom maintenance reminders
Figure 2-5 Add Maintenance Reminder dialog box

Items on the Add Maintenance Reminder dialog box
• Name: Type the name of the component or maintenance task you wish to
create.
• Description: Type a meaningful description for this maintenance task.
• Days: Type the number of days after which an alert should appear to
remind you to perform maintenance on this component.
• Days before alert: Type the number of days prior to the actual alert point
at which a warning should appear to let you know that required
maintenance is imminent.
Torch Position tab

Use this tab to view, define, and edit the torch X, Y, and Z parameters. You will
generally update the torch X, Y, and Z parameters through the SmartTune™
Torch Alignment and Torch Sampling Depth optimization functions. However, you
can also manually control the individual motor positions here.
Note: The X position is somewhat dependent on the Y position due to the circular nature
of the possible torch path.
Figure 2-6 Control screen System View panel Torch Position tab
Items on the Torch Position tab
• Description: This column describes the parameter.
• Status: This column indicates the current status or parameter for a given
parameter.
• Step: Type a step value, in millimeters, to indicate how big the intervals
between value settings should be.
• Value: The Value column indicates the current position for a given
parameter. Use the arrow controls to modify the current position in mm.
For the horizontal and vertical (X and Y) axes, the position is charted
visually on the XY graphic above. For the Z axis, torch depth is charted
visually on the Torch graphic above.
Device and Instrument Control

The Devices panel contains a series of vertical tabbed displays containing the
controls for the main ICP-MS instrument functions, as well as externally attached
peripheral devices, including the peristaltic pump, autosamplers and autodiluters,
and the optional Peltier cooler.
Devices Panel Tabs

The Devices panel contains a variety of tabs depending on what peripherals you
have attached to your system.
ICP-MS Tab
The ICP-MS tab contains the main instrument controls. Use the buttons here to
run the vacuum, plasma system, and cone access door. Beside each button is a
color-coded status indicator bar with a message about the status of the
component above it. A green bar indicates a ready state; red indicates a fault;
and gray indicates a power failure or loss of communication with the instrument.
Figure 2-7 Control screen Devices panel ICP-MS tab

Items on the ICP-MS Tab
• Plasma Start/Stop: Use this control to start and stop the plasma system.
The plasma status indicator bar must be green and read Ready before
you can click Plasma Start. The status indicator bar is blue during plasma
ignition.
• Vacuum Start/Stop: Use this toggle control to start and shut down the
vacuum system. Generally, you should leave the vacuum system on
unless you will not be using the instrument again for a period of three days
or longer. When you shut down the vacuum, the instrument takes
significantly longer to return to running pressure the next time you start it.
The status indicator bar is blue when the system is pumping, and the
vacuum is attempting to reach the minimum value. If the bar is yellow, it
indicates that the vacuum is on, but the high voltage power supply is off.
• Cone Access Open: Use this control to open the cone access door.
When fully open, the system is in service position; when fully closed, the
system is ready for XYZ calibration and general operation.
Note: While the Cone Access door can be opened via the software controls on
this panel, it must always be closed manually at the instrument. This is a
deliberate safety measure, designed to ensure that care is taken when closing the
door, so that no object or person is inadvertently trapped or pinched when the
internal mechanism slides into place and the door latches.
Pump Tab
Use this tab to control either the integrated peristaltic pump, or any external
peristaltic pump connected to your instrument.
Figure 2-8 Control screen Devices panel Pump tab

Items on the Pump Tab
• Status: Indicates the status of pump communications, the pump speed,
and the direction of rotation.
• Pump Speed: Type to set a numeric pump speed between ±150rpm
(2000 series instruments) or ±48rpm (300/350 series instruments). Use
the related control buttons to increase (+ button) or decrease (- button) the
speed. Click ++ to jump immediately to full speed: ±100rpm (2000 series
instruments) or ±48rpm (300/350 series instruments).
The curved arrow buttons set the direction of pump rotation—clockwise or

counter-clockwise. Click the stop/go toggle button to halt or start the pump.
• Use internal pump: Select this check box to indicate that the instrument
should communicate with the internal peristaltic pump. This also activates
the remaining controls on this panel.
If this check box is not selected, the instrument communicates with

whatever external pump is connected to the system and the Connect /
Disconnect toggle control becomes enabled.
• Connect / Disconnect: Use this toggle control to establish and terminate
communication between the external pump and the software. When the
pump is connected, a message appears in the Status field.
• Stop pump on software shutdown: Select this check box to
automatically turn off the peristaltic pump when the software is shut down.
• Start pump on plasma ignition at: Select this check box and type the
speed in rpm to turn on the peristaltic pump automatically when the
plasma is ignited. The pump goes to the selected speed when the
nebulizer gas turns on following plasma ignition.
• Enable tubing saver after a delay of: To enable the tubing saver option,
select this check box and type number of minutes the instrument should
wait after the plasma is shut down before activating the tubing saver. The
tubing saver feature extends the life of the peristaltic pump tubing by
operating the pump at a low speed in alternating clockwise and
counterclockwise rotations when the plasma is not on.
Autosampler Tab
Use this tab to select the type of autosampler used, the communications port, and
the autosampler tray.
A note about pump tubing: The instrument ships with a standard size of peristaltic

pump tubing, and the system pump defaults are designed to work with that tubing in this
system. However, if you are using a different tubing diameter or quality, you may need to
adjust your peristaltic pump speed accordingly. Smaller, stiffer tubing requires a faster
pump speed, while larger tubing may require longer conditioning time and may lead to
system drift over time. Also, high speed autosamplers and autodiluters require higher
speeds, and accordingly cause tubing to degrade at a faster rate. Contact your
PerkinElmer Service Representative or Product Specialist for more information.
Figure 2-9 Control screen Devices panel Autosampler tab

Items on the Autosampler Tab
• Autosampler Type: In the Autosampler Type list, select the type of
autosampler you are using.
If you select an autodiluter (such as the Cetac ADX-500), one or more of

the following Auto Diluter fields become available on the Method panel
Sampling tab (see Sampling Tab on page 191):
 Dil. Factor: Enter a dilution factor from 2 to 1 000, as required. The
default dilution factor is 10. A dilution factor of n will lower the
measured intensity by a factor of n.
 Dil. To Vol: Specify the volume, from 2mL to 50 mL, of the diluted
samples the autodiluter will create. The default volume is 10mL.
 1st Dil. Pos.: Specify the position of the first diluted sample to be
created. Successive tubes are numbered accordingly.
 Probe Purge Pos.: This is used when the software is initializing the
autodiluter. In order to accurately measure the volumes of liquid
involved in each dilution, the dilution probe and associated tubing must
be full of diluent before any dilutions are done. To accomplish this, 10
mL of diluent are pumped into the dilution probe as part of the
initialization. To contain any excess diluent you can specify the
position of the large tube at the back right.
Selection of an autodiluter also activates autodilution functions in the
Sample Batch and Quality Control management sections of the software.
If you select an ESI autosampler or autodiluter (such as the ESI

prepFAST), additional controls become available in this tab. Consult your
ESI user documentation for more information.
• Port: In the Port list, select the communications port to be used.
• Tray File: Click Browse to select a sampling tray file. For some devices,
such as the ESI and ESI prepFAST, you will select a file shortcut, linking
you to an external folder structure (in this case, the ESI folder structure).
• Initialize: Click to initiate communication with the autosampler.
• XYZ positioning graphic: Select the autosampler location according to the
X, Y, and Z coordinates, and then click Go to XYZ location. (This option is
unavailable for ESI and ESI prepFAST devices.)
Slide the tube positioning scroll bars to select the X, Y, and Z coordinates
for the tube location. The corresponding tube number appears below the
scroll bar.
• Go to XYZ location: Moves the autosampler probe to the selected X, Y,
and Z coordinates.
• Go to rinse: Moves the autosampler probe to the wash solution.
• Go to standby: Click to move the probe to the standby position—the rinse
position with the probe raised. This is useful when you want to change the
probe or load a new tray.
• Interactive tray graphic: Use the interactive tray to move immediately to
the selected position.
FIAS Tab
This tab is displayed only if a FIAS system is installed and enabled, and selected
in an active method. Use this tab to establish communication with and manually
run the FIAS™ program without making measurements. Note that these controls
cannot execute a Read command, even if the FIAS step contains the Read.
Figure 2-10 Control screen Devices panel FIAS tab

Items on the FIAS tab
• Status: Indicates the status of communication and the current step in the
FIAS program.
• Reference A/S (Auto Sampler) Location: Displays an autosampler
location. This location is used as the Reference Location for blank or
relative autosampler location entries in the FIAS tab. If a location is not
entered prior to selecting Run Current Step/Program, an error message is
displayed.
• Initialize: Initializes communication with the FIAS device. A message
appears in the Status field.
• Run Current Step: Runs the step. The software performs the step where
the cursor is located. There must be an entry in the Reference A/S
Location field to run this step.
• Run Current Program: Performs the FIAS program in the active method.
This will not execute a Read command. There must be an entry in the
Reference A/S Location field to run this program.
PC3 Tab
This tab is displayed only if a PC3 Peltier cooler is installed and enabled.Use this
tab to start and control the Peltier PC3 cooler.
Figure 2-11 Control screen Devices panel PC3 tab

Items on the PC3 tab
• Start / Stop: Use this toggle control to start or stop the Peltier PC3 cooler.
• Reset Plot: Click the Reset Plot button to clear and reset the displayed
plot.
• Plot: Displays the progress of the Peltier PC3 cooler, tracking temperature
in degrees Celcius against time in minutes.
• Current Temperature: This field displays the current temperature at the
Peltier cooler output in degrees Celcius.
• Setpoint Temperature: Type the desired temperature for the Peltier
cooler output in degrees Celcius, and then click Set.
• Set: In the Setpoint Temperature field, type the desired temperature for
the Peltier cooler output in degrees Celcius, and then click Set.
• Automatically turn PC3 on/off with plasma: Select this check box to
automatically turn the Peltier cooler on when the plasma is ignited, and off
when the plasma is extinguished.
System Status panel

This panel displays critical system status messages, fault warnings, and
maintenance reminders. It works in conjunction with the System View graphic;
when a fault occurs, the related component is outlined in red on the graphic and a
descriptive message appears on the System Status panel.
Instrument Diagnostics Panel

Use the comprehensive Instrument Diagnostics panel to view the status and
operating conditions for checkpoints in the cooling, vacuum, gas, and plasma
systems. An expanded version of the diagnostics component on the Control
screen, all components of the instrument subsystem are monitored on this panel,
and their present status is continually updated. Diagnostics functions are
organized via pre-defined and custom filters, which you can design to display only
the diagnostics information relevant to your system usage. Double-click any
component to view its details. In the diagnostics list, read-only components
appear against a gray background, while components with modifiable values
appear against a white background.
Supplemental Sample and Realtime panels are also provided here, so that you
can make changes and monitor your results while adjusting or troubleshooting the
system. See Sample Panel Software Reference on page 244 and Realtime Panel
on page 291 for details regarding these additional panels.
Note: UCT instruments only. The Cell Voltages filter displays parameters related to the
DRC system. Many of these parameters are linked, so that if you change the value of one
parameter, the software automatically adjusts the value of one or more additional related
parameters.
Figure 2-12 Instrument Diagnostics panel

Items on the Instrument Diagnostics panel
• Filter: Click the list to select the diagnostics filter you wish to use.
• Edit List: Click to open the Edit List dialog box where you can modify the
diagnostics included in an existing filter, or create a new filter.
• Diagnostics Table Columns:
 System: Indicates the system where this component resides.
 Subsystem: Indicates the subsystem where this component resides.
 Component: Indicates the component being monitored.
 Status: Indicates the current status or value of a given component.
 Override: (Service mode only) When you click a diagnostics
component row, a check box appears if the option to override this
parameter exists. When you override a value, a check mark appears in
the row.
 Value: Use the Value arrow controls to modify the current value.
• Alerts: Displays any fault state warnings detected in the system.
• Reset All Overrides: Click to return any overridden parameters to their
default system values.
• Logger: Click to open the Logger dialog box, where you can define
logging parameters and start the logging function.
Figure 2-13 Logger dialog box

Items on the Logger Dialog Box
 Export Folder: In the Export Folder field, click Browse to select a
location for the log file.
 Criteria: In the Log Every fields, indicate the frequency with which
logging should occur. In the Log For fields, indicate the duration over
which logging should occur. In the Start section, indicate when you
want to start logging: select Now or select a Date and Time in the
future to start logging.
 Data Collection: In the Filter list, click a filter to select the data to be
logged.
 Start: Click Start to start logging.
 Export Now: To export logging data to the specified file location, click
Export Now.
Getter Regeneration
UCT instruments only. You must regularly regenerate, or clean, the getter in the
DRC gas assembly to purge it of impurities from DRC gases. In most cases, you
should plan to run this process overnight or on the weekend, as regeneration
takes approximately eight hours to complete. You cannot run KED or DRC mode
methods during the regeneration process. Plasma ignition is not required for this
process.
The Getter Regeneration Wizard leads you through the regeneration process,
providing instructions and progress messages along the way.
Note: The getter is always installed on the physical gas channel A; it will never be
installed on a different channel.
Chapter 2
Enhanced Security™ Software Administration

This section provides an overview of the Syngistix™ for ICP-MS
Enhanced Security™ software (ES) and its features.
• Introduction to the Syngistix™ for ICP-MS Enhanced Security™ software
on page 73
• Getting Started — Administrator’s guide on page 75
• Logging in for the first time on page 76
• Running as an Administrator on page 76
• Overview of the ES Setup Utility on page 77
• Selecting Enhanced Security features on page 78
• Setting up and managing users on page 80
• Setting up and managing groups on page 85
• Defining signature points and challenge reasons on page 94
• Understanding challenge dialog boxes on page 96
• Overview of the ES Tools Utility on page 98
• Managing audit trails on page 100
• Managing the file history on page 105
• Understanding the Review, Approve, and Reject functions on page 107
• To show differences between two versions of a file on page 109
Introduction to the Syngistix™ for ICP-MS

Enhanced Security™ software
The Enhanced Security software is an additional component that can be installed
on top of the basic Syngistix for ICP-MS software package to provide the security
and integrity your lab requires for electronic records. System administrators can
manage user access to various software functions through configurable
permissions. During routine operation, Syngistix ES automatically records
changes to key operational profiles such as method, mass calibration, and
conditions files, and tracks system operations in the audit trail.
Note: To achieve full compliance with regulatory requirements that pertain to your
laboratory, you may require the establishment of laboratory policies in addition to the
features provided by the ES software.
73
Key features
Security
• Administrators of the Syngistix ES software can configure Syngistix users
and assign them to different groups with each group assigned a specific
set of permissions. Your ES administrator defines these groups and
assigns permissions based on the needs of your users and lab
environment. Along with the use of passwords to gain access to the
software, these features permit overall access to be managed
appropriately in a regulated environment.
• The system administrator can determine whether different users can
normally access the same files such as method, mass calibration,
conditions, sample, and report files. Files can be located on the instrument
computer or on other computers connected to the controller across the
network.
Traceability
• Significant actions performed by the user are recorded in the Syngistix
Audit Trail with the date and time of the action, what was done, the name
of the user, and the reason the action was performed, together with any
relevant comments. The Syngistix Audit Trail can be filtered by several
data fields and then viewed onscreen or printed.
• New e-signature and file review functions can capture user credentials,
action reasons, and comments at every stage of the workflow for all key
files in the system, from the development of methods through sample
batch quality control. Challenge dialogs can collect e-signature information
every time a file is created, modified, or reviewed. Together with the
version control functions, this ensures complete traceability for all data
captured and decisions made.
• The software also provides file version control, automatically creating
version numbers for all key files and maintaining legacy versions in the
database. Differences between versions can be reviewed in the ES Tools
File History window.
• The Syngistix ES software does not permit analyses to be performed
without saving the resultant data. The security features also ensure that
analyses are conducted only with methods and other parameter files that
have been saved. These restrictions ensure that a proper audit trail is
maintained for all activities.
Every time an analysis is performed, the Syngistix ES software saves a

copy of all pertinent analysis parameters with the analytical results. The
data saved includes method and instrument parameters, analytical
calibrations, and the report template.
Integrity
• The Enhanced Security software applies a checksum to all data files
completely transparently to the user. If someone alters the data outside of
the Syngistix ICP-MS software (for example, by altering the analysis time
or changing the concentration value) this alteration is detected by the
Enhanced Security software when the file is next accessed.
• Reprocessing does not change the stored data, but rather new data is
written to the dataset along with a notation that the data represents
reprocessed data rather than original data. This provides a permanent
record of all results regardless of whether they are from the initial analysis
or from post-analysis reprocessing.
• Data archival tools are also provided in the Syngistix ES software to
facilitate complete and accurate archival of data on other storage media.
Once archived, the analytical data along with the respective audit trail
entries can be restored at a future date for review or audit purposes.
Note: During the Enhanced Security installation process, either the Configurable
or Non-Configurable version of the software was selected. If the Configurable
option was chosen, some features can be disabled and enabled (see Selecting
Enhanced Security features on page 78). If the Non-Configurable option was
chosen, all features and functions are available at all times.
In this guide, many sections describe features which may or may not be available
to the user depending on the option selected during installation, and the
subsequent ES Setup configuration. If you are running the Non-Configurable
version of the software, disregard the conditional references and assume that all
functions are available to you.
Getting Started — Administrator’s guide

To set up your system, you will log into your Windows account and launch ES
Setup; you will be prompted for your User name and Password; and you will then
be required to change that password immediately. See Logging in for the first time
on page 76, and Overview of the ES Setup Utility on page 77.
Based on your site’s security and audit trail policies and the level of regulatory
compliance you require, you will select which enhanced security features you
want activated. See Selecting Enhanced Security features on page 78.
Note: This functionality is only available if you have selected the Configurable option on
the Enhanced Security Installation Type page of the ES software installation wizard. If the
Non-Configurable option was selected, then you cannot turn off any ES features. Also,
turning off any of these features might compromise your audit trail capabilities and your
compliance with regulatory protocols.
Before users can log into the ES software, you must perform the following tasks to
set up the appropriate project folders and ensure proper privileges are assigned:
Windows tasks
• Set up new users in Windows
• Set up the Windows display properties for each user
• Enable the auditing of file deletion inside project folders
ES software tasks
• Log into ES Setup
• Select enhanced security features
• Define groups
• Create and set up users
• Assign users to groups

• Create project folders
•
Assign project folders to users
See Setting up and managing users on page 80 to set up new ES software users.
Logging in for the first time

After your PerkinElmer service representative has installed and configured the
software, you will be able to log into Windows as an administrator and set up your
Windows display properties. You will then be able to log into the ES software with
the privileges of the Administrators group.
To log into Windows
1. Log into the administrator account created for you in Windows. If you did
not supply a name, use the default Windows Admin account. Enter your
temporary password (initially 123456).
2. As this is the first time that you are logging into Windows, you are
prompted to change your password now. Type your new password and
repeat the same password in the Confirm New Password field. Write
down your new password.
To log into Syngistix™ ES
You can now log into Syngistix ES as follows:
IMPORTANT! You will not be able to open the Syngistix software until at least one
project folder has been defined and assigned to your user profile. If this was not done
during installation, proceed to Creating and managing project folders on page 88
before continuing with the steps following.
ICP-MS > Syngistix for ICP-MS (or double-click the Syngistix ICP-MS
icon on your desktop, if applicable). A login window appears.
2. At the prompt, type the user name and password for your Syngistix
administrator’s account. If this is the first time that you are logging into
Syngistix, you are prompted to change the password (initially 123456).
Type the new password and repeat the same password in the Confirm
Password box. Write down your new password.
3. Click OK. The Syngistix ICP-MS software starts and establishes
communication with the instrument.
Running as an Administrator
Depending on what functions you are performing, sometimes you will need to log
into the Syngistix ES software or the ES Tools utility as an administrator. For the
Syngistix ES software, you will need to run the program as an administrator only if
you are cleaning up data files, or installing an upgrade of the software. For the ES
Tools utility, you need log in as an administrator to use advanced functions, such
as accessing the security audit trail; viewing data for multiple users and folders;
repairing and compacting database files; and archiving data.
Note that both successful and failed attempts to log in as administrator are logged
in the audit trail.
Note: To run the Syngistix Enhanced Security software or the ES Tools utility as an
administrator, you must perform both parts of the following instructions (that is, you must
first be logged into Windows as an Administrator and then you must right-click and select
Run as Administrator); just logging in as a Windows Administrator is not sufficient in itself.
To run the software and utilities as an administrator

1. Log into Windows as an Administrator.
2. On the Windows Start menu, locate PerkinElmer Syngistix for ICP-MS,
and then right-click the desired program (Syngistix for ICP-MS or ES
Tools); select Run as Administrator. The PerkinElmer Login dialog box
appears.
3. Type in your User Name and Password, and then click OK. The program
opens.
Overview of the ES Setup Utility

The ES Setup window allows the Enhanced Security software administrator to
add users and groups and modify their settings; manage working folders;
configure e-signature and challenge dialog reasons settings; and select which ES
system features are available.
This window contains the following sections, which allow you to manage various
parts of the system:
• Users & Groups
• Project Folders
• Electronic Signatures
• Select ES Features
To log into the ES Setup utility
ICP-MS > ES Setup. The PerkinElmer Login dialog box appears.
2. Type in your User Name and Password (the user must have administrator
privileges), and then click OK. The ES Setup window appears.
If any users have been locked out from the ES software, a dialog box
appears allowing you to unlock them. A user is locked out of the ES
software if they have exceeded a specific number of unsuccessful login

attempts:
Figure 3-1 ES Setup window
Selecting Enhanced Security features

If, during installation of the ES software, you selected the Configurable option on
the Enhanced Security Setup Type page of the install wizard, you can choose to
enable or disable certain features of the ES software. If you selected the Non-
Configurable option during installation, you will run the full set of features, and this
tab will be unavailable to you.
CAUTION! Be aware that turning off any of these features may compromise your audit
trail capabilities and your compliance with regulatory protocols.
To select your ES features

1. In the ES Setup window, double-click Select ES Features. The Select
Enhanced Security Features dialog box appears:
Figure 3-2 Select Enhanced Security Features dialog box.
2. In the Select Enhanced Security Features dialog box, select the desired
check boxes:
 Rights Checking: When selected, users can only perform actions as
defined by their group membership.
 File Versioning: When selected, the Syngistix ES software saves old
versions of key operational files to a database for full traceability,
ensuring that information is never obscured.
 Audit Trail: When selected, an audit trail is kept of key user actions in
the Syngistix ES software; this is displayed as the ES Tools Syngistix
Audit Trail panel. Note that system administration tasks (such as
operations performed in ES Setup) are always logged in the Security
Audit Trail.
 Challenge and Electronic Signatures: When selected, users are
required to provide their system ID credentials (their E-Signature)
and detail their reasons for performing selected actions.
Because the challenge and electronic signature features are part of

the audit trail functionality, this check box is disabled if the Audit
Trail check box is not selected.
Enabling this check box adds Review, Approve, and Reject

buttons and columns to the ES Tools > File History window to
create signature points and help implement strict file version
control. Quality control personnel and lab managers can use these
functions to review file changes and additions, ensuring that
outdated or incorrect files are closed, and that the right files are
always available.
Enabling this check box also adds Review, Approve, and Reject
buttons to the Syngistix software > Report View panel data tabs
to create additional signature points in the user workflow. Related
columns also appear on the Report View results tabs — along with
an e-signature credentials column — if the Display Signed By,
Display Reviewed By, and Display Approval Status check
boxes on the Advanced Report View Display Options dialog box
are also selected. These functions allow managers and lab
personnel to track e-signatures and review acquired data.
 Quality Control Signoff: When selected, a QC Signoff button is
added to the Syngistix software > Report View panel QC tab to
create a QC-specific signature point for acquired data. This
replaces the Review button which appears on the other data tabs
(and which appears on the QC tab if the Challenge and Electronic
Signatures options is enabled, but the Quality Control Sign off
options is disabled). The signatory information from the QC Signoff
appears in the existing Reviewed By column on the QC tab. (The
Display Reviewed By check box on the Advanced Report View
Display Options dialog box must also be selected for this column to
appear.)
Because the electronic signature features are part of the audit trail
functionality, this check box is also disabled if the Audit Trail check
box is not selected.
3. Click OK.
Setting up and managing users

Follow the procedures in this section to set up a new user in Syngistix ES as a
member of the appropriate groups (for example, Chemists or Technicians), and
assign a project folder. The new user will then be ready to log into Windows and
Syngistix ES and use the instrument.
To set up a new Enhanced Security user
1. Log into Windows as an Administrator. Enter your Administrator password.
2. If you have not already done so, set up this user in Windows (see To set
up a new Enhanced Security user in Windows on page 84) and then
configure their Windows display properties (see To enable the auditing of
file deletion inside project folders on page 90).
3. On the Windows Start menu, locate and select All Programs >
PerkinElmer Syngistix for ICP-MS > ES Setup. The PerkinElmer Login
window appears.
4. At the prompt, type the User Name and Password for your Enhanced
Security Administrator account. Click OK. The ES Setup dialog box
appears.
Note: If this is the first time that you are logging in to the software, you are
prompted to change your password (initially set to a default of 123456). Type the
new password and repeat the same password in the Confirm Password box.
Record your new password somewhere safe.
5. Double-click Users and Groups. The Users, Groups, Password Control

and Summary dialog box appears. Click the Users tab:
Figure 3-3 Users & Groups > Users tab
6. On the Users tab, click New. The New User dialog box appears:
Figure 3-4 New User dialog box

 In the User Name field, type the user’s User Name or unique ID. This
is a shorter identifier which will be used in tables and audit trails
throughout the system.
 In the Full Name field, type the user's full name.
 In the Password field, type 123456 to serve as an initial default
password. (You can specify the minimum length of passwords when
you manage password settings in the Password Control tab.)
 In the Confirm Password field, type 123456 again.
 Specify whether the user is Enabled or Disabled. You might disable a
user if they have not started on a given project yet, or later if you no
longer not want them to have access to the software (for example, if
they leave your laboratory).
 Click OK.
Note: The Enhanced Security software requires all new users to change their
passwords when they first log in. As a result, the User must change password
at next login check box is automatically selected and unavailable.
7. In the Available groups for user list, select a group (such as Chemists),
and click Add to move the group name to the User is a member of list.
Click Apply, and then click OK. See Setting up and managing groups on
page 85 for more information.
8. A message appears instructing you to assign a project folder for the new
user. Click OK.
9. Double-click Project Folders. The Setup dialog box appears.
10. Click the Users and Project Folders tab, and select the user’s name from
the drop-down list. Select a folder from the list of Available folders, and
then click Add to move it to the list of Assigned folders for the user. Click
Apply, and then click OK.
11. Close the ES Setup dialog box.
12. Write down the user’s name and the temporary password (123456) and
give it to the user. The user must change their password when they first
log into the software.
Note: You can specify the same project folder for all users until it becomes
necessary to use additional folders.
Note: You can set up additional administrator accounts using alternate names
and passwords, if desired.
To edit a user
1. On the Users tab, select a user from the Name drop-down list, and then
click Edit. The Edit User dialog box appears:
Figure 3-5 Edit User dialog box.

2. If desired, change the Full name or Password (and re-enter the password
in the Confirm password box).
3. To force the user to change their password, select the User must change
password at next login check box.
Note: You cannot change the User name. You can specify the minimum length
of passwords when you manage password settings in the Password Control tab.
4. You can choose to enable or disable the user by clicking Enabled or

Disabled. You might disable a user if they will no longer be using the ES
software. For instance, you might want to keep track of user IDs for former
employees. If you enable a previously disabled user, you must change the
user’s password.
Note: Do not disable all users in the Administrator group; there must always be
at least one enabled Administrator.
Note: You cannot disable the user who is currently logged into ES Setup.
5. When you are finished, click OK.

To delete a user
When a particular user name is no longer required, you can delete it.
Note: A deleted user name cannot be used again for a new user.
1. On the Users tab, select a user from the Name drop-down list, and then
click Delete.
2. When prompted to confirm the deletion, click Yes. The user is removed
from the Name drop-down list.
Note: You cannot delete all users from the Administrator group; there must
always be at least one active Administrator.
To unlock a user
If a user attempts unsuccessfully to log in to the software too many times, their
user name is locked, and the ES administrator must unlock it before the user can
log in and resume their work. The administrator sets the number of unsuccessful
login attempts after which the user is locked out. For more information, see
Managing password settings on page 92.
Note: The unlock function is unrelated to the user enable and disable functions.
1. Launch ES Setup. When prompted, enter your administrator user name

and password.
2. If any users have been locked out, the Locked Out Users dialog box
appears, showing the Full Name and User Name of any users who have
been locked out.
3. Select the user you want to unlock, and click Edit.
4. In the Edit User dialog box, type a new password in the Password box,
and retype the password in the Confirm Password box. Click OK.
5. In the Locked Out User dialog box, the user no longer appears. When you
are finished unlocking users, click OK. You do not have to unlock all
locked users to continue to use ES Setup.
To set up a new Enhanced Security user in Windows
1. If you are not logged in, log into the administrator account created for you
in Windows. If you did not supply a name, use the default Windows Admin
account. Enter your temporary password (initially 123456).
2. If this is the first time that you are logging into Windows, you are prompted
to change the password. Type your new password and repeat the same
password in the Confirm New Password box. Write down your new
password.
3. On the Windows Start menu, locate and select Control Panel.
4. In the Control Panel, select the Small Icons view, and then click
Administrative Tools > Computer Management.
5. Navigate to Local Users and Groups > Users.
6. Click Action > New User. The New User dialog box appears.
7. In the User Name field, type the user name. Type a default password of
123456 in the Password field; and then type it again in the Confirm
password field.
8. Click Create, and then click Close.
9. Now, in the list of users, right-click the new user name and then click
Properties.
10. On the General tab, ensure that the User must change password at
next logon check box is selected.
11. Click the Member of tab, and ensure that Users appears in the Member
of list. (If it does not, click Add and, in the Enter the object names to
select field, type Users and click OK. Users appears in the Members of
field.)
12. Click Apply, and then click OK.
13. Windows 10: Click the Windows button; click the User button; and then
click Sign Out. The new user is now available from the Start menu; click
the user’s icon. The user must change their password when they first log
into Windows.
OR
Windows 7: Click Start > Shut Down > Log Off. The Select user window
appears. The new user is now available. The user must change their
password when they first log into Windows.
Note: Do not create accounts with names that are difficult to remember. We
suggest that you use the exact same name for the Syngistix ES account as the
Windows account for the same user.
Setting up and managing groups

When the ES software is installed, a user belonging to the Administrators group is
already created for you. You can log in as the administrator (using the user name
specified during installation) to define additional groups and users. You cannot
edit the Administrators group, but you can add other users to the Administrators
group so that they can also manage ES settings.
Groups are categories to which users belong that give the users certain
permissions. There are a number of pre-defined groups in the system, most of
which you can edit to suit your needs. For example:
• The Administrator group is pre-defined and cannot be edited (nor does it
appear) on the Users & Groups > Groups tab; however, users can be
assigned to this group on the Users & Groups > Users tab.
Administrators have full rights for activities pertaining to user and group
setup, permissions, and administrative functions. A user must have
administrative rights in order to access the security audit trail; view data for
multiple users and folders; repair and compact database files; and archive
data. See Running as an Administrator on page 76 for more information.
Administrators have full access to the ES Setup functions and ES Tools

screens, but do not automatically have Review and Approve rights, and
they are not granted permissions for creating or modifying workflow files
(such as methods).
• Chemists are high-level staff with full workflow rights. By default, they are
given the appropriate permissions to edit system configuration and
optimization files, and to create and modify all analytic files (including
conditions, method, mass calibration, sample, batch, and report options
files). Chemists can also run sample analyses using unapproved sample
and conditions files.
• Technicians have more modest workflow rights, with the permissions to
create, modify, and run a subset of those functions allowed Chemists.
• The Method Developers group is meant as a secondary level of
permissions, adding the right to run analyses with unapproved conditions,
method, mass calibration, sample, and report options files to allow for trial
and error during the method development process.
• Reviewers and Approvers have very narrow rights, specific to the review
and approve functions (respectively).
You can assign users to multiple groups if their duties cross the defined functional
definitions, and you can also add and define new groups according to your
company needs and policies, as required.
To add a group
1. In the ES Setup window, double-click Users & Groups. The Users,
Groups, Password Control and Summary dialog box appears. Click the
Groups tab:
Figure 3-6 Users & Groups > Groups tab

2. On the Group tab, click New. The New Group dialog box appears:
Figure 3-7 New Group dialog box

3. Enter a Group name for the group, and then click OK. The new group
appears and is selected in the Name drop-down list.
Note: The number that appears in square brackets after each permission is how
that permission is referenced in the Security Audit Trail. If the permission is
referenced in the Security Audit Trail, it is this number that appears, not a text
description of the permission. To determine which permission is being referenced

in the Security Audit Trail, you must look at this list.
To assign users to groups

After you create a user, you must assign that user to one or more groups to define
their permissions. For more information about groups, see Setting up and
managing groups on page 85.
1. On the Users tab, select a user from the Name drop-down list.
2. In the Available groups for user list, click the group or groups to which
you want to assign the user, and then click Add. The groups appear in the
User is a member of list.
3. To remove a user from a group, click in the User is a member of list, and
then click Remove. The group disappears from the list.
To edit a group
You change the properties of a group in the Permissions section of the Groups
tab. Members of that group will be able to perform the actions that you specify.
1. On the Groups tab, select a group from the Name drop-down list. The
members of this group are able to box displays the permissions associated
with that group in a tree structure.
2. In the Members of this group are able to box, set permissions for the
group as follows:
 Select the check boxes of the permissions you want to assign to
members of this group.
 To remove a permission from a group’s capabilities, clear the
corresponding check box.
 To select all of the permissions within a branch, click the check box
beside the parent of that branch.
 To expand a branch, click the plus-sign icon. To collapse it, click the
minus-sign icon.
 If you select a check box within a branch, the check box beside the
parent permission in the tree contains a grayed-out check mark.
3. When you are finished, click OK.
To delete a group
When a particular group is no longer needed, you can delete it.
Note: If you delete a user’s only group, that user cannot use the ES software until you
assign that user another group. Ensure that any affected users belong to a group.
1. On the Group tab, select a group from the Name drop-down list, and then
click Delete.
2. You are prompted to confirm the deletion. If the group you are trying to
delete has users assigned to it, the confirmation dialog box informs you of
this. To confirm deletion, click Yes. The group disappears from the Name
drop-down list.
Creating and managing project folders

Project folders are locations where users store all files used in a specific software
session. Each user is assigned one or more project folders in which they save
files. Users designate one project folder as their current one, and can only save
files in that folder. A project folder can be assigned to more than one user. You
add project folder settings from the Setup dialog box.
To add a project folder
1. In the ES Setup window, double-click Project Folders. The Setup dialog
box appears. Click the Project Folders tab:
Figure 3-8 Setup dialog box Project Folders tab
2. On the Project Folders tab, type the full path of the project folder in the
New Project Folder box, or click Browse to locate the folder or create a
new one.
3. Click Add. The new project folder appears in the Project Folder list.
Note: If you add a project folder with a name identical to an existing project
folder (or import a similar folder from outside of the ES project folder), and this
existing project folder is not registered or defined, its read only default files get
overwritten by the added project folder. All other default files are preserved.
To assign project folders to users

After you have created a project folder, you can specify which project folders will
be used by which users. You do this from the Setup dialog box, Users & Project
Folders tab. To access it from the ES Setup window, double-click Project Folders,
and then click the Users & Project Folders tab. To apply the changes you make
and continue working in this dialog box, click Apply. To apply changes and close
the dialog box, click OK.
1. On the Users & Project Folders tab, select a user from the Name drop-
down list.
2. In the Available list, click the project folder you want to assign to the user,
and then click Add. The project folder appears in the Assigned list.
3. To remove a project folder assignment, click the project folder to remove in
the Assigned list, and then click Remove. The project folder disappears
from the Assigned list.
To reassign project folders
After you have created a project folder, you can specify which project folders will
be used by which users. You do this from the Setup dialog box, Users & Project
Folders tab. To access it from the ES Setup window, double-click Project Folders,
and then click the Users & Project Folders tab. To apply the changes you make
and continue working in this dialog box, click Apply. To apply changes and close
the dialog box, click OK.
1. On the Users & Project Folders tab, select a user from the Name drop-
down list.
2. In the Available list, click the project folder you want to assign to the user,
and then click Add. The project folder appears in the Assigned list.
3. To remove a project folder assignment, click the project folder to remove in
the Assigned list, and then click Remove. The project folder disappears
from the Assigned list.
To delete a project folder
When a particular project folder is no longer required, you can delete it from the
list of available project folders. This action does not delete the folder from your file
system. Note that if you delete a user’s only project folder, that user can no longer
use the ES software.
1. In the Project Folder list, select the project folder, and then click Delete.
2. When prompted to confirm the deletion, click OK. The project folder
disappears from the Project Folder list.
Note: This operation does not delete the folder from your system. If you later
add a previously deleted project folder (or import a folder from outside the ES
project), the software overwrites only the default files, and leaves any files that
you have created intact.
To enable the auditing of file deletion inside project folders

2. On the Windows Start menu, locate and select Control Panel.
3. In the Control Panel, select the Small Icons view, and then click
Administrative Tools.
4. In the file list, double-click Local Security Policy. The Local Security
Settings window appears.
5. In the Security Settings tree, double-click Advanced Audit Policy
Configuration.
6. Double-click System Audit Policies - Local Group Policy Object.
7. Double-click Object Access, and then double-click Audit Detailed File
Share.
8. On the Policy tab, select the Configure the Following Audit Events
check box, and then select the Success check box.
10. Close the Local Security Settings window and the Control Panel.
11. Open Windows Explorer and click Organize > Folder and Search
Options.
12. On the View tab, in the Advanced Settings section, clear the Use
Sharing Wizard (Recommended) check box.
14. Locate the project folder you want to audit for successful deletion events.
15. Right-click the folder, click Properties, and then click the Security tab.
16. Click Advanced, and then click the Auditing tab.
17. To set up auditing for all users, click Edit, and then click Add. In the Enter
the object name to select field, type Everyone and then click OK.
18. In Auditing Entry for File or Folder, in Apply onto, select where you
want auditing to take place.
19. In the Access field, select the Successful check box for Delete
Subfolders & Files and Delete to audit successful events.
20. Click OK.
21. Repeat steps 14-20 for each project folder you want to audit for successful
deletion events.
Viewing a summary of your security settings

When you want to review your user, group, and password settings in one
summary report, you can view the Summary tab.
To view a summary of your security settings
Summary tab:
Figure 3-9 Users & Groups > Summary tab

The Summary tab lists the settings under the following categories:
 Password control
 Permissions
 Users
 Groups
To print this text summary, click Print. To export this summary to a comma-
separated or raw text file, click Export.
Managing password settings

If your corporate security policies require it, you can specify how users manage
their passwords.You modify password settings from the Password Control tab.
Note: The settings on this tab apply to all users. You cannot define different password
control settings for different users or groups.
To specify password settings for users

Password Control tab:
Figure 3-10 Users & Groups > Password tab

2. In the Maximum password age group, select one of the following options:
 Password never expires: Users never need to change their
passwords.
 Password expires after (days): Users must change their passwords
after the number of days specified in the box.
3. In the Minimum password age group, select one of the following options:
 Allow changes immediately: Users can change their passwords right
away.
 Allow changes after (days): Users cannot change their passwords

until the specified number of days has passed.
4. In the Minimum password length group, type the lowest number of
characters allowed in users’ passwords in the At least (characters) box.
The default number is 6.
5. In the Password uniqueness group, type the number of passwords that
must be used before a user can repeat one in the Number of passwords
to remember box. This prevents the user from repeating recently used
passwords. The default number is 24.
6. To specify account lockout settings, click Account Lockout. The Account
Lockout dialog box appears:
Figure 3-11 Account Lockout dialog box

7. In the Lockout group, specify the number of times a user can attempt
unsuccessfully to log in before they are locked out of the ES software.
8. In the Lockout duration group, select one of the following options:
 Permanent: The user remains locked until an ES administrator
unlocks the user name.
 Duration (minutes): The user remains locked for the specified period
of time, in minutes.
Note: Never select a Permanent Lockout duration for an administrator, or there

will be a risk that the administrator will be locked out of the software indefinitely.
You may choose this option for a user if desired.
We strongly suggest that you create a secondary or backup administrator account

to use in the event of an unintended lockout.
9. Click OK.
10. On the Password Control tab, to apply the changes you made and
continue working in this dialog box, click Apply. To apply changes and
close the dialog box, click OK.
Defining signature points and challenge reasons

The Signature dialog box allows you to configure a series of predefined Signature
Points in the software workflow at which users are presented with a Challenge
dialog box requiring them to enter their e-signature information (short user ID and
password) and indicate a reason for their action, as well as providing any
additional comments or information.
For each action or signature point, you can enable or disable the e-signature
function and/or a freeform comments field. This can be handled in the same way
for all signature points, or configured differently for different actions.
Here you can also edit and add to a list of pre-defined reasons from which users
can choose to describe their actions when they perform various tasks in the
Enhanced Security software. A selection of default reasons for each signature
point is provided by the software.
Note: Users are required to enter reasons for the operations listed in this dialog box only
when the Audit Trail and Challenge and Electronic Signatures check boxes are
enabled in the Select Enhanced Security Features dialog box.
To open this dialog box, on the ES Setup window, double-click Electronic

Signatures:
Figure 3-12 Signature dialog box

To define signature points and challenge reasons for user operations
1. In ES Setup, click Electronic Signatures to access the Signature dialog
box.
2. In the Signatures section, in the Name list, select an operation. The
operations which can serve as signature points are:
 Analyze Sample
 Append Sample
 Approve and Sign
 File Save
 Insert Priority Sample
 Modify Configuration
 Reject and Sign
 Reprocess Data
 Review and Sign
3. To require users to enter their e-signature credentials when they perform
this operation, enable the Signature Required check box.
4. To prompt users to enter relevant comments when they perform this
operation, enable the Prompt for Comments check box.
Note: If you wish to apply the same settings to all of the operations in the Name
drop-down list, click Update All. The Update All Signature Point Settings dialog
box appears. Here you can apply either option across all or no operations as
desired.
5. Define selectable reasons for the operation.

When you select an operation from the Name drop-down list, the Reasons
list box is populated with the reasons that have already been assigned to
that operation.
 To edit an existing reason, select the reason in the list and then click
Edit. Edit the reason text in the resulting dialog box, and then click OK.
 To add a new reason, ensure that the desired operation is selected in
the Signature points drop-down list, and then click New. Type the
reason text in the resulting dialog box, and then click OK.
 Use the up and down arrows to change the order in which the reasons
appear to the user. The first reason in each list appears as the default
option on any challenge dialog box.
 To delete an existing reason, select the reason in the list and then click
Delete.
6. When you are finished changing the reasons for an operation, click Apply
to save your changes. You can now select another operation to define, or
click OK to exit the Signature dialog box.
7. To close the dialog box without changing settings for the current operation,
click Cancel. Changes already made for other operations remain in effect.
Understanding challenge dialog boxes

“Sign” challenge dialog boxes are used to track user actions and decisions in the
software, and can help you maintain traceability for QC and regulatory compliance
purposes. You can set up with system to present a challenge dialog box at any of
the designated signature points in the software, and can configure these dialog
boxes to gather several different kinds of information.
When a user performs one of the flagged operations, a challenge dialog box
appears, requiring that they enter the specified information.
Note: Users are able to perform only those actions permitted to the groups to which they
belong (see Setting up and managing groups on page 85). Actions not permitted for
their group members are disallowed and will trigger an error message rather than a
challenge dialog box if attempted.
For each operation in the Signature Points Name drop-down list, you can select
one or both of the following options:
• Signature required — If this check box is enabled, User name and
Password fields appear at the top of the challenge dialog box for this
action. These are the shorter user ID (not the full name) and password
specified for this user in their ES Setup user profile (see Setting up and
managing users on page 80):
The e-signature fields are mandatory when enabled. A user will not be
allowed to continue with or complete the signature point action if a valid
user ID and password are not entered.
• Prompt for comments — If this check box is enabled, a Comment text

field appears at the bottom of the challenge dialog box for this action:
The Comment field is a freeform text field in which users can type any
notes; however, it does not constitute a mandatory field and no system
checks are run to determine whether or not a user has entered any
information here. If your SOPs require that users enter comments here,
this must be enforced either via the Review/Approve/Reject functions or
through management and training practices.
A challenge box with all options enabled looks like this:
At the top of each box, a text field describes the action for the given signature
point.
A Reason drop-down list will always appear unless you delete all of the reasons
for a given signature point. For each signature point, there are one or more pre-
defined reasons in the system when you install the software. You can add your
own reasons to each list; and edit or delete the existing reasons. Arrow buttons
allow you to change the order of the reasons in the list; the first reason in the list
will always be the default selected on the challenge dialog box. If selection of a
valid reason is important to your company’s SOPs, this can be enforced via the
Review/Approve/Reject function or through management and training practices.
Overview of the ES Tools Utility

This section describes the features available in the ES software ES Tools utility.
The ES Tools window allows you to do the following:
• View and print user workflow and validation information using the Syngistix
Audit Trail
• View e-signature details and review cycle progress; and perform Review,
Approve, and Reject functions on File History entries
• Compare different versions of the same file
• Compact the audit trail and file versioning databases
• Archive and restore files in users’ project folders
• View and print system and administrative events using the Security Audit
Trail
To open the ES Tools window
ICP-MS > ES Tools:
Figure 3-13 ES Tools window
Running ES Tools as an Administrator

Depending on what functions you are performing, sometimes you will need to log
into the ES Tools utility as an administrator. Generally, you need log in as an
administrator only to use advanced functions, such as accessing the security audit
trail; viewing data for multiple users and folders; repairing and compacting
database files; and archiving data.
Note that both successful and failed attempts to log in as administrator are logged
in the Security Audit Trail.
Note: To run the ES Tools utility as an administrator, you must perform both parts of the
following instructions (that is, you must first be logged into Windows as an Administrator
and then you must click Run as Administrator); just logging in as a Windows Administrator
is not sufficient in itself.
To run ES Tools as an administrator

ICP-MS, and then right-click ES Tools; select Run as Administrator. The
PerkinElmer Login dialog box appears.
3. Type in your User Name and Password, and then click OK. The ES Tools
dialog box appears.
Managing audit trails

The Enhanced Security administration software provides two audit trails:
• Syngistix Audit Trail: a record of user workflow and validation actions
performed in the ES software.
• Security Audit Trail: a record of administrative actions performed in ES
Setup and ES Tools, and login events for Syngistix. Because ES Setup
features can be used only by someone with Administrative permissions,
this audit trail is not visible to all Syngistix users.
Managing the Syngistix™ Audit Trail

To view and refine Syngistix ES software user workflow events
After logging into your computer as an administrator, launch the ES Tools window
(on the Windows Start menu, locate and select PerkinElmer Syngistix for ICP-
MS, and then right-click ES Tools; select Run as Administrator).
In the ES Tools window, click Audit Trail. The Syngistix Audit Trail window
appears:
Figure 3-14 Syngistix Audit Trail window
The title bar of the window shows the location of the XML file generated. A series
of icons and filter drop-down selectors appear in the menu bar along the top of the
panel, and a calendar selection tool to the right of the menu bar lets you define a
date range for the data you wish to review:
Click the Refresh button to update the current view with the most
recent data.
Click the Clear Filters button to remove filtering options and
return to the complete file view.
In the date selection fields, select start and end dates for the date
range you want to view, and then click the Filter Date Range
button.
Note: The calendar shows only those dates for which there is existing
data.
For every event, the Syngistix Audit Trail table displays the relevant Record
Number, Time Stamp, User ID, User Name (their full name), the Action Type,
Action Details, Reasons, and Comments (if any). If the Audit Trail and Challenge
and Electronic Signatures options are enabled in the Select ES Features dialog
box, this panel also includes e-signature and reviewer/approver/file rejection
details. If the Quality Control Sign off check box is also selected, QC review
information is also displayed
You can change the view of the audit trail events in the following ways:
• To sort the rows alphanumerically by column, click the column heading
(except for Rec # or Reasons). The column by which the rows are sorted is
highlighted and an arrow appears beside the column heading. An arrow
pointing up indicates ascending sort order, while an arrow pointing down
means descending. The Time Stamp column defaults to descending, and
is selected by default when you first open the Syngistix Audit Trail window.
• When you first open the Syngistix Audit Trail window, all events are shown.
To display only events of a particular type, click one of the filters in the
Select a Filter drop-down list:
 Syngistix log in/out
 File Save
 Syngistix System Event
 Sample Analysis
 Dataset Operations
 Modify Configuration Parameters
 Print Report
 ES Setup
 Archive/Restore Operation
 Review
 Approve
 Reject
 QC Review
• To display only those events attributed to a project folder, click the folder
name in the Select a Project Folder drop-down list. Individual users can
see only their own project folder. Administrators can see all project folders.
• To display only those events attributed to a particular user, click the user
name in the Select a User drop-down list.
• To display only those events signed by a particular user, click the user
name in the Select Signed By drop-down list.
• To display only those events reviewed by a particular reviewer, click the
user name in the Select Reviewed By drop-down list.
• To display only those events approved by a particular user, click the user
name in the Select Approved By drop-down list.
• To display only those events rejected by a particular user, click the user
name in the Select Rejected By drop-down list.
• To display only those events with QC signoff attributed to a particular user,
click the user name in the Select QC Reviewed By drop-down list.
• display events between two particular dates, select the dates from the
drop-down boxes, and then click the Filter Date Range button.
• To remove filtering and display all events, click the Remove Filtering
button.
• To update the view with the most current information from the Syngistix
audit trail database, click the Refresh button.
• To print the filtered list of events, click File > Print.
Managing the security audit trail

The Security Audit Trail allows you to view a history of login attempts and actions
performed in the ES Setup and ES Tools utilities. You view this information in the
Login History & Audit Trail dialog box.
To view ES system login events
In the ES Tools window, click Security Audit Trail, and then click the Login
History tab:
Figure 3-15 Login History & Audit Trail dialog box Login History tab
The Login History tab shows a history of user login and logout actions, both
successful and failed, together with the following information:
• Full Name: The user’s full name, as defined in ES Setup
• User Name: The user’s shorter user name or ID, as defined in ES Setup
• Computer: the name or ID of the computer on which the function was
performed
• Status: An indication of whether the user’s login attempt was successful
or failed
• Logged In: The date and time at which they performed the login or failed
attempt
• Logged Out: The date and time at which they performed the logout
To print the contents of the current tab, click Print. To export the contents of the
current tab to a comma-separated or raw text file, click Export.To clear the
contents of the current tab, click Clear History (note that if the events have not
yet been archived, they are not cleared).
To view ES system administrative events

In the ES Tools window, click Security Audit Trail, and then click the Audit Trail
tab
Figure 3-16 Login History & Audit Trail dialog box security Audit Trail tab
The security Audit Trail tab shows the following information for administrative
actions performed in ES Setup:
• Function: The function performed
• Previous Value: the previous setting or value of the field that was
changed
• Current Value: the new setting or value to which the field was changed
• Full Name: the administrator’s full name, as defined in ES Setup
• User Name: the administrator’s shorter user name or ID, as defined in ES
Setup
• Computer: the name or ID of the computer on which the function was
performed
• Date Modified: the date and time when the function was performed.
To print the contents of the current tab, click Print. To export the contents of the
current tab to a comma-separated or raw text file, click Export.To clear the
contents of the current tab, click Clear Audit (note that if the events have not yet
been archived, they are not cleared).
Managing the file history

The File History window provides a history of key working files created and
modified in the system. Here you can examine files, compare different versions of
the same file, and perform file review/approve/reject functions.
If the File Versioning option is selected in the Select ES Features dialog box, the
software performs file version control to maintain traceability across the system.
The version control function stores successive versions of each file as users
open, modify, and save them. The ES software provides version control for the
following file types:
• Method .mth files
• Mass calibration .tun files
• Sample .sam files
• Report options .rop files
• Conditions files .dac files
• Calibration files
• Response .rsp files
The differences function compares only two versions of the same file — you
cannot compare more than two files, nor can you compare files of different types,
or having different names.
Note: You cannot show differences between version one of a Syngistix software default
file with any subsequent version.
To view the File History

In ES Tools, click File History. The File History window appears.
Figure 3-17 File History window
The File History window contains three panels with a row of filters and action
buttons running along the top of the window. The buttons provide the following
functionality:
• Project Folder — In the Project Folder drop-down list, select the project
folder containing the file you want to review. The list will contain only those
folders associated with your name in ES Setup.
• Refresh — To ensure that all the latest files and actions are reflected in
the File History window, click Refresh.
• Show Differences — Select two versions of a file in the File Versions
table and then click Show Differences to view a detail of the differences
between the two versions in the results panel at the bottom of the window.
• View File — Select a file version row in the File Versions table and then
click View File to display detailed information about this version of the
selected file (such as date created or modified, file location, and
configuration details) in the results panel at the bottom of the window.
• Signature Details— Select a file version row in the File Versions table and
then click Signature Details to display e-signature information for users
who have performed actions and provided e-signature credentials for this
version of the selected file in the results panel at the bottom of the window.
This information will also include e-signatures provided during Review,
Approve, and Reject functions either in this window, or in the Syngistix
software Report View panels.
Note: Default, pre-defined files provided with the software will list PerkinElmer
Inc. as the initial signatory, reviewer, and approver.
• Review — Select a file version row in the File Versions table and then click
Review to provide your e-signature credentials and comments (as
required) to indicate that you have reviewed the selected record.
• Approve — Select a file version row in the File Versions table and then
click Approve to provide your e-signature credentials and comments (as
required) to indicate that you approve the selected record.
• Reject — Select a file version row in the File Versions table and then click
Reject to provide your e-signature credentials and comments (as
required) to indicate that you reject the selected record.
The panels display the following information:
• The small File Types panel in the top-left corner provides an expandable
tree list of viewable files in your system. Expand the tree and select the file
you want to view.
• The larger panel in the top-right corner contains the File Version table,
listing all versions of the selected file.
• The bottom panel displays details or difference information for the file
version or versions selected, depending on the action button selected.
Select a row in the File Version table and then click an enabled button to
view details here; or select two rows and then click Show Differences to
display the delta here.
To perform review and version control functions in the File History

1. In the ES Tools window, click File History. The File History window
appears.
2. In the Project Folder drop-down list, select the project folder containing
the file you want to review.
3. To ensure that all the latest files and actions are reflected in the File
History window, click Refresh.
4. In the File Types box, expand the tree and select the file you want to
Review, Approve, or Reject. When you select a file, a list of all versions of
that file appear in the File Versions table.
5. In the File Versions table, select the version of the file you want to Review,
Approve, or Reject, and then click the appropriate button. When you click
one of these buttons, a Sign challenge dialog box appears, in which you
must provide your user credentials and (depending on how your system is
configured) provide a reason and relevant comments describing your
actions.
Note: The Review, Approve, and Reject buttons are available only if the Audit
Trail and Challenge and Electronic Signatures options are enabled in the ES
Setup window Select ES Features dialog box. These button are enabled only if
the user belongs to a group with the appropriate permissions for the given action
AND if the action is appropriate to the selected file version.
 Click Review to provide your e-signature credentials and comments

(as required) to indicate that you have reviewed the selected record.
 Click Approve to provide your e-signature credentials and comments
(as required) to indicate that you approve the selected record.
 Click Reject to provide your e-signature credentials and comments (as
required) to indicate that you reject the selected record.
Understanding the Review, Approve, and Reject functions

In addition to the workflow-related signature points (such as Analyze Sample and
Save File), enabling the Audit Trail and Challenge and Electronic Signatures
check boxes on the Select ES features dialog box adds Review, Approve, and
Reject functions to the software. You can use these functions to validate user
workflow actions such as sample and batch analyses and reprocessing sessions
in the Syngistix software > Report View acquired data tables; or to validate
actions and monitor file version control in the ES Tools > Syngistix File History
window.
Syngistix software Review, Approve, and Reject functions
In the Syngistix software > Report View data acquisition tables, these functions
appear as a set of buttons at the bottom of each of the Raw and Net Intensities,
Concentrations, Unfactored Concentrations, and QC tabs. Users who are
members of groups with the appropriate permissions can look over the data in the
reports; click to select a single acquired data row (or CTRL + click to select
multiple rows); and then indicate review, approval, or rejection of the selected
data. Samples, appended samples, batches, and reprocessed data can all be
validated in this way. Graphic calibration rows cannot be selected for these review
functions; however, the component Blank and Standard rows for any calibration
may be reviewed.
Multiple reviews can be performed on any data row (by one or more users); for
example, a reviewer can perform a subsequent review to add more details, add an
additional reason, or comment on another reviewer’s signature. Approve and
Reject functions cannot be performed on a row until at least one Review has been
logged.
If the Audit Trail > Quality Control Sign off option is also enabled on the Select
Enhanced Security Features window, the Review button on the Report View QC
tab is replaced by a QC Signoff button. You can configure a user Group for quality
assurance personnel to perform QC validation, and use this function to add it to
your workflow.
Because the Reporter currently displays information for quantitative analyses
only, acquired data records for other types of analyses — such as Isotope Ratio or
TotalQuant analyses — cannot have the review functions applied to them.
ES Tools File History Review, Approve, and Reject functions
All file types except data files can have Review, Approve, and Reject functions
applied to them only in the ES Tools > File History window. Here, the Review,
Approve, and Reject functions appear in the row of action buttons at the top of the
window. The File History window contains a comprehensive record of all key
workflow files in the system. Here users who are members of groups with the
appropriate permissions can select from any of their accessible project folders, to
isolate and examine all versions of any file contained therein. They can then click
on any file version that has not been closed to select a particular file version (or
CTRL + click to select multiple rows); and then indicate review, approval, or
rejection of the selected data.
Multiple reviews can be performed (by one or more users) on any file version that
has not been marked Version Closed. For example, a reviewer can perform a
subsequent review to add more details, add an additional reason, or comment on
another reviewer’s signature. Approve and Reject functions cannot be performed
on a file version until at least one Review has been logged.
Approved files are labeled Approved, and become the new in-use version of that
particular file in the system; all previous unapproved versions of that file are
marked Version Closed. When a file is rejected, it is labeled Rejected, and a
version of the file tagged with a _rejected suffix is created and kept in the project
folder for future examination; the previous version of the file is restored to use.
If your system has been configured to not require e-signature information (or
some subset of e-signature information) at certain points in the workflow, the
relevant cells in the File History table are marked NA (Not Applicable).
To show differences between two versions of a file

1. In the ES Tools window, click File History. The File History window
appears.
Figure 3-18 File History window — view differences

2. In the Project Folder drop-down list, select the project folder containing
the file versions you want to show differences between. To repopulate the
Project Folder list and update the File Types list, click Refresh. The File
Types box displays the types of files stored in the specified working folder:
method files, mass calibration files, sample files, report files, conditions
files, calibration files, and response files.
3. In the File Types box, expand the tree and select the file whose versions
you want to show differences between. When you select a file, a list of all
versions of that file appear in the File Versions table.
4. In the File Versions table, select two versions. When you click any version
other than version one, the version you clicked and the previous one are
selected by default. To select two non-consecutive versions, click one
version, hold down the Ctrl key, and then click the other version.
5. When you have selected the two versions for which you want to show the
change delta, click Show Differences. A detail of the differences between
the two versions appears in the results panel at the bottom of the window.
6. To print the contents of the results pane, click File > Print.
Repairing and compacting the databases

The audit trail and file version control databases may become large and
cumbersome over time, leading to slower performance. These databases can
also sometimes become corrupted. For instance, if your computer or operating
system stops responding while the software is saving information to a database,
the database could become corrupt. To avoid database corruption or performance
issues, you should compact your databases regularly.
Note: Before repairing and compacting the databases, ensure that the ES Setup and
Enhanced Security software applications are not running, and that no other application is
using the databases.
To repair and compact the databases

1. In the ES Tools window, click Repair/Compact.
2. When prompted to confirm this operation, click Yes. ES Tools uses
standard database utilities to repair and compact the databases.
Archiving system data and audit files

You can archive dataset files along with other supporting data so that they can be
periodically backed up to a secure storage medium and restored later if required.
You specify a project folder, and the ES Tools utility archives the following
information:
• Audit trail database entries related to the specified project folder
• File version control database entries related to the specified project folder
• Dataset files (containing conditions, calibration, method, report options,
and configuration information)
You also specify an end date and a destination folder. Then the ES Tools utility
browses the specified project folder, collects the above information that has a date
stamp before or on this end date, compresses them in one ZIP file, and saves this
file to the destination folder specified. Finally, the ES Tools utility deletes the
archived dataset files and audit trail records from the source location.
Note: When you archive these files, the Syngistix databases are automatically
compacted. Before running the archiving utility, ensure that the ES Setup and Enhanced
Security software applications are not running and that no other application is using the
databases.
To archive system data and audit files

1. In the ES Tools window, click Archive.The Archive dialog box appears.
Figure 3-19 Archive dialog box

2. In the Archive Date group, specify one of the following options:
 All: Archives all files regardless of date stamps
 End Date: Archives all files that have a date stamp identical to or
preceding the specified date
3. In the Archive group, specify one of the following options:
 Project Folder: archives all audit trail and file versioning records
related to the specified project folder. Select a project folder from the
drop-down list.
 Other: archives all non-project-related audit trail records, specifically
those related to ES Setup and Archive/Restore
4. Specify the location in which the archive should be placed by typing a full
path name or clicking Browse and selecting a folder.
5. If you want to include text to distinguish this archive from others, type the
text in the Add a description text box.
6. Click Archive.
7. When prompted to confirm the operation, click Yes. The Status area
shows the progress of the operation.
8. When the archive is complete, click Exit.
Restoring archived data and audit files

To restore archived files, first specify the location of the archived data file or
project folder, then specify the destination folder to which you want to restore the
archived data. If you select a destination folder that contains Syngistix data, this
Syngistix data will be overwritten.
When the restore process is complete, you must run ES Setup to ensure that the
destination folder you restored to is a valid project folder. You must also assign the
destination folder to the appropriate users. Then you can use the destination
folder containing the restored data like any other project folder. You can then also
archive the restored data file or project folder at any time.
Note: Before running the restore utility, ensure that the ES Setup and Enhanced Security
software applications are not running. Also, ensure that the destination folder specified in
the restore procedure does not contain any files that you do not want overwritten.
To restore archived data and audit files

1. In the ES Tools window, click Restore.The Restore dialog box appears:
Figure 3-20 Restore dialog box

2. Type the full path and name of the archive file to restore, or click Browse
to locate the file. Any descriptive text that was entered during the archiving
process appears in the Archive Description box.
3. Choose a folder into which to restore the file by typing the full path of the
folder, or click Browse to locate a folder.
4. Click Restore. A confirmation dialog box appears, reminding you that any
files in the destination folder that have names identical to those in the
archive will be overwritten.
5. To confirm the restore operation, click Yes. The Status bar shows the
progress of the operation. When the operation is complete, a dialog box
appears reminding you to launch ES Setup to define the restored folder as
a project folder and assign it to a user.
6. Click Exit.
Chapter 4
Optimization Processes
This section discusses the optimization and tuning functions of the software. The
SmartTune tools allow you to perform regular performance checks and
optimizations at varying levels of granularity. And each method you run includes
mass calibration and conditions files that specify the hardware parameters under
which determinations will occur.
• The SmartTune™ Functions on page 115
• Custom Mass Calibrations on page 143
• Deadtime Corrections on page 144
• Mass Calibration panel Software Reference on page 145
• Conditions screen on page 132
• LogBook on page 147
Optimizing and Calibrating the Instrument

In most cases, you should optimize and calibrate the instrument using the
SmartTune functions. However, advanced users can also use the Mass
Calibration and Conditions windows to perform custom resolution, condition
adjustments, and manual cell gas parameter optimization where applicable.
The SmartTune™ Functions

The Syngistix SmartTune™ functions provide a full range of tuning and
optimization options to provide exactly the level of control you need to keep your
system running at peak performance. A sophisticated automated optimization
tool, SmartTune Express makes daily tuning quick and easy. For more specific
needs and less-frequent system adjustments, the SmartTune Manual suite of
optimizations lets you select just the tuning parameters you want, and adjust them
to suit the particular requirements of your lab. A comprehensive Results panel,
shared by both the SmartTune Manual and Express applications, captures and
displays the most recent results for the selected optimization. You can then
manipulate the data shown interactively to adjust your data and fine-tune your
settings. For manual sample runs (not using an autosampler), an intelligent Smart
Sampling™ function detects and determines when two sequential functions use
the same solution. When this is the case, you are no longer prompted between
optimizations to manually aspirate the sample. The data from any SmartTune
Express or Manual Performance Check is automatically recorded in the LogBook
as part of the system’s performance tracking and diagnostics function.
115
The SmartTune™ Express Optimization Tool

IMPORTANT! (UCT instruments only) The pre-defined Standard acquisition profile,
Ammonia DRC profile (assigned by default to cell gas channel A), and Helium KED profile
(assigned by default to cell gas channel B) are required to run the SmartTune Express
optimizations. To run an Express optimization, the default profile or profiles for the modes
being optimized must be assigned to their default gas channels.
SmartTune Express was designed to be a one-button optimization solution to get

your ICP-MS system tuned up and running quickly each day. This application runs
an automated set of pre-determined optimizations that proceed dynamically and
intelligently until satisfactory sensitivity and background levels are achieved. For
many labs, this will constitute sufficient tuning for daily operations. During a
SmartTune Express run, the following optimizations may be performed (note that,
on UCT instruments, the optimizations performed depend also on the profiles and
modes selected; these functions may also be run in STD, KED, or DRC mode-
specific versions, depending on your settings):
• Background and sensitivity performance check
• Torch alignment
• QID optimization
• Nebulizer gas flow
• Cell rod offset (CRO) (UCT instruments only)
• Cell entrance/exit voltage (UCT instruments only)
• Mass calibration
• Detector voltages
As the optimization proceeds, the processes being run are displayed in the
SmartTune list box. This is a dynamic process, however — when the desired
sensitivity and background levels are detected, the optimization process stops, so
there is no guarantee that all possible procedures will be run. If your lab
regulations mandate that certain processes are run every day (or on a particular
schedule), you should create a SmartTune Manual file containing those
processes that you can run as required.
Note: The data from any pre-defined performance checks performed as part of a
SmartTune Express optimization is automatically recorded in the LogBook as part of the
system’s performance tracking and diagnostics function.
The Syngistix Options Performance Check Defaults tab

The SmartTune Express software is designed to optimize the instrument to its
factory specifications. This is generally sufficient for most applications. However,
for some purposes; to meet the standards set by certain regulatory organizations;
or to offset natural changes in sensitivity due to environmental factors or an aging
instrument, you may wish to adjust the optimization criteria. To do so, there is a
tab in the Syngistix Options dialog box where you can change and save these
criteria (on UCT instruments, these settings are further organized by mode).
When you run SmartTune Express thereafter, it will optimize to those new
specifications.
These Performance Check Defaults are also used in the SmartTune Manual
Performance Check optimizations. To reset the defaults back to their original
factory settings, simply click Reset. See Performance Check Defaults tab on
page 41 for more information.
The SmartTune™ Manual Optimization Tool

The SmartTune Manual function optimizes the instrument by running a series of
procedures you select. Here, you can also perform a mass or dual detector
calibration and resolution, and adjust torch parameters. All optimization
procedures have default parameters and methods that you can modify as
required. If you modify a default method file, you should save it with a new name,
and revise any affected SmartTune files accordingly. You use the SmartTune
setup panel to select which procedures to run in sequence and to fine-tune the
procedures. You select which acquisition profile to optimize against; which
method files; to use, and the start, step, and end values for each procedure.
You can select additional optimization runs for each procedure, and change the
start, step, and end values to extend the optimization range in the event that an
optimum parameter is not achieved on the previous pass. The software
automatically selects the same method and criteria for the subsequent passes as
those used on the previous run.
The SmartTune™ Manual Pre-defined Files

The SmartTune Manual function comes with three main pre-defined files to cover
regular optimization tasks — SmartTune Daily, SmartTune Monthly, and
SmartTune Full. You can run these files as they are, or modify them to meet your
specific needs.
Daily Optimization Process
The daily optimization process targets the sample introduction system, torch, and
cones. If the SmartTune Express function is not sufficient to your needs, you can
perform this process daily, adjusting the settings and adding additional
optimization processes as best suits your needs.
If performance is not adequate after this procedure, check the hardware of the
sample introduction system, torch, and cones, and clean or replace as needed. If
this fails to produce adequate performance, run a monthly or full optimization.
If your instrument has been modified or had heavy use since the last optimization,
run a daily optimization, and then proceed through a monthly, and then a full
optimization.
For UCT instruments, mode-specific DRC Performance Check.mth, KED
Performance Check.mth and STD Performance Check.mth files are available
for optimizing the instrument when switching between profiles using different
modes.
Monthly Optimization Process
This process builds on the daily optimization process, adding Detector Voltages
and Dual Detector optimizations. Run a monthly optimization process on a
regular—approximately monthly—basis, or whenever you want to verify that the
detector voltages are optimized.
Full Optimization Process
This process builds on the monthly optimization process, adding a Mass
Calibration and Resolution adjustment. Perform this process only when the state
of the instrument is unknown, after a major subsystem has been serviced, or
when all else fails to explain poor performance.
SmartTune™ Manual Optimization Procedures

On UCT instruments, some optimization types will have the relevant profile name
(gas and mode) added to the beginning of the optimization name (for example:
[Oxygen DRC] CRO or [Helium KED] Performance Check) to allow you to

optimize for the specific acquisition conditions. Optimization types without a mode
or gas specified in the name apply to all profiles and modes.
• Auxiliary Gas Flow: Use to optimize the Auxiliary Gas Flow.
• Cell Entrance/Exit Voltage STD: Available on UCT instruments only. Use
this procedure to optimize the DRC cell path voltage for standard mode.
The DRC system acts like a long AC-only section, exhibiting mass-
dependent focusing and multiple maxima for analyte versus voltage
profiles. Similar mass-dependence and multiple optima are seen when
optimizing the cell path voltage and cell RF voltage. Optimization for these
parameters cannot consist of a single mathematical criteria, but must take
into account mass bias (the relative balance of low, mid, and high mass
intensity) and the continuum background, which is influenced by ion path
voltages. The ultimate measure of the power of an instrument lies in the
ability to achieve extremely low detection limits. The most important factor
contributing to the detection limit measurement is the chemical
background signal. In many instances, the measurement is governed by
the continuum background. When optimizing, try to trade off signal
intensity for reduced background. An increase in background from 1 cps to
2 cps typically requires a four-fold increase in analyte sensitivity to
maintain the same detection power.
• Cell Rod Offset STD [CRO]: Available on UCT instruments only. Use this
procedure to set up the DRC rod offset voltage for standard mode.
• Deflector Voltage: Use this procedure to optimize the deflector voltage
parameters. In most cases, you should use the QID functions — use this
procedure only when you require maximum sensitivity for reading a single
element.
• Detector Voltages: This process optimizes the voltages for both the pulse
and analog stages to improve detector performance. Service mode only.
Additional controls become available so that you can optimize either of the
voltages separately or do them both at the same time.
Note: Some systems may not be able to meet the performance values indicated
in the pre-defined SmartTune files. These criteria reflect the factory specifications
to which your instrument was certified when manufactured. Laboratory conditions
and normal instrument use can affect performance over time, as can
modifications to instrument operating parameters, sample introduction systems,
and other hardware. Consequently, these criteria may no longer be achievable
following initial performance verification. In this event, you can still obtain
excellent analytical results in most cases by employing the appropriate QC
protocols.
• Differential Aperture: Available on 300/350Q instruments only. Use this

procedure to set up the Differential Aperture optimization parameters. This
lens aperture separates the analyzing quadrupole from the QID — this
optimization process optimizes the lens voltage on the bell housing to
regulate the flow of ions through the aperture, while accounting for the
difference in pressure between the two regions.
• Dual Detector Calibration: Dual detector calibration extends the dynamic
range of the detector by normalizing the analog stage to the pulse stage.
The calibration must contain each analyte you want to quantitate using
extended dynamic range. Perform a dual detector calibration only as
required. Before doing this procedure, you must calibrate the detector
voltages.
• ICP RF Power: Use this procedure to optimize the ICP RF power only
when required. You will seldom need to perform this procedure. The ICP
RF power is set to a value of between 1000 and 1600 watts, depending on
the sample introduction system used and the nature of the sample matrix.
• Lab Performance Check: Use this procedure to set up a custom
performance check for your lab, and to validate that background count,
sensitivities, and oxides are all within the desired ranges.
Note: The data from any Lab Performance Check is automatically recorded in
the LogBook as part of the system’s performance tracking and diagnostics
function. You can use the Lab performance Check option to check system
performance for custom acquisition profiles and non-standard cell gases.
• Makeup Gas Flow: Available on 300/350Q instruments only. This option

is available only if the makeup gas function is installed and enabled in the
software. Use this procedure to set up a makeup gas optimization to
achieve optimum sensitivity while also meeting the oxide ratio criterion.
• Mass Calibration and Resolution: Use this procedure to set up the mass
calibration and resolution optimization parameters. You can alter the peak
search window (amu) and custom resolution DAC in the Mass Calibration
panel. The SmartTune function performs the calibration based on the
definitions in the mass calibration .tun file, using an advanced centroiding
algorithm for maximum precision. Note that mass calibration and
resolution is not normally performed daily — you should perform this
process daily only if you are using certain EPA methods, such as US EPA
method 200.8 or 6020a.
• Nebulizer Gas Flow: Available on 300/350Q instruments only. Use this
procedure to optimize the nebulizer gas flow. The nebulizer gas flow rate is
a key operating parameter. An excessive flow rate cools the plasma and
can decrease ionization efficiency while increasing molecular ion
formation. Decreasing the flow reduces the analyte introduction rate and
warms the plasma, reducing the analyte signal and molecular species, and
increasing the number of doubly-charged ions.
When run as part of a SmartTune Express optimization, this function
employs a dynamic range-finding feature, wherein the software
automatically detects the optimum range settings for successive retries of
the optimization and configures them for you, decreasing the amount of
time spent on each run.
• Performance Check: Available on 300/350Q instruments only. Use this
procedure to set up a performance check, and to validate that background
count, sensitivities, and oxides are all within the necessary ranges.
Note: The data from any Performance Check is automatically recorded in the
LogBook as part of the system’s performance tracking and diagnostics function.
• Plasma Gas Flow: Use this procedure to set up the plasma gas flow
optimization parameters.
• QID (Quadrupole Ion Deflector): Available on 300/350Q instruments
only. Use to optimize QID parameters to adjust the lens scanning system
for maximum efficiency measuring the isotopes of interest. The QID

function compensates for matrix suppression and space charge effects in
the ion optics, enabling the software to achieve optimum sensitivity for
each isotope.
IMPORTANT! You must use the default method provided for all QID
calibrations. Also, ensure that the mass range used for your calibration includes
the range specified for your analytical determinations. Any deviation from these
protocols will compromise analytical performance.
• Torch Alignment: Use this procedure to optimize the X and Y axis torch
alignment. The instrument firmware uses an optimization algorithm to
determine the torch XY coordinates at which the maximum signal intensity
will be produced. The convergence criterion of the algorithm is that the
RSD between successive points must be less than 5%. The optimization
algorithm runs a maximum of 50 steps, after which, if the RSD criterion is
not yet met, the optimum is set to those coordinates where the maximum
intensity was recorded. The optimization fails if no intensities encountered
exceed 1000 cps.
• Torch Sampling Depth: Use this procedure to optimize the Z axis torch
depth alignment. This process may help to increase optimal performance
when determining for low oxide samples.
• [STD] Performance Check: Available on UCT instruments only. Use this
procedure to set up a STD mode performance check for your lab, and to
validate that background count, sensitivities, and oxides are all within the
desired ranges. Use this check when switching to STD mode from another
mode.
• [STD] QRO (Quadrupole Rod Offset): Available on UCT instruments
only. Use this procedure to optimize the quadrupole rod offset in standard
mode.
• [STD/DRC] QID (Quadrupole Ion Deflector): Available on UCT
instruments only. Use to optimize QID parameters to adjust the lens
scanning system for maximum efficiency measuring the isotopes of
interest. The QID function compensates for matrix suppression and space
charge effects in the ion optics, enabling the software to achieve optimum
sensitivity for each isotope.
• [STD/KED] AMS Gas Flow: Available on 2000 instruments only. This

option is available only if the AMS/O2 gas function is enabled. Use this
procedure to set up a gas optimization for a Standard or KED mode profile.
• [STD/KED] Makeup Gas Flow: Available on 300/350 UCT instruments
only. This option is available only if the makeup gas function is installed
and enabled in the software. In Standard or KED mode, use this procedure
to set up a makeup gas optimization to achieve optimum sensitivity while
also meeting the oxide ratio criterion.
• [STD/KED] Nebulizer Gas Flow: Available on UCT instruments only. Use
this procedure to optimize the nebulizer gas flow for Standard or KED
mode. The nebulizer gas flow rate is a key operating parameter. An
excessive flow rate cools the plasma and can decrease ionization
efficiency while increasing molecular ion formation. Decreasing the flow
reduces the analyte introduction rate and warms the plasma, reducing the
analyte signal and molecular species, and increasing the number of
doubly-charged ions.
• [KED] QID (Quadrupole Ion Deflector): Available on UCT instruments
only. Use to optimize QID parameters to adjust the lens scanning system
for maximum efficiency measuring the isotopes of interest. The QID
function compensates for matrix suppression and space charge effects in
the ion optics, enabling the software to achieve optimum sensitivity for
each isotope.
• [KED Profile] Cell Entrance Voltage: Available on UCT instruments only.

Use this procedure to optimize the cell path entrance voltage for KED
mode.
• [KED Profile] Cell Exit Voltage: Available on UCT instruments only. Use
this procedure to optimize the cell path exit voltage for KED mode.
• [KED Profile] CRO (Cell Rod Offset): Available on UCT instruments only.
Use this procedure to optimize the cell rod offset for KED mode profiles.
• [KED Profile] Performance Check: Available on UCT instruments only.
Use this procedure to set up a KED mode performance check for your lab,
and to validate that background count, sensitivities, and oxides are all
within the desired ranges. Use this check when switching to KED mode
profile from a profile in another mode.
Note: The data from any KED Performance Check is automatically recorded in
function.
• [KED Profile] QRO (Quadrupole Ion Deflector): Available on UCT

instruments only. Use this procedure to optimize the quadrupole rod offset
for KED mode profiles.
• [DRC Profile] AMS Gas Flow: Available on 2000 instruments only. This
option is available only if the AMS/O2 gas function is enabled. Use this
procedure to set up a gas optimization for a DRC profile.
• [DRC Profile] Cell Entrance/Exit Voltage: Available on UCT instruments
only. Use this procedure to optimize the cell entrance and exit voltages for
DRC mode profiles. Your aim is to select a value that results in minimum
background while maintaining maximum analyte signal.
• [DRC Profile] CRO (Cell Rod Offset): Available on UCT instruments only.
When optimizing the cell rod offset in DRC mode profiles, your aim is to
select a value that results in minimum background noise while maintaining
the maximum analyte signal.
• [DRC Profile] Makeup Gas Flow: Available on 300/350 UCT instruments
only. This option is available only if the makeup gas function is installed
and enabled in the software. Use this procedure to set up makeup gas
optimizations in DRC profiles to achieve optimum sensitivity while also
meeting the oxide ratio criterion.
• [DRC Profile] Nebulizer Gas Flow: Available on UCT instruments only.
Use this procedure to optimize the nebulizer gas flow in DRC mode
profiles. When optimizing nebulizer gas flow in DRC mode, aim for a value
that results in minimum background while maintaining maximum analyte
signal.
• [DRC Profile] Performance Check: UCT instruments only. Use this
procedure to set up a DRC mode performance check for your lab, and to
validate that system sensitivities are within the desired ranges. Use this
check when switching to a DRC mode profile from a profile in another
mode.
Note: The data from any DRC Performance Check is automatically recorded in
function.
• [DRC Profile] QRO (Quadrupole Rod Offset): Available on UCT

instruments only. To obtain sufficient transport through the quadrupole
mass filter, the DRC mode quadrupole rod offset must be made more
negative than the DRC mode CRO. This is because the ions are
collisionally dampened within the DRC system when it is pressurized. In a
sufficiently pressurized cell, the ions are nearly thermalized and have a
potential energy nearly the same as the cell rod offset. In most cases, the
DRC mode QRO value can be set without optimization according to the
relationship: DRC mode QRO = DRC mode CRO - 5.5. When optimizing
the DRC mode QRO, your aim is to select a value that results in minimum
background while maintaining maximum analyte signal.
• [Service] AC Rod Offset: Service mode only. Available on 300/350Q
instruments only. Use to optimize the AC Rod Offset.
• [Service] Discriminator Threshold: Service mode only. A bracket with
two capacitors connected in parallel sits on the ion detector high voltage
power supply board to reduce the ripple noise on the pulse stage positive
high voltage. This bracket has EMI fingers for grounding purposes. By
reducing the ripple, the instrument can operate at a lower discriminator
level and a lower multiplier gain, thereby extending the life of the detector.
The factory parameter for the discriminator threshold is printed on the data
sheet that is shipped with the instrument. The optimum discriminator
threshold is set so the instrument can distinguish between real pulses and
electronic noise. If, after a period of time, the noise increases, optimize the
discriminator. When you have finished, optimize the detector voltages.
• [Service] Torch XY Intensity Plot: Service mode only. Use this
procedure to set up a torch XY intensity plot at high or low resolution.
When to Perform SmartTune™ Manual Optimization Procedures

Generally you will simply run a daily SmartTune Express optimization to prepare
your system for normal operation. However, there are a number of individual
optimizations available that you may choose to run to meet particular lab
requirements; to correct for performance issues; or to provide tuning following a
hardware change or adjustment. The following charts provide some guidance
regarding when you might need to run these optimization procedures.
Note: When run, a Mass Calibration and Resolution should come first in a complex
optimization, but it is not normally a daily procedure. Run it daily only if you are using
certain EPA methods, such as US EPA method 200.8 or 6020a.
Table 4-1 Optimization procedures: 300/350Q Basic Quadrupole instruments
Procedure When to perform
Deadtime Correction When the detector is replaced, in which
case you should do it after the detector
optimization.
See Deadtime Corrections on page 144 for
more information.
Deflector Voltage When you require maximum sensitivity for
reading a single element.
Detector Voltages Monthly, or when sensitivity cannot be
recovered through other cleaning or
optimization methods, or when the
detector is replaced.
Table 4-1 Optimization procedures: 300/350Q Basic Quadrupole instruments
Dual Detector Calibration When you require an extended dynamic
range above two million counts per second
in a quantitative analysis. A detector
calibration is always necessary if you have
selected the Dual Detector mode on the
Method panel Processing tab. You must
calibrate for each analyte you want to
quantitate. A minimum of two masses is
required for cross‐calibration.
Nebulizer Gas Flow Daily.
Performance Check Daily, or as required.
QID Daily if your methods use the QID™
function. Also, perform a QID calibration
when sample matrices are significantly
different to achieve the best performance.
Torch Alignment Daily, or after you clean or replace the
cones, or perform any maintenance
procedures in the torch chamber.
Table 4-2 Standard mode optimization procedures: UCT™ instruments
Deadtime Correction When a detector has been replaced, and
after the new detector has been optimized.
See Deadtime Corrections on page 144 for
more information.
Deflector Voltages When you require maximum sensitivity for
reading a single element.
Detector Voltages Monthly, or when sensitivity cannot be
recovered through other cleaning or
optimization methods, or when the
detector is replaced.
Dual Detector Calibration When you require an extended dynamic
range above two million counts per second
in a quantitative analysis. A detector
calibration is always necessary if you have
selected the Dual Detector mode on the
Method panel Processing tab. You must
calibrate for each analyte you want to
quantitate. A minimum of two masses is
required for cross‐calibration.
Table 4-2 Standard mode optimization procedures: UCT™ instruments
Mass Calibration When the sensitivity cannot be recovered
through optimization or when there are
changes made to the quadrupole power
source electronics.
Torch Alignment Daily, or after you clean or replace the
cones, or perform any maintenance
procedures in the torch chamber.
STD Performance Check Daily, or as required (i.e., when switching to
STD mode from another mode).
[STD] Cell Entrance/Exit Voltage When the performance check does not
meet specifications.
[STD] CRO (Cell Rod Offset) When the performance check does not
meet specifications.
[STD/KED] AMS Gas Flow Daily, if the AMS gas option is installed.
[STD/KED] Makeup Gas Flow Daily, if the makeup gas option is installed.
[STD/KED] Nebulizer Gas Flow Daily.
[STD/DRC] QID (Quadrupole Ion Daily if your methods use the QID™
Deflector) function. Also, perform a QID calibration
Table 4-3 DRC™ mode optimization procedures: UCT™ instruments
Cell Gas Flow When measured detection limits do not
meet requirements.
See the help system for more information.
Detection Limits When measured detection limits do not
meet requirements.
[DRC Profile] Cell Entrance/Exit When measured detection limits do not
Voltage meet requirements.
[DRC Profile] CRO When measured detection limits do not
meet requirements.
Table 4-3 DRC™ mode optimization procedures: UCT™ instruments
[DRC Profile] Makeup Gas Flow When measured detection limits do not
[DRC Profile] Nebulizer Gas Flow meet requirements.
[DRC Profile] QRO (Quadrupole Rod When measured detection limits do not
Offset) meet requirements.
[DRC Profile] Performance Check Daily, or as required (i.e., when switching
to DRC mode from another mode).
Table 4-4 KED mode optimization procedures: UCT™ instruments
Cell Gas Flow When measured detection limits do not
meet requirements.
[KED] QID (Quadrupole Ion Daily if your methods use the QID™
Deflector) function. Also, perform a QID calibration
[KED Profile] Cell Entrance Voltage When measured detection limits do not
meet requirements.
[KED Profile] Cell Exit Voltage When measured detection limits do not
meet requirements.
[KED Profile] CRO (Cell Rod Offset) When measured detection limits do not
meet requirements.
[KED Profile] Performance Check Daily, or as required (i.e., when switching
to KED mode from another mode).
[KED Profile] QRO (Quadrupole Rod When measured detection limits do not
Offset) meet requirements.
SmartTune™ Software Reference
Figure 4-1 SmartTune screen showing a SmartTune Express function
Figure 4-2 SmartTune screen showing a SmartTune Manual function
SmartTune™ Setup Panel

The SmartTune setup panel is common to both the SmartTune Express and
SmartTune Manual functions; here you select which function you are going to use,
and configure all relevant criteria.
If you are using the SmartTune Express function, the setup panel contains default
file selection controls; autosampler position settings; pump settings; and (on UCT
instruments) options for selecting the modes for which you want to optimize the
instrument, and defining cell gas flows for those modes. The large display field in
the setup panel then acts as a tracking tool, displaying a list of each optimization
process run, and detailing the process in progress.
When using the SmartTune Manual function you use the setup panel to select
which procedures to run in sequence and to fine-tune the procedures. You select
which method file to use, and the start, step, and end values for each procedure.
You can select additional optimization runs for each procedure, and change the
start, step, and end values to extend the optimization range in the event that an
optimum parameter is not achieved on the previous pass. The software
automatically selects the same method and criteria for the subsequent passes as
those used on the previous run.
SmartTune Common Optimization controls
You must configure the following overall parameters before running an
optimization. In SmartTune Express, these options are always displayed; in
SmartTune Manual, you must select Optimization in the list box in order to
access these parameters:
• Optimize: Starts the selected SmartTune optimization.
• SmartTune function drop-down list: Click to select SmartTune Express or
SmartTune Manual.
• Edit List: SmartTune Manual only Accesses the optimization procedure
selection dialog box where you can select and order your procedures.
Note: For UCT instruments, a drop-down list at the top of the Edit List dialog box
displays all acquisition profiles in the system. You can choose any profile (or
multiple profiles) when creating or saving a SmartTune optimization file, but you
can only run optimizations for which the selected profiles are currently assigned to
a gas channel.
Depending on the mode or profile chosen, some optimization types will have the
relevant profile name (gas and mode) added to the beginning of the optimization
name (for example: [Oxygen DRC] CRO or [Helium KED] Performance Check) to
allow you to optimize for the specific acquisition conditions.
• Mode: SmartTune Express only and UCT instruments only Displays the
mode or modes to which the optimization will apply. Click Set to specify
the modes you will be optimizing for when setting up a SmartTune Express
optimization. Here you can also indicate the appropriate cell gas flow for
each mode (in liters per minute).
IMPORTANT! (UCT instruments only) The pre-defined Standard acquisition

profile, Ammonia DRC profile (assigned by default to cell gas channel A), and
Helium KED profile (assigned by default to cell gas channel B) are required to run
the SmartTune Express optimizations. To run an Express optimization, the default
profile or profiles for the modes being optimized must be assigned to their default
gas channels. See Acquisition Profiles tab on page 37 for more information.
• Optimization list box: In SmartTune Express, this box on the left side of
the SmartTune setup panel initially displays instructions for using
SmartTune Express; when an optimization is running, it lists the processes
being run as they are run.
In SmartTune Manual, this box on the left side of the SmartTune setup
panel shows a list of optimization procedures to be processed in
sequence. Click Edit List to add procedures. You can change the
optimization sequence by dragging entries in the list. You can also click an
entry in the list to show the details for that procedure. Or right-click a
procedure in the list, and then click:
 Delete to remove a procedure from the list
 Quick Optimize to run the selected procedure only
• Use Manual Sampling (No Autosampler): Select this check box if you do
not use an autosampler. Note that, if using manual sampling, you will be
prompted to aspirate each optimization solution in turn — Read and Flush
delays will not apply. (See also Use Smart Sampling, following.)
• Use Smart Sampling: For manual sample runs (not using an
autosampler), if selected, this intelligent sampling function detects and
determines when two sequential functions use the same solution. When
this is the case, you are no longer prompted between optimizations to
manually aspirate the sample.
• Stop if optimization fails: Select this check box if you want the
SmartTune process to stop immediately following any unsuccessful
optimization. Unavailable in the SmartTune Express function.
• Send Results to Printer: Select this check box if you want to
automatically print the result summary reports following optimization.
• Autosampler: These parameters specify autosampler locations for each
procedure:
 Procedure displays read-only entries that are updated when entries in
the optimization procedure list are added, deleted, or moved
 A/S Location lists the autosampler tray positions for the solution to be
used for each optimization. This entry is ignored if a manual analysis
with no autosampler is being performed
• Peristaltic Pump: This table provides peristaltic pump parameters
derived from the Global Pump parameters. Change these to override
these parameters when running a SmartTune optimization:
 Sample Flush Time: Specifies the time in seconds during which the
sample tubing is flushed with sample solution. Type a value between 0
and 99 999
 Sample Flush Speed: Specifies the pump speed in rpm during the
flush cycle. Any value between ±150 (2000 series instruments) or ±48
(300/350 series instruments) is valid
 Read Delay Time: Specifies the time in seconds between the end of
the flush cycle and the beginning of data acquisition. Type a value
between 0 and 99 999
 Read Delay Speed: Specifies the pump rate in rpm used during the
read delay cycle. Any value between ±150 (2000 series instruments)
or ±48 (300/350 series instruments) is valid. A negative value indicates

counter-clockwise rotation of the pump head and a positive value
indicates clockwise rotation
 Analysis Speed: Read only. Displays the pump rate in rpm used during
the determination. A negative value indicates counter-clockwise
rotation of the pump head and a positive value indicates clockwise
rotation
 Wash Time: Specifies the time in seconds during which the sample
tubing is rinsed with wash solution following completion of data
acquisition. Type a value between 0 and 99 999
 Wash Speed: Specifies the pump speed in rpm used during the wash
cycle. Any value between ±150 (2000 series instruments) or ±48
(300/350 series instruments) is valid. A negative value indicates
indicates clockwise rotation. During a wash cycle, you can use a more
rapid pump rate to quickly wash sample solution from the sample
tubing
• Files group: These fields let you specify the target Conditions, Mass
Calibration, and Dataset files in which to store your optimization data. Use
the pre-defined files displayed, or browse to select different files.
SmartTune Manual Common Procedure parameters

Most of the optimization procedures available through the SmartTune Manual
function share common parameters. These are listed here.
Table 4-5 SmartTune™ Manual Common Parameters
Control Function
Method Displays the method file used with this optimization
procedure. Use the default method displayed, or click
Browse to select a different file.
Criteria These options define the criteria against which the
instrument optimizes for this function. Typically, you
will click to choose one analyte for Intensity
optimization or one analyte Formula; use the formula
option when you want to optimize on a relationship
between two signals.
For some functions, you may choose All Analytes, and
the system will automatically select all the available
analytes in the related method, and provide a
secondary option for then excluding ratio and
background analytes as required.
Other functions employ a dynamic range‐finding
feature, wherein the software automatically detects
the optimum range settings for successive retries of
the optimization and configures them for you,
decreasing the amount of time spent on each run.
Specific criteria are listed with the individual
procedures.
Range These parameters define the range the instrument will
measure. During optimization, the system moves
through a series of values, with data acquired at each
value. You control the start and end flow values, and
the step size.
Ramp Select the Ramp check box to specify that the software
should conduct an optimization, but should return to
the original value when completed. Use this option
when you want to review the data before making any
parameter changes, or want to select a value that
does not result in the highest possible signal.
SmartTune™ Results Panel

A Results panel fills the right-hand portion of the SmartTune screen, and is shared
by both the SmartTune Express and SmartTune Manual applications. There are
two tabs on this panel — a Summary tab, which displays detailed summary
report information for the current (or most recent) optimizations run, and an
Optimization Details tab, which captures and displays the most recent results for
the selected optimization process. On the Optimization Details, you can review
your results and then manipulate them interactively to adjust your data and fine-
tune your settings. This information is persisted between sessions, and this tab
will always display the most recent data for any given optimization, whether the
data was gathered during a SmartTune Express or SmartTune Manual
optimization; and whether the individual optimization components were run
together, or disparately, over time.
SmartTune Results panel controls
This section describes the shared controls on the SmartTune Results panel
Optimization Details tab (the Summary tab has no controls: it simply records
summary report information for the current or most recent optimization process).
• Optimization selection drop-down list: Click to select the optimization you
want to display.
• Linear/logarithmic plot buttons: Use to select a linear value or

logarithmic value Y-axis plot.
• Grid off/on buttons: Use to select no grid (with tick marks) or a

full grid plot background.
• Print: Click to print the current optimization results. Opens the Print
selection dialog box.
• Print All: Click to print the complete set of most recent optimization
results. Automatically uses the default printer.
Conditions screen
Note: Generally, you should optimize and calibrate the instrument using the SmartTune
function. However, advanced users can use the Mass Calibration and Conditions panels
to perform high-precision or custom calibrations.
The Conditions screen is accessed via the Conditions icon on the ribbon, and
consists of a Conditions panel with multiple functional tabs, together with Sample
and Realtime panels, so that you can make changes and monitor your results
while optimizing the system. Use the Conditions panel to fine-tune the hardware
subsystems in the torch/quadrupole assembly. Here you can adjust control
parameters for the DACs (digital-to-analog converters) associated with these
functions. When opened, this panel displays the last file accessed. The Conditions
panel has several tabs:
• QID tab: Use this tab to view ion lens scan data. On UCT instruments, this
tab is further divided into subtabs for standard/DRC and KED modes, as
well as for any custom QID acquisition profiles.
• Dual Detector Calibration tab: Use this tab to view the performance of
each detector element (pulse and analog) and the crossover points
between the two detector systems.
• Manual Adjust tab: Use this tab to manually adjust the DAC values, so
you can make DAC adjustments without having to perform the full
optimization procedure.
• Advanced Optimize tab: Use this tab to control advanced optimization
routines for cell gases, rejection parameters, and Axial Field™ (AFT)
voltage. UCT instruments only.
• Cell Parameters tab: Use this tab to view advanced optimization routines
for cell gases and rejection parameters. You can also edit these values
here, and send them to the method. UCT instruments only.
QID Tabs
Use this tab to review lens scan data to ensure the instrument is experiencing
maximum efficiency measuring the isotopes of interest. The QID™ (Quadrupole
Ion Deflector) function compensates for matrix suppression and space charge
effects in the ion optics. It also helps the software to achieve optimum sensitivity
for each isotope in an analysis. You optimize the QID settings using the
SmartTune™ function. Use the QID tab only to review current QID calibration
data, or to reprocess a calibration using previously acquired data.
During acquisition profile creation, custom QIDs can also be specified, causing
additional tabs to appear here (the tab name will match the originating profile).
See Understanding Acquisition Profiles on page 31 for more information.
Note: On UCT instruments, this tab is further divided into subtabs for standard/DRC and
KED modes, as well as for any custom QID acquisition profiles. Although the algorithms
and parameters used for each mode are different, the controls on each of these subtabs
are identical.
Figure 4-3 Conditions panel QID tab
Items on the QID Tab

• Get Analyte List: Copies the list of analytes that are included in the active
method. Before a calibration can proceed, analytes must be listed in the
lens scanning data table, and a method that measures the listed analytes
must be loaded in the Method panel. If you have the proper analytical
method loaded, you can copy the list of analytes in the Lens Scanning
data table by clicking the Get Analyte List button.
• Clear Calibration: Clears current QID calibration data before creating a
new calibration or before loading calibration data from previously acquired
data.
• Calibrate From Dataset: Reads QID calibration information from
previously acquired data as long as at least one data file corresponding to
a QID calibration is selected. When data is acquired, the lens scanning
information is stored along with other operating parameters in the dataset.
This information can be used to calibrate the system for current analytical
determinations. Any valid dataset data can be used, regardless of the
original method type, as long as the data was acquired with a QID
calibration. To use the Calibrate From Dataset command, first click Clear
Calibration to remove any existing calibration data. Next, select the
relevant entry in the Dataset panel, and then click Calibrate From Dataset.
• Dataset Pathname: Indicates the name and location of the dataset used.
• Sample Filename: Indicates the name of the sample file used.
• Date: Indicates the date of the calibration.
• Points Acquired: Specifies the number of unique voltage values
measured during the lens scanning procedure. This value is determined
by the Start Value, End Value, and Step Size parameters. The Points
Acquired value is the total DAC range (End Value - Start Value) divided by
the Step Value +1.
• Correlation Coefficient: Specifies the voltage to mass coefficient on the
QID voltage-versus-mass graph.
• Intercept: Specifies the offset on the deflector voltage-versus-mass
graph, when the mass is zero.
Parameters in the QID Table
• Analyte: Specifies the analytes that will be used in the lens scanning
calibration. The analytes listed here should match the list of analytes in the
method. To import all of the analytes in the active method, click Get
Analyte List.
• Mass: Specifies the exact mass at which the QID calibration will be
performed for the analyte listed. To populate the Analyte and Mass fields,
click Get Analyte List; this imports the analyte and mass data from the
method. To add a new analyte, add it to the Method panel Timing tab, and
then click Get Analyte List.
• Points: Indicates the number of measurements taken during QID
calibration. This entry is read-only.
• DAC Value: Lists the DAC Value that will be used for the lens during
determinations. This value represents the DAC parameter that yielded the
highest signal intensity during the lens scanning calibration procedure.
This entry is read-only.
• Max Intensity: Lists the maximum intensity value obtained for the listed
analyte during the QID calibration. This entry is read-only.
Dual Detector Calibration Tab

Use this tab to review the dual detector parameters, to ensure the two stages of
the detector provide a linear response over the entire dynamic range of the
system. You perform a dual detector calibration using the SmartTune function.
Use the Dual Detector Calibration tab only to view current dual detector calibration
parameters, or to reprocess a calibration using previously acquired data.
Figure 4-4 Conditions panel Dual Detector Calibration tab

Items on the Dual Detector Calibration Tab
• Get Analyte List: Copies the list of analytes that are included in the active
method. Before a calibration can proceed, analytes must be listed in the
dual detector calibration data table, and a method which measures the
listed analytes must be loaded in the Method panel. If you have the proper
analytical method loaded, you can copy the list of analytes in the Dual
Detector Calibration data table by clicking the Get Analyte List button.
• Clear Calibration: Clears the current dual detector calibration data before
a new calibration is created by collecting new data or using Calibrate From
Dataset.
• Calibrate From Dataset: Reads dual detector calibration information from
previously acquired data, as long as two data files corresponding to a dual
detector calibration are selected. When data is acquired, the dual detector
calibration information is stored along with other operating parameters in
the dataset. This information can be used to calibrate the system for
current analytical determinations. Any valid dataset data can be used,
regardless of the original method type, as long as the data was acquired
using both detectors.
• Points Acquired: Specifies the number of unique voltages measured
during the dual detector calibration procedure.
Parameters in the Dual Detector Table
• Analyte: Specifies the analytes that will be used in the dual detector
calibration. The analytes listed here should match the list of analytes that
are being examined in the method. To automatically list all the analytes in
the active method, click Get Analyte List. When you require extended
dynamic range (above 2 million counts per second) in a quantitative
analysis, you must calibrate for each analyte you want to measure.
• Mass: Specifies the exact mass at which the dual detector calibration will
be performed for the analyte listed in the same row of the Dual Detector
Calibration data table. Populate the Analyte and Mass fields by clicking
Get Analyte List. This imports the analyte and mass from the method. To
add an analyte, add it to the Method panel Timing tab, and then click Get
Analyte List.
• #Points: Lists the number of crossover data points included in the dual
detector calibration curve. This entry is read-only. When the software
calibrates the dual detector system, response curves are generated for
both the pulse and analog stages of the detector. These two response
curves are integrated to yield a single curve which will serve as the
detector response curve for analytical determinations. For accurate dual
detector calibration, the system should have as many common data points
(that is, crossover points) as possible. These are data points at which the
system acquired both analog and pulse count data during the calibration
sequence.
• Coefficient: Lists the correlation coefficient for the composite response
curve that the software creates during dual detector calibration. This
correlation coefficient is generated during the linear regression of the data
points and is a measure of the quality of the final calibration curve. This
entry is read-only. A poor correlation coefficient is an indication that the
two response curves had very different slopes prior to their integration. In
this event, it is recommended that you recalibrate the system before
proceeding with analytical determinations.
• Gain: Lists the gain factor that will be used for the analyte in the same row
of the Dual Detector Calibration data table. This entry is read-only. The
gain value is used to decide how the software translates an analog current
signal into usable pulse count data during measurements.
• N(max): This read-only entry is the dynamic range of the detector using
the extended dynamic mode (dual mode), in counts per second. Signal
intensities above the N(max) value are considered to be in shutdown (S).
• Conversion Factor: Indicates the ratio of the analog signal to pulse
signal. It is the slope of the line on the dual detector calibration graphs.
These values are plotted in the Detector Response Function. This entry is
read-only.
Manual Adjust Tab

This tab displays the active optimization parameters for the current optimization
.dac file in the data table. Use this tab to make fine adjustments to the hardware
subsystems without having to perform a full optimization routine.
These parameters are intended for trained service representatives and
experienced users only. If you are unfamiliar with these parameters, use the
SmartTune functions instead.
UCT instruments only: The data table differentiates between standard, DRC, and
KED mode profiles by placing them against different colored column
backgrounds: Standard mode values appear against a white background; KED
mode values appear against a green background; and DRC mode values appear
against a yellow background.
A link graphic indicates a dependency between values; when one linked value is
changed, the software automatically updates the others accordingly. In the
Syngistix Options dialog box Acquisition Profiles tab, you can also specify that a
profile be unlinked, an option that severs some of the links between values in this
table. This frees you to independently adjust more parameters when working with
cold plasma analyses, and dealing with specific issues and interferences. When a
profile is unlinked, the following .DAC parameters can be adjusted individually for
that profile: Nebulizer Gas Flow, Plasma Gas Flow, Auxiliary Gas Flow, Makeup
Gas Flow (300/350 instruments only), Oxygen Gas Flow, ICP RF Power, and
Deflector Voltage.
Figure 4-5 Conditions panel Manual Adjust tab

Items on the Manual Adjust Tab
• Profile: UCT instruments only. Click to select an active acquisition profile
(or any Standard mode profile); this changes both the view in this tab and
the active operating mode of the instrument.
• View DAC Values: UCT instruments only. Click Active to view DAC values
for the selected profile only. Click All to view DAC values for all active
profiles (including Standard).
• DAC: Lists the current DAC value of the selected component. Use the
arrow controls to change the current value, or click and type directly in any
table cell.
Parameters in the Manual Adjust Table
• Profile/Value columns: UCT instruments only. Lists the active DAC value
of the hardware parameter selected for the profile indicated. Used when a
determination is run using the active Conditions file. To change a value,
click in the relevant table cell, delete the old entry, and type a new value.
The acceptable range for entries is listed in the Minimum Value and
Maximum Value fields.
A link graphic indicates a dependency between two values; when one

linked value is changed, the others are automatically updated accordingly.
During acquisition profile creation, you can also create unlinked profiles,
severing some of the links between values in this table. This frees you to
independently adjust more parameters when dealing with specific issues
and interferences.
• Current Value: 300/350Q instruments only. Lists the active DAC value of
the hardware parameter selected. Used when a determination is run using
the active Conditions file. To change the value, click in the relevant cell,
delete the old entry and type a new value. The acceptable range for
entries is listed in the Minimum Value and Maximum Value entries.
• Description: Describes the hardware subsystem associated with the
DAC. The software is shipped with descriptive information already filled in.
• Step Value: Lists the default Step Value that will be used in an automated
optimization.
• Settling Time (sec.): Shows the amount of time in seconds that the
instrument waits after a parameter value has changed before making the
analyte measurement. This delay lets the analyte signal stabilize.
• Minimum Value/Maximum Value: Displays the acceptable parameter
range for each DAC. The DAC Resolution value must not be set outside
the limits defined by these numbers.
Advanced Optimize Tab

UCT instruments only. Advanced users only can use this tab to perform
advanced optimization routines for cell gas flows, rejection parameters, and Axial
Field voltage. Generally, you should optimize these parameters using the
SmartTune option. Use the Advanced Optimize tab only when you need to
examine the process more closely.
Figure 4-6 Conditions panel Advanced Optimize tab

Items on the Advanced Optimize Tab
• Optimize: Initiates automated optimization of the subsystem selected in
the Parameter Description list. The new optimal DAC value for the
parameter appears in the Current Value field when optimization is
complete.
• Parameter Description: Lists the available hardware subsystems that
can be optimized using the automated optimization protocol. The following
parameters are available for optimization:
 Gas Flow: Adjusts the flow rate of the reaction cell gas associated with
the selected profile.
 Axial Field Voltage: Adjusts the AFT voltage, which improves DRC
system performance by applying a linearly accelerating axial field. The
net effect is that matrix effects are decreased, analyte signal is
stabilized, and the speed of analysis is significantly improved
The AFT voltage does not require frequent optimization because it has
a very broad optimization peak. However, if you suspect that the AFT
voltage requires optimization, run this process. Because the AFT
voltage optimization value is dependent on the deflector voltage, cell
path voltage, and cell rod offset, you should optimize it after these
parameters. If the value changes by greater than 100 V, you should
then re-optimize the deflector voltage, cell path voltage, cell rod offset,
and AFT voltage.
 RPa: Adjusts the DC voltage applied to the reaction cell quadrupole
 RPq: Adjusts the RF voltage applied to the reaction cell quadrupole
• Analyte: Specifies the element-mass-profile (generally gas and mode) on
which you want to optimize. If no analytes are listed, click Get Analyte List
to retrieve the list of analytes from the active method.
• Start Value: Specifies the start value for the optimization.
• End Value: Specifies the final value for the optimization.
• Step Value: Specifies the amount the value will be increased during
successive measurements of the optimization procedure. During
optimization, the software ramps the DAC value between the Start Value
and the End Value, increasing in successive measurements by the Step
Value. The intensity for the selected analyte is then plotted as a function of
the parameter value to find the optimum parameter. Click Get Defaults to
retrieve the default system values for the Start, End, and Step values.
• Maximum Intensity: Specifies that the software should calculate the
parameter value which creates the highest signal intensity during an
optimization.
• Minimum Intensity: Specifies that the software should calculate the
parameter value that creates the lowest usable signal intensity during an
optimization.
• Ramp: Specifies that the software should conduct an optimization, but
should return to the original value when completed. This option is selected
when you want to review the data before making the parameter change, or
want to select a value which does not result in the highest possible signal.
• Formula: Use this option to optimize on a relationship between two
signals. The most common relationship is signal-to-noise ratio. This
involves placing the analyte of interest in the first window under the
Formula option. Then select an operation (+, -, × or / ). Select the second
analyte and determine the relationship of either greater than, less than or
max (<, >, or max). In the final field insert a value. For example: CeO
156/Ce 140 < 0.03 (formula used to optimize the oxide ratio).
• Spike Concentration (ppb): RPq optimizations only. Use this entry to
specify the concentration in ppb of the standard solution or spike when
performing an automated RPq optimization. All analytes in this solution
must have the same concentration.
• LOD (Limit of Detection): RPq optimizations only. Select to choose Limit
of Detection as the optimization criterion. The LOD, expressed as the
concentration or quantity, is derived from the smallest measure that can be
detected with reasonable certainty for a given analytical procedure.
• BEC (Background Equivalent Concentration): RPq optimizations only.

Select to choose Background Equivalent Concentration as the
optimization criterion. BEC is the background signal represented as an
equivalent concentration and provides an excellent means of gauging the
true magnitude of noise.
Cell Parameters Tab

UCT instruments only. This tab displays the active cell gas parameters for the
current optimization .dac file in the data table. Entries on this tab are sorted in
parallel with the entries on the Method panel Timing tab — when the content and
order of the analytes on the Timing tab changes, the content and order of the
analytes on the Cell Parameters tab changes. When opened, this tab displays the
most recently optimized or edited cell parameter values for the analytes in the
current method.
Figure 4-7 Conditions panel Cell Parameters tab

Items on the Cell Parameters Tab
• Send Parameters to Method: Click to load the reaction cell parameters
displayed to the current Method Timing tab.
• Reset: Highlight a row in the table, and then click this button to reset the
values for the cell gas flows and the RPa (rejection parameter a) and RPq
(rejection parameter q) parameters. The elemental library maintains the
default system values for the gas flows and rejection parameters for each
element. The Elemental Library.xml may be edited by advanced users
only; contact your local service representative for more information.
Parameters in the Cell Parameters Table
• Analyte: Displays the analyte symbol corresponding to the mass of the
isotope the instrument will examine in each measurement. Taken from the
current method.
• Mass (amu): Specifies the mass at which the isotope will be measured.
This is a read-only parameter whose value is configured in the Method
panel Timing tab.
• Begin Mass (amu): (Data Only and TotalQuant methods only) Defines the
start of an atomic mass range for each measurement. The scanning range
defined by a single row in the table is the range between the Begin Mass
and End Mass values set in that specific row. This is a read-only
parameter whose value is configured in the Method panel Timing tab. To
populate a row with the default system cell parameter values, highlight the
row and then click Reset.
• End Mass (amu): (Data Only and TotalQuant methods only) Defines the
end of an atomic mass range for each measurement. This is a read-only
parameter whose value is configured in the Method panel Timing tab.
• Profile: Displays the acquisition profile to be used for the determination.
• [Gas] Flow columns (ml/min): These columns specify the flow rate in
ml/min at which the specified cell gas flows into the reaction cell.
• RPa (Rejection Parameter a): Specifies the DC voltage applied to the
reaction cell quadrupole for all methods. In normal operation, this entry is
automatically filled by the software when you type the atomic symbol or
isotope number in the Analyte column. To enter information in this column,
click the relevant cell and type the exact voltage at which the
measurement should occur.
• RPq (Rejection Parameter q): Specifies the RF voltage applied to the
reaction cell quadrupole for all methods. In normal operation, this entry is
automatically filled by the software when you type the atomic symbol or
isotope number in the Analyte column. To enter information in this column,
click the relevant cell and type the exact voltage at which the
measurement should occur.
Custom Mass Calibrations

Note: Generally, you should optimize and calibrate the instrument using the SmartTune
function. However, advanced users can use the Mass Calibration and Conditions panels
to perform high-precision or custom calibrations.
The mass calibration .tun file manages the instrument's quadrupole mass filtering
performance. The mass calibration functions permit custom parameter
configuration for mass calibration and resolution. You should calibrate the
instrument whenever there are changes to the electronics, or if you need to modify
resolution for one or more elements.
Note: The instrument must run for at least 30 minutes with the plasma on before you
perform a mass calibration.
Mass Calibration Controls

The mass calibration controls are used to perform a custom calibration or to adjust
the resolution of the mass spectral peaks. The procedure is quick to perform and
is good for fine-tuning the spectrometer for optimum performance.
The results from each set of mass calibration adjustments are initially stored in the
file default.tun. You can elect to save the results in a separate file with a name that
you specify. Each analytical method used to acquire data contains a mass
calibration .tun file.
DAC Files
The software tuning, optimization, and calibration controls include several entries,
controls, and files that use the acronym DAC. A DAC is a digital-to-analog
converter channel connected to a specific hardware subsystem. An electronically
controlled hardware component is adjusted by varying the parameter of its related
DAC.
Calibration Adjustments
Mass calibration and resolution adjustments affect the DAC parameters for the
quadrupole subsystem. The quadrupole systems act as a mass filter; calibration
affects the timing of ions through this filter, and the shape of the resulting mass
spectral peaks. Use the mass calibration controls to perform the following
operations:
• A mass calibration to adjust the instrument's electronics and guarantee the
accuracy of the mass spectrometer
• A resolution check and adjustment to ensure that the resolution at each
mass of interest is within the defined range
When running either operation, you can view the results as they happen in the
accompanying Realtime graphics panel.
Mass Calibration
When a mass calibration is performed, the Interactive panel displays a series of
graphs corresponding to the individual elements measured during the calibration.
During calibration, the instrument performs a determination on a test solution,
typically a solution covering a broad mass range. The instrument finds the
maximum intensity of each isotope in the solution and its atomic mass relative to
its intensity — the measured mass of the isotope.
During this measurement, the system scans for a peak within a predefined scan
width region centered around the exact, or known, mass for that isotope. The
instrument can then compensate for the differences between the apparent and
exact mass.
Resolution Check or Adjustment
Resolution is measured as the peak width at 10% peak height. The hardware is
preset to scan the entire mass range at 0.7 amu resolution. This parameter
provides the best balance between peak separation and signal-to-noise ratio for
most applications. The resolution can be adjusted on an individual mass basis, for
example to correct for spectral interferences. Again, a test solution covering a
broad mass range is typically employed. However, when adjusting resolution, you
may want to use the analytes included in your analysis method.
The system scans the specified analytes within a predefined scan width region
centered around the known mass for each analyte isotope, then measures the
peak width at 10% peak height. This value should normally be approximately 0.7
amu. Resolution should be within ±0.10 amu of the expected resolution or an
adjustment should be made.
Deadtime Corrections
Deadtime correction is a mathematical equation that is used to correct for
erroneous readings at high count rates (pulse counting) caused by the finite width
of the detector output pulses. At these high count rates (> 1,000,000 cps
approximately) there is a finite probability that two pulses will arrive at the detector
output simultaneously. The deadtime correction function corrects for this anomaly.
Deadtime Calculation
Characteristic of all ion detection systems, deadtime (t) is the amount of time
required for the detector to process the signal from an incident ion. Following an
ion strike, the detector is unable to record another strike for a short period of
time—this deadtime is typically 50 - 60 ns. If two ions arrive at the detector within t
seconds of each other, the second ion is not counted. At low count rates of less
than 1e5 cps, only 0.5% ions arrive during this period, and the count rate
measured by the detector is 0.5% less than the count rate impinging upon the
detector. At higher count rates, however, the effect is more significant and follows
the relation:
Rtrue = R0 / (1  R0t)
where:
Rtrue xis the ion count rate arriving at the detector
R0 xis the ion count rate measured by the detector
t xis the deadtime
When the deadtime of the system has been measured, the above equation can be
applied to correct for it. The software uses the deadtime correction to compensate
for counting loss at high ion arrival rates. When measuring using signals above
2e5 cps, you must ensure that the deadtime correction is set accurately.
Mass Calibration panel Software Reference

This section describes the Mass Calibration panel, which is accessed via the arrow submenu located
below the Conditions icon on the Ribbon menu.
Figure 4-8 Mass Calibration screen

Items on the Mass Calibration panel
• Start MassCal: Initiates a mass calibration and peak width measurement.
Results from a resolution measurement are displayed numerically in the
Peak Width (amu) column of the data table on this panel, and graphically
in individual isotope graphs in the Interactive panel. Typically, this
measurement takes only a few minutes to complete.
• Peak Width Only: Specifies that the mass calibration DAC value will not
be adjusted based on the measured mass. This is used to adjust the
resolution DAC value independently of the mass calibration DAC value.
Note: Because changes made exclusively to the resolution DAC affect the mass
calibration, you should always adjust the resolution and mass calibration in
tandem.
• Peak Search Window (amu): Specifies the width of the search window in
which the software will look for a peak for the isotope being measured. The
value entered defines a window in atomic mass units centered around the
known mass for each isotope used in the calibration. For example: If you
are calibrating for Mg (24), with a known mass of 23.985 amu, and have
set the Peak Scan Width to 1 amu, then the search range extends from
23.485 amu to 24.485 amu. Reduce the value to avoid accidentally
calibrating on an interfering peak. If you need to use a value above 1 amu
to find the peak, you should perform a hardware optimization, because

some performance irregularity is affecting the mass discrimination
functionality.
• Resolution DAC: Adjusts the digital-to-analog converter parameter, which
controls the peak width. The text following the field identifies which analyte
in the data table is selected. To change the DAC value for a specific
isotope, click in the Resolution DAC value cell for that isotope and type the
new value. To verify the effect of the change on the peak width, you must
perform the resolution measurement again. The new results are displayed
in the Peak Width (amu) field.
• Analyte: Lists the name of an element being included in the calibration
measurement. To enter a new element, type the abbreviated symbol for
the element.
• Mass (amu): Identifies which isotope of the element shown in the Analyte
entry will be used during the calibration. Normally, you use the isotope with
the highest natural abundance. To enter a mass value, type the exact
known mass for the isotope of interest.
• Measured Mass (amu): Lists the atomic mass for the isotope at the point
of maximum intensity — the apparent, or measured, mass after a
measurement is completed. When the Mass Calibration panel is first
opened, this field is empty. Because the exact, or actual, mass is known,
the instrument can then compensate for the differences in all future
determinations and calculations.
If applicable, you can use the Resolution DAC Value entry to adjust the
Measured Mass result so that it is closer to the actual mass value. When
you make an adjustment in the Resolution DAC Value entry, you should
always rerun the mass calibration procedure to verify its effect on the
Measured Mass value.
• Mass Calibration DAC Value: Makes adjustments to the mass
discrimination functionality in order to correct for differences between the
measured and known mass values. To make a change for a specific
isotope, click in the Mass Calibration DAC Value cell for that isotope and
type the new value. To verify the effect of the change on the calibration,
you must perform the mass calibration again. The new results are
displayed in the Measured Mass (amu) field.
• Resolution DAC Value: Lists the current parameter for the Resolution
DAC and permits you to modify the value. To adjust the DAC parameter,
click in the Resolution DAC Value cell for the relevant analyte and type the
new DAC value. You may also use the DAC field which appears above the
data table.
To adjust resolution, make changes to the DAC as follows:
 To increase resolution (narrow the peak width), increase the DAC
parameter
 To decrease resolution (broaden peak width), decrease the DAC
parameter
• Measured Peak Width (amu): Lists the peak width at 10% of peak height
after a measurement is completed. When the Mass Calibration panel is
first opened, this field is empty. If applicable, you can use the Resolution
DAC field to adjust the peak width. When you make an adjustment in the
DAC entry, you should always rerun the resolution adjustment procedure
to verify its effect on the peak width value.
• Custom Resolution: Identifies any analyte that has a different resolution.
This entry does not affect the actual spectrometer controls, and is used
only as a reminder for the user.
LogBook
When any pre-defined SmartTune Express or Manual Performance Check is run,
the results of the optimization, together with all the relevant instrument parameters
used in that optimization, are recorded in the LogBook grid. This creates a
continuous performance history of the instrument, which you can review to track
instrument performance trends over time, and to troubleshoot problems. This can
be of particular use to lab managers and service personnel: you can export the
data to Microsoft Excel in .xls or .xlsx format, in order to perform further statistical
analyses, or send the data to an offsite PerkinElmer Customer Support
Representative to aid in remote diagnostics in the case of instrument malfunction.
In the tables, sample data is displayed in alternating rows of white and gray to
improve readability. Additional color cues employed in the tables include the use
of a red font to indicate performance check failures, and the Syngistix software
standard KED mode green and DRC mode yellow used in the column headers to
indicate analytes processed using profiles in these modes (UCT instruments
only). Note that all tables take their base colors from your system colors; if you
change from the default Windows system colors, you may change the table
background colors.
Note: Mass Calibration values are stored for every performance check; they cannot,
however, be displayed on the plot.
LogBook screen Software Reference
Figure 4-9 LogBook screen

The LogBook screen has several panels:
• Syngistix LogBook panel: Use this panel to define the data you want to
view in the main LogBook table, and to review the raw data collected from
your system performance checks.
• Instrument Parameters panel: Use this panel to view the parameter
values that existed at the time the selected sample was run. Here you can
also load Conditions and MassCal parameters from the last known good
conditions. You can select any parameter displayed to be factored in on
the Statistics panel.
• Statistics panel: Use this panel to view historical trends for any analyte
intensity or parameter selected in the other two panes.
Main LogBook panel

Use the main LogBook panel to define the data you want to view in the main
LogBook table, and to review the raw data collected from your system
performance checks.
On UCT instruments, this panel is further divided into tabs for each mode, using
the default acquisition files that ship with the software: Standard, Helium KED, and
Ammonia DRC. These profiles are used for all the pre-defined Performance
Checks run via the SmartTune Express and Manual functions.
To optimize analytes using other gases or profiles, create a Lab Performance

Check file in SmartTune Manual, and associate it with a method running analytes
in the chosen profile.
Figure 4-10 LogBook screen Main LogBook panel

Items on the Syngistix LogBook panel
• Show sample ID: Enable this check box to include sample ID information
in the LogBook table.
• Show failed performance checks: Enable this check box to include
information about failed performance optimizations in the LogBook table
(that is, optimizations wherein the specified sensitivity, background, or
RSD targets were not met).
• Export All... : Click to export current data from the LogBook table to
Microsoft Excel in .xls or .xlsx format.
Instrument Parameters panel

When you click on an item in the main LogBook table, the parameter values that
existed at the time the sample was run are displayed on the Instrument
Parameters panel. Here you can also load Conditions and MassCal parameters
from the last known good conditions. You can select any parameter displayed to
be factored in on the Statistics panel (press CTRL + click to select multiple
parameters). Your selections are then persisted when you leave the given tab or
panel.
Figure 4-11 LogBook screen Instrument Parameters panel Conditions tab
Items on the Instrument Parameters panel Conditions tab

• Mode: (UCT instruments only) In the drop-down list, select the mode
/profile for which you want to view Conditions information. You can select
from any of the default performance profiles: Standard, Helium KED, or
Ammonia DRC.
Figure 4-12 LogBook screen Instrument Parameters panel MassCal tab

Parameters in the MassCal table
• Analyte: Lists the name of the element included in the calibration
measurement.
• Mass (amu): Identifies which isotope of the element shown in the Analyte
entry was used during the calibration.
• Measured Mass (amu): Lists the atomic mass for the isotope at the point
of maximum intensity — the apparent, or measured, mass after a
measurement is completed.
• Mass Calibration DAC Value: This value makes adjustments to the mass
discrimination functionality in order to correct for differences between the
measured and known mass values.
• Resolution DAC Value: Lists the current parameter for the Resolution
DAC.
• Measured Peak Width (amu): Lists the peak width at 10% of peak height
after a measurement is completed.
• Custom Resolution: Identifies any analyte that has a different resolution.
Figure 4-13 LogBook screen Instrument Parameters panel Diagnostics tab

Items on the Instrument Parameters panel Diagnostics tab
• Filter: Click the drop-down list to select the diagnostics filter you wish to
use. (Note that the filters that begin with the prefix 350_ are used to define
the parameters that appear for each subsystem on the Control screen
System View panel Diagnostics tab.)
• Edit List: Click to open the Edit List dialog box where you can modify the
diagnostics included in an existing filter, or create a new filter.
Statistics panel
The Statistics panel displays historical trends for any analyte intensity or
parameter selected in the other two panes. Select one or more cells or columns in
the main LogBook or Instrument Parameter tables to display the related
information on this panel (press CTRL + click to make multiple selections). On the
plot, a floating Legend displays a reference of the colors used to plot the selected
parameters or analytes. Horizontal and vertical sliders allow you to adjust the area
of focus along each axis; click the square arrows button in the bottom right corner
of the graph to return to the original view. Click the small, square, gray button in
the upper right corner to expand this panel for better viewability.
Figure 4-14 LogBook screen Statistics panel
Chapter 5
Method Development
This section provides background information about creating analytical methods
for your determinations.
• Modes of Operation on page 153
• Analytical Techniques on page 155
• Fundamentals of Data Acquisition on page 159
• Data Processing on page 164
• Fundamentals of Calibration on page 168
• Method Panel Software Reference on page 175
Modes of Operation
The NexION® 300/350Q instrument operates in a single mode (Standard mode)
to perform typical ICP-MS analyses of samples having no significant
interferences. NexION instruments with UCT™ functionality (all 2000 series
instruments; 300/350X, D, and S models) have three available operating modes
— Standard mode, DRC™ mode, and KED mode. The mode you choose to apply
depends on the samples you will be analyzing and the types of interference you
expect to encounter. In the software, you create acquisition profiles to pair mode
assignments with the cell gases used, and to define the related gas flow rates,
and other parameters. See Acquisition Profiles tab on page 37 for more
information.
Standard Mode
The NexION standard mode provides excellent ICP-MS analysis for most of the
isotopes in the periodic table where complex spectral interferences are not an
issue, or where it is not critical that you use the most abundant isotope of each
element. If an element experiences an interference, you can find and use an
alternate isotope. Or, if you are using an instrument with UCT functionality, you
can move on to KED mode or DRC mode.
KED Mode
This mode uses collisions with an inert gas together with kinetic energy
discrimination to reduce polyatomic interferences. While not as sensitive as DRC
mode, this method can be applied to all polyatomic interferences using a single
set of operating conditions, and does not require an in-depth knowledge of the
sample prior to analysis. This system discriminates between the kinetic energy of
analyte ions and that of their interferences by creating a positively-biased voltage
between the mass analyzer and the cell. The system then relies on the higher
probability of collisions of an inert gas (for example, He) with the polyatomic
interferences based on their relatively larger collisional cross-section —
polyatomic species cannot overcome the positive energy barrier established
between the mass analyzer and the cell. KED mode is especially useful in
applications where moderate detection limits are required for multi-element
analyses in complex matrices, such as in high salt samples.
153
DRC™ Mode
DRC mode provides ultimately low detection limits and high-sensitivity for
complex spectral interferences including polyatomics and atomic isobars. The
DRC technology uses ion-molecular reactions and band-pass tuning to chemically
correct for interferences. This allows you to remove difficult-to-avoid interferences
(such as those formed in the plasma or present in the sample) before they reach
the mass spectrometer, without limiting the detection capabilities of the system.
This mode uses controlled gas-phase reaction chemistry inside an enclosed cell
containing an additional quadrupole mass filter equipped with Axial Field™
Technology. The result is a dramatically improved detection capability into the sub
parts-per-trillion range for most elements.
Ions extracted from the plasma are focused within the ion optics and directed into
the cell. The standard mode is achieved by turning off the reaction gas flow into
the cell and opening the vent to the analyzer chamber. In this mode, the cell is a
quadrupole device which transfers the ions to the mass spectrometer’s analyzer
chamber. DRC mode is achieved by closing the vent to the analyzer chamber and
introducing a reaction gas into the cell. In this mode, ion-molecule reactions are
promoted to selectively eliminate interferences.
The specificity of interference rejection is obtained through the selection of the
reaction gas and the operating conditions. Both RF and DC electrical components
are applied to provide control over the extent of ion-molecule reactivity in the cell.
This chemical band pass is used in concert with the selected reaction gas to
reduce interferences by interrupting the sequence of reactions that would
otherwise create an interference. The RF provides an intercept for reaction
intermediates of lower mass; the DC suppresses chemistry involving higher mass
reaction intermediates. The system introduces the reaction gas through a gas
assembly function; you create acquisition profiles to define the type of gas used
and the flow rate at which the cell operates.
Mode Application Example

For example, if you want to examine the isotopes 56Fe and Ar40O16, you will
encounter an isotopic interference, as the mass of the two isotopes is identical. To
deal with this:
• In standard mode, select a less abundant isotope, such as 54Fe rather
than 56Fe, to avoid the interference
• In KED mode, helium gas introduced into the cell reduces the interferent
isotopes through collision and kinetic energy discrimination
• In DRC mode, the cell gas triggers an ion-molecule reaction that obviates
the interference, without affecting the isotope of interest:
NH3 + 56ArO+xxxxxNH3+ + 56Ar O
NH3 + 56Fe+xxxxxx no reaction
You define acquisition profiles to specify the desired mode and cell gas
combinations and then, when you create a new method, you select one or more
profiles to be applied when analyzing the analytes. You can mix profiles of
differing modes within a single method to best deal with specific interferences, but
you should choose a single profile for specialized methods, such as Isotope Ratio
and Isotope Dilution.
Method Development
Analytical Techniques
Developing a method involves defining your analysis goals, selecting the
analytical technique best-suited to achieving those goals, and configuring the
method parameters to provide the best possible combination of accuracy,
precision, and analysis speed.
The most important consideration when selecting an analytical technique is the
degree of precision required in your results. For survey measurements or semi-
quantitative testing, TotalQuant™ analyses provide the most convenient method,
providing both analytical effectiveness and fast results. However, with the addition
of standards in a TotalQuant determination, many quantitative requirements are
also satisfied. While Quantitative Analysis methods are generally selected when
accuracy and precision are the primary considerations, some applications may
benefit from the added precision achievable using an Isotope Dilution method.
The software provides several different ways of managing data acquisition:
• Quantitative Analysis
• TotalQuant III Analysis
• Isotope Dilution
• Isotope Ratio
• Data Only
Quantitative Analysis Methods

This technique establishes the concentrations of specific elements in an unknown
sample. It provides accurate results across a wide range of concentrations and
generates results suitable for certification, specification, and litigation work.
In Quantitative Analysis, you calibrate the instrument by measuring standards for
all the elements you are interested in determining. You analyze standards at
different concentrations to ensure instrument response is accurate across the
range of concentrations you are likely to encounter in your sample solutions. As
you analyze the standard solutions, the software creates a calibration graph of the
measured intensity versus concentration for each element in the standard
solution. These individual calibration curves are updated after each standard
solution is measured.
After calibration data is acquired, you run your sample solutions. The
concentrations for the analytes of interest are automatically calculated. The
technique can be used in conjunction with QC (quality control) procedures to
monitor the results of your determination and flag samples which fall outside of
default ranges.
Although Quantitative Analysis methods are suitable for the majority of
requirements, should your application require even greater analytical precision,
the Isotope Dilution application may offer a slight improvement. However, Isotope
Dilution methods require the use of enriched isotopes, making them less suitable
for routine use.
TotalQuant™ III Methods

For the rapid analysis of a total unknown, the software provides a unique, fully
automated, semi-quantitative method called a TotalQuant analysis. With this
technique, you can automatically find the concentrations of up to 81 elements in a
single sample measurement. A TotalQuant analysis measures the entire mass
spectrum, so you do not need to specify the individual elements you want to
examine. The software automatically corrects for isotopic interferences and
interfering molecular species, and produces a comprehensive report listing each

element present in your sample and its concentration.
TotalQuant analyses afford an excellent approach to characterizing unknown
solutions. They can be used without standards to perform a rapid survey
determination, providing a simple means of identifying unexpected components in
a solution. After you characterize a solution in this manner, you can select to use a
TotalQuant method with standard solutions to improve analytical accuracy, or
switch to the Quantitative Analysis technique to focus on specific elements and
detect their concentrations with even greater accuracy and precision.
While you can perform a TotalQuant determination without using a series of
standards, we recommend you do use standards to adjust the instrument
parameters for improved accuracy. Unlike Quantitative Analysis methods, in
which you analyze standards for all the elements you want to examine, TotalQuant
calibration is achieved using just a few elements distributed throughout the mass
range of interest. The calibration process updates internal response data that
correlates measured ion intensities to the concentrations of elements in a solution.
During calibration, the software adjusts this response data to account for changes
in the instrument's sensitivity due to variations in the sample matrix.
Isotope Dilution Methods

You can use the Isotope Dilution method for extremely high accuracy and
precision measurements of the concentrations of elements in an unknown
sample. Isotope Dilution is an absolute means of quantitation based on altering
the natural relative abundance of two isotopes of an element by a known amount,
and then measuring the results. It is one of the most accurate approaches to
elemental analysis.
To use Isotope Dilution, you add a known weight of the spike solution to your
sample. Given a known weight for the spike and a sample weight or volume that
includes the spike, the software applies natural abundance ratios to calculate the
sample concentration. It measures the isotopes in the same sample, eliminating
potential errors introduced by sample preparation.
The software uses this equation to calculate the sample concentration (c):
W  A' –  B' 
c = Kx -------------------------------
MB – A
where:
K = natural atomic weight of the element
xxxx atomic weight of the spike isotope
W = weight of the isotopically enriched material added
M = weight or volume of the sample
a = element isotope of highest natural abundance
b = highest abundance isotope in enriched isotope solution
A,B = natural abundances of sample isotopes a and b
A’,B’ = isotopic abundances of a and b in the spike
ñ = ratio of isotope a to isotope b measured in the sample
Method Development
If W is given in micrograms and M is given in grams, then c is the concentration of

the element in micrograms per gram by weight.
This technique does have some weaknesses:
• Requires polyisotopic elements: Because calculations are based on the
ratio of one isotope to another in the same element, the element you are
determining must have more than one isotope.
• Requires certified enriched isotopic standards: These standards can
be expensive, especially those that deviate significantly from the normal
isotopic abundance of the element.
• Does not compensate for spectral interferences: Although the
technique compensates for interferences due to signal enhancements or
suppressions, you must subtract a blank to compensate for spectral
interferences.
Autodilution Methods
You can use an autodiluter with dilution methods, but be aware of the following
issues:
• You can use an autodiluter only when running samples in batch mode.
• Batch mode analysis with more than one method in the batch: In order to
use dilution positions sequentially, only the first method in the batch needs
to have a rack position entered for the 1st Dil Pos field on the Sampling
tab. All methods that follow must have a zero in this field.
• When using internal standards, the diluent must contain internal standard
elements at the same concentration as the blank, standards, and samples.
• To prevent uncontrolled mixing of sample and diluent within the dilution
probe, the instrument introduces a small air bubble between the two
liquids. Each sample is transferred to the dilution tube in quantities that are
small enough to keep the air bubble confined within the tubing. The
maximum and minimum amounts of sample that can be transferred in one
pass is approximately 1.3 mL and 1.7 µL, respectively. Thus, when small
dilution factors are combined with large diluted sample volumes, several
passes can be required to transfer sufficient sample to the dilution tube. In
order to make a 50 mL diluted sample with a dilution factor of two, 25 mL
of sample are needed — this would take 20 passes. Therefore, we
recommend that you optimize the dilution factor and dilution volume to
reduce multiple passes.
• The autodiluter performs successive dilutions in response to a quality
control action until the out-of-limit condition — upper sample
concentration, S (shutdown), or EEE (elemental equation error) — is
remedied.
Autodilution Controls
The following Method panel Sampling tab controls apply specifically to
autodilution method development:
• Dil. Factor: The system has been designed to operate typically with
dilution factors ranging from 2 to 1 000, with a default value of 10. A
dilution factor of N should lower the measured intensity by a factor of N.
• Dil. to Vol.: Specifies the volume of the diluted samples the autodiluter will
create. This volume ranges from 2mL to 50 mL, with a default value of 10
mL.
• 1st Dil. Pos: Here you can specify which tubes should be used when
diluted samples are created. The first diluted sample is created in the tube
number corresponding to the value entered in the 1st Dil. Pos field, the
second in the next higher numbered tube, and so on. To use dilution
positions sequentially, only the first method in the batch must have a rack
position entered for the 1st Dil. Pos field on the Method panel Sampling
tab. All methods that follow must have a zero in this field.
• Probe Purge Pos: Here you can specify that an empty tube be used for
autodiluter initialization. In order to accurately measure the volumes of
liquid involved in each dilution, the dilution probe and associated tubing
must be full of diluent before any dilutions are done. Ten milliliters of
diluent are pumped through the probe into the tube at the Probe Purge
Position. The default value for this tube position is 10.
If the autodiluter is to be under QC control, on the QC Sample tab, right-click in
the Action 1 and Action 2 columns to view a menu of available actions. For
analyte upper limit measurements, the menu item Wash For X, Dilute, and Rerun
Current is available.
You can also dilute samples before measurement by right-clicking in the
Measurement Action column on the Sample panel Batch tab and choosing one of
the following actions:
• Run Diluted Sample
• Run Blank and Diluted Sample
• Run Stds. and Diluted Sample
• Run Blank, Stds. and Dil. Sample
Note: The following solution types cannot be pre-diluted: spike, duplicate and dilution
pairs, blanks, reagent blanks, calibration standards and QC standards.
Isotope Ratio Methods

This specialized technique enables measurement of the exact ratio of two
isotopes of an element. It is a sensitive indicator of age, reaction, or metabolism in
nuclear, geochemical, and biomedical applications.
With the Isotope Ratio technique, you compare the isotope of interest to a
reference isotope of the same element. For example, you might compare the
concentration of Pb204 to Pb206. Alternately, you can compare more than one
isotope or all remaining isotopes of an element to your reference isotope,
obtaining a ratio for each. For example, you could compare the ratio of Pb204 to
Pb206, Pb204 to Pb207, and Pb204 to Pb208. The ratio is presented in the
following format:
ratio = isotope of interest / reference isotope
Method Development
Data Only Methods

The Data Only option supports the acquisition and reporting of raw or minimally
processed mass spectral data from the instrument. You can apply external data
processing routines to analyze your data, to selectively apply a minimum set of
the processing routines, and to view and then reprocess the raw data using
another analytical technique.
You should use the Data Only technique for advanced method development or
when your sample set requires data processing using algorithms other than those
supplied in the software processing set. Because the main purpose of the
technique is the acquisition and reporting of raw data with minimal processing, it
does not support the acquisition of standard solutions — only blank and sample
solutions. No concentration calculations are performed as sample data is
collected. The system does permit you to specify analytes using either a mass
range or individual analyte parameter for greater flexibility in defining acquisition
than other techniques.
In addition to reporting the raw data, the technique permits you to select from a
minimum set of data processing routines, including peak processing, signal profile
smoothing, signal profile processing, elemental equations for interference
correction, and blank subtraction.
Fundamentals of Data Acquisition

The instrument is comprised of two major components: an Inductively Coupled
Plasma source for ion production and a Mass Spectrometer for ion detection and
quantification.
For solution analyses, the sample is nebulized into the inductively coupled
plasma. Within the plasma, the sample solvent is evaporated and a large
percentage of the atoms are ionized by the energetic plasma environment. A
fraction of these ions are captured in the interface region of the system and
channeled into the mass spectrometer. The mass spectrometer serves as a mass
filter and selectively transmits ions according to their mass-to-charge ratio. The
ions are then captured by an electron multiplier and quantified by the pulse and
analog stages of the dual detector assembly. The entire operation of sample
introduction, ionization and detection is controlled and monitored by the system
computer, which also generates the final reports on sample composition.
The inductively coupled plasma is usually employed as a means of dissociating
sample solutions and generating excited atoms for atomic emission spectrometry.
However, ICP is also an excellent ion generator. Under typical plasma conditions
(~6000 °C), only a few elements in the periodic table are less than 90% ionized. In
addition, the ICP is extremely efficient in the production of singly versus doubly
charged ions. Only a few elements possess sufficiently low ionization potentials to
permit generation of an appreciable quantity of doubly charged species, and even
then, the relative percentage of doubly charged ions is typically less than 2%.
NexION® instruments use a classic quadrupole design mass spectrometer
operating in a vacuum of less than 1 x 10-5 Torr as the detection device. This
mass analyzer generates a spectrum by linearly varying the RF and DC voltage
amplitudes on the quadrupole rods. The mass of the ions that reach the detector
is a linear function of the applied voltage. The entire mass range from 1 to 269
amu (atomic mass units) can be scanned in milliseconds. Using the software, you
can select scanning over the entire mass range, over a portion of the mass range,
or scanning of only the individual masses of interest while intervening masses are
skipped.
Mass Discrimination and Spectral Scanning

During a measurement, the instrument measures signal intensity by counting the
rate at which ions of each mass reach the detector system. By skewing the charge
conditions across the quadrupole rods, the mass spectrometer selectively passes
ions through to the detector according to their mass-to-charge ratio. This mass
filtering process is not conducted in discrete fashion, that is, the spectrometer
actually passes ions distributed over a range of mass-to-charge ratio-varying from
slightly below to slightly above the actual mass of interest.
The width of the range is established by the resolution parameters in the mass
calibration file. In most cases, resolution is set to 0.7 amu per mass, covering from
half an amu below the actual mass to half an amu above the mass. Resolution is
also individually adjustable by atomic mass, meaning that you can selectively
narrow the range of masses to less than one amu to help compensate for spectral
interferences. The primary consideration in narrowing the resolution for an
individual mass is the reduction in the total counts, and therefore, the signal-to-
noise ratio for that mass. If you set too narrow a resolution, you will adversely
impact the precision of the acquired data.
To this point, we have described operations that physically discriminate ions
according to their mass-to-charge ratios. Mass discrimination defines a spectrum
of intensity values. If you sampled all the possible data for each measurement you
made, you would end up acquiring a vast amount of data. In any method, you
instruct the instrument how to scan across this spectrum while acquiring only the
data of importance to your analysis.
The software provides two different functions for acquiring mass spectral data
during a determination:
• Peak hopping
• Scanning
Peak Hop Acquisition

The most common method for ICP-MS data acquisition is peak hopping. In peak
hop mode, the instrument measures the signal intensity at only the center point in
the mass range defined for each element of interest. The spectrometer spends a
specified amount of time, the dwell time, measuring signal intensity at this point,
and then hops to the next element in the method. The data from each
measurement constitutes a reading. Multiple sweeps through the mass range can
be set, with the data from each of the individual sweeps averaged into a single
final value for each atomic mass.
Method Development
Figure 5-1 Single sweep peak hop acquisition
Scanning: Data Acquisition

Acquiring a single point directly at each atomic mass of interest is the most time
efficient means of acquiring data. However, this approach does not provide
information about potential interferences from adjacent peaks. To more accurately
characterize the mass spectrum and identify potential interferences during data
acquisition, scanning is commonly employed. Scanning acquires data from
multiple points in the mass range defined for the element being measured. The
spectrometer ramps — steps incrementally — through the mass range, acquiring
intensity data at each point. The number of data points acquired in the range is
decided by the number of MCA channels, which can be set from 1 to 20, centered
around the exact mass for the element being measured.
Figure 5-2 Scanning data acquisition

During scanning, because the total number of data points being acquired is larger,
the time spent acquiring each point is shorter relative to the time spent during
peak hop mode. The total time spent at each element is decided by the Dwell
Time value. The time spent acquiring each individual data point is therefore the
dwell time divided by the number of MCA channels being measured. As in Peak
Hop mode, multiple Sweeps/Reading can be acquired to improve measurement
precision.
Signal Profile and Scanning

In a traditional ICP-MS determination, the sample solution is continually nebulized
into the ICP torch during a measurement. As sample introduction starts, the signal
strength gradually increases until the system reaches a steady-state condition at
maximum signal intensity. At this point, the signal measurements are taken. Under
steady-state conditions, the peak maximum can be measured at any time after the
steady-state is achieved.
Figure 5-3 Steady state signal

In the preceding illustration, one Reading/Replicate was used to collect several
data points along the signal. Because the sample is continually aspirated, the
Readings parameter is typically set to one, as there is no reason for multiple
sample injections.
Although it is the most common, a peristaltic pump is only one of the sampling
techniques used to continually introduce sample into an instrument. Other
commonly used techniques include:
• Flow injection
•Laser ablation
Flow injection uses transient signals.
Method Development
Transient Signal Processing

Flow injection introduces a discrete volume of sample into the ICP-MS system. In
this situation, the signal intensity gradually increases to a maximum intensity, then
decreases back to zero; this is termed a transient signal.
Figure 5-4 Transient signal

For a transient signal, you must acquire enough readings to accurately profile the
shape of the signal before it disappears. This means careful evaluation of the
timing parameters, balancing Dwell Time, Sweeps/Reading, and
Readings/Replicate to complete data acquisition in the available time. This is
especially crucial if scanning is used. The signal profile is a representation of the
composite mass spectral peaks — that is, behind each point along the signal
profile is a set of mass spectral data.
Figure 5-5 Data processing in a transient analysis
Data Processing
The raw data acquired during a determination must be processed before it is
passed along for the analytical technique-specific calculations. Making the correct
selections requires you to consider the mixture of the analytes, the sample matrix,
instrument conditions and analytical requirements. The processing functions are
divided into two broad classes:
• Functions used to process the mass spectral data
• Functions used to process the time-based signal profile
Spectral Peak Processing

Mass spectral peaks are actually a set of individual data points whose spacing is
based on the resolution and the number of points per peak.
Figure 5-6 Ion intensity versus mass plot

The raw data for each mass is processed to produce a single value for that mass
by using one of three algorithms: Average, Sum, or Maximum. The Average
function calculates the average intensity value of the channels acquired for the
mass. The Sum function is a mathematical summation of the individual intensity
values in counts. The Maximum function establishes the maximum intensity
channel for each mass being examined.
To improve analytical precision, you can acquire more than one sweep through
the mass spectrum for each reading. The spectral peaks from each sweep are
summed to create the final reading. This reading is then plotted as a function of
time to create the signal profile.
Method Development
Figure 5-7 Mass spectral peaks
Signal Profile Processing

Following acquisition, the data consists of a series of intensity data readings
plotted against time. This intensity versus time signal profile is processed to
produce a final intensity value used in the analytical technique calculations. The
software provides three options for processing the signal profile data: Average,
Sum, and Maximum.
The Average function calculates the average intensity for all readings in a
replicate. The Sum function calculates the total counts measured for all readings,
a particularly useful option when a low number of readings per replicate have
been specified. The Maximum option identifies the reading with the largest
intensity value and selects it for use in further calculations.
In situations where the sample matrix causes a high background reading, greater
precision may be achieved by adjusting the background level before performing
signal profile processing. The Baseline Readings entry in the Process Signal
Profile group is used to designate a specific number of readings at the start of
each acquisition as background points. These readings are then used to set the
baseline level for all subsequent readings.
Figure 5-8 Baseline readings set to 3

Finally, for measurements with a low signal-to-noise level or in other cases where
the signal profile readings are subject to baseline shift effects, the software
permits you to smooth data before applying the signal profile processing
algorithm. The Smooth Signal Profile option uses a Savitzky-Golay moving point
average over a defined number of readings to reduce the effects of noise on the
signal profile.
Method Development
Figure 5-9 Signal profile data for an individual replicate
Fundamentals of Calibration
Calibration is a fundamental part of acquiring the best possible data from your
instrument. In Quantitative Analysis, you calibrate the instrument by analyzing
standards for all the elements you are interested in measuring. You analyze
standards at different concentrations to ensure instrument response is accurate
across the range of concentrations you are likely to encounter during your
determinations.
As you measure standard solutions, the software plots the measured intensity
versus the concentration for each element in the standard solution. These
individual calibration curves are updated as each subsequent standard is
measured. You view and edit calibration curves in the Calibration panel. If a point
seems aberrant, you can remove it and recalculate the curve. You can also store
any calibration data to use in future determinations.
In a TotalQuant determination, the instrument uses stored response tables to
correlate measured ion intensities with known concentration values. This internal
response data indicates how many ions per second should be observed for a
concentration of one milligram/Liter for each element in a sample. The response
table takes into account variations in instrument sensitivity to different elements.
However, changes in overall instrument sensitivity can occur from day to day.
Because instrument sensitivity for all elements generally changes to the same
degree, you can update the responses for all elements by measuring the
responses for a few calibration elements.
Both Isotope Dilution and Isotope Ratio are effectively self-calibrating techniques.
In Isotope Ratio, you compare the isotope of interest to a reference isotope of the
same element. For example, you might measure Pb204 compared against Pb206.
Because this ratio can be calculated from within a single sample measurement
calibration is not required, although it is recommended to run a standard of known
isotopic composition to verify that the instrument is not biasing the results due to
mass discrimination.
One additional calibration technique, internal standardization, is commonly
employed in methods. You can use internal standards to correct for changes in
instrument hardware response or for sample-to-sample variations in sensitivity. An
internal standard is a non-analyte isotope that is added to the standards and
samples before you analyze them. During the determination, the software uses
the ratio of analyte and internal standard intensities to adjust the final analyte
intensity values. Internal standards are used in both Quantitative Analysis and
TotalQuant methods. Isotope Ratio methods use the principles of internal
standardization as the basis for ratio measurement. Isotope Dilution
measurements do not require internal standards.
Calibration in Quantitative Analysis

The instrument offers these methods of calibration in the Quantitative Analysis
technique:
• External standardization
• Standard addition
• Addition calibration, as a variant of standard addition
The method you select defines how you prepare and run your samples. Review
the following descriptions to select the calibration method best suited to your
analytical requirements.
Method Development
External Standardization
For samples that are not subject to sample-specific matrix interferences that
change the overall instrument sensitivity between measurement of the standards
and samples, external standardization is a simple and effective way to calibrate
your instrument.
External standardization involves measuring a blank solution followed by a set of
standard solutions to create a calibration curve over the concentration range of
interest. Typically, you run two or three standard solutions containing different
concentrations of all the elements you are determining. Increasing the number of
points on the calibration curve — that is, increasing the number of standard
solutions — may improve accuracy in circumstances where the calibration range
is very broad. However, it is seldom necessary to run more than five standard
solutions. After the standards have been measured, you continue with the
measurements of your unknowns.
The following figure summarizes the measurement procedure when using
external standardization:
Blank

Standard solution 1

Standard solution 2

Standard solution 3

Sample 1

Sample 2

Sample 3

and so forth
Standard Addition Calibration
Standard addition calibration provides an effective way to minimize sample-
specific matrix effects through the use of spiked samples.
In standard addition calibration, you first measure a blank solution. Next, you
measure the sample solution spiked with a known concentration of each element
you want to examine. The software measures the response for the spiked
samples and creates a calibration curve for each element for which a spike has
been added. This curve is based on the known concentration values which you
entered. The calibration curve plots the measured intensity of each spike element
against its concentration. Based on the slope of the calibration curves, the
software calculates the unspiked concentration of the analytes in the unknown.

After creating the calibration curve, you run your unspiked sample solution.
The following figure summarizes the measurement procedure when using
standard addition calibration:
Blank

Spiked sample 1 (spike conc. 1)


Unspiked sample 1

Blank



Unspiked sample 2

Blank

and so forth
Method Development
Addition Calibration
Addition calibration is a variant of standard addition. It is used when all samples
have a similar matrix. The following figure summarizes the measurement
procedure when using standard addition calibration:
Blank



Unspiked sample 1

Unspiked sample 2

Unspiked sample 3
Calibration in TotalQuant™ Methods

The software uses response tables to correlate measured ion intensities with
known concentration values. The data in these tables can be updated by
calibrating the instrument. You can calibrate the full mass range using just a few
calibration solutions.
Two response tables are supplied with the software: TotalQuant.rsp and
current.rsp. The TotalQuant.rsp table contains reference response data for the
instrument. When you perform a calibration, changes to the response table are
automatically saved in the file current.rsp. Response tables can be saved under a
user-defined name so that you can recall them for future determinations on similar
samples.
The software offers two methods for updating the internal response data:
• External calibration
• Sample addition calibration
External Calibration
Use external calibration when you are interested in a few specific elements or
when you are running a large number of samples of simple composition with little
sensitivity variation between samples. By updating the calibration of the elements
you are most concerned with, you guarantee that the instrument measures those
elements with the highest accuracy possible. Although it is typical to use three to
six elements for external calibration, the software permits calibration using up to
100 elements. In general, the more elements you use, the more accurate your
results are.
Using external calibration, you measure a blank, then a calibration solution
containing known quantities of specific elements prior to measuring your
unknowns. You then identify the elements in the calibration solution and their
concentrations to the software.
The software establishes the intensities for each of the calibration elements and
then calculates the response based on the concentrations you have specified. It
then adjusts the response factors in the response table for all elements in
proportion to the calibration elements.
For example, using cobalt and rhodium in the calibration solution, the software
finds the response for cobalt at mass 59 to be 5% greater than the internally
recorded response and the response for rhodium at mass 103 to be 15% greater.
It adjusts these elements by 5% and 15% respectively. For other elements that
have isotopes between cobalt and rhodium, the adjustment is based on the
relative mass difference between the measured analyte and the calibration
elements. The adjustment value for an individual element (c) is calculated as
follows:
Adjustment = a + [(b-a) * (c-d) / (e-d)]
where:
a = % difference for calibration element with lower mass
b = % difference for calibration element with higher mass
c = mass of element
d = mass of lower calibration element
e = mass of higher calibration element
For example, the adjustment for arsenic at mass 75 is:
Adjustment = 5 + [(15-5) * (75-59)/(103-59)] = 8.6%
For the most accurate results for all detectable elements, use a calibration
solution that contains five or six elements from a wide mass range, with the
elements concentrated at the lower masses. This provides reference points for
adjustments across the entire spectrum. A typical calibration solution might
contain 1µg/L of Li, Mg, Co, In, Tb, and Pb.
You can measure your standard solution once during a determination, after
measuring the blank, or periodically during the determination (for example, to
correct for time-dependent drift, or to re-standardize between groups of samples
with dissimilar matrices).
When you change the software's internal response data through external
calibration, the changes remain in effect until you update the response data. This
means the updated response information is used for all subsequent samples until
you perform another external calibration or load a different calibration file.
Method Development
Sample Addition Calibration

Sample addition calibration corrects for sensitivity changes specific to each
sample, so you might use this technique if you expect the physical or chemical
characteristics of an individual sample to affect instrument sensitivity. For
example, if a sample has a high concentration of ions, instrument sensitivity will
not be accurate because the high ion concentration will alter the readings for all
ions in the sample.
By performing a sample addition calibration, you guarantee the highest possible
accuracy for each sample in your analysis.
Blank Blank
 
Standard solution Standard solution
 
Sample 1 Sample 1
 
Sample 2 Sample 2
 
Sample 3 Sample 3
 
Sample 4 Sample 4
 
Sample 5 Standard solution
 
Sample 6 Sample 5
 
and so forth and so forth
Sample addition calibration involves adding known quantities of specific elements

to your unknown sample before measuring it, or requires that you know the
concentration of some elements in the sample. If you are adding elements, the
elements you add must not already be present in significant quantities in the
unknown. As with external calibration, you identify the elements that you are
adding or the elements that you know the concentrations of, indicating the
concentrations for each of these elements. The software calculates the response
data based on the concentrations you specify. It then adjusts the internal response
data for all remaining analytes relative to the calibration elements.
Blank

Sample 1 + Calibration standards




and so forth
When you modify the software's internal response data using sample addition
calibration, the changes remain in effect for the individual sample only. However,
the response data can be saved for later use. You can correct any sensitivity drift
that may occur during a determination by measuring each sample using sample
addition calibration. However, because you have to add calibration elements to
each sample you measure, this technique can be time-consuming. Generally,
sample addition calibration is only applicable when performing determinations on
complex samples of unknown concentration.
Internal Standards
An internal standard is a non-analyte isotope added to standards and samples
before a determination. You can use internal standards to correct for changes in
instrument hardware response or sample-to-sample variations in sensitivity.
The implementation protocol for internal standards varies according to the
analytical technique in which it is used. For Quantitative Analysis methods, the
Internal Standard entry clusters elements with similar ICP-MS response
characteristics into a standard group, then specifies which element within the
group will serve as the standard or reference isotope. The software assumes that
all elements within the standard group are similarly affected by instrument drift or
matrix interferences. Therefore, changes in the measured intensity of the internal
standard are used to create the ratios for correcting measured intensities of the
analytes.
Method Development
For example, during the measurement of Pb in water, you must account for the
effect of salinity. High Na concentrations typically result in a matrix interference.
For these measurements, Bi (mass 209) can be used as an internal standard to
correct the measured intensities of Pb (mass 208).
Table 5-1 Quantitative Analysis Internal Standard Example
Tl Pb Bi
Standard solution
Intensity 4.078 6.117 2.039
Sample solution
Measured intensity 4.820 6.234 1.78
Adjusted intensity 5.521 7.141
For TotalQuant determinations, the internal standard function is similar in purpose,

but somewhat different in implementation. A TotalQuant internal standard is used
to continually compensate for instrument drift or for interferences for a defined
mass range. If you use a single internal standard, it is used to cover all the
masses selected for the determination. You can also define more than one
internal standard which is valuable when conducting measurements over a large
mass range. When multiple internal standards are used, the software interpolates
any resulting adjustment to intensity values according to the distance in mass
between the analyte and the nearest internal standard element.
Method Panel Software Reference

All method development takes place within the Method screen, accessed via the
Method icon on the ribbon. The Method screen consists of the Periodic Table
panel, wherein you select the analytes for your methods, and the main Method
panel, which is divided into nine functional tabs. On these tabs you can set the
data acquisition, processing, and calibration information that will be used to
control the determination. The Method panel is also used to specify any quality
control checks that will be employed during automated quantitative analysis
determinations.
Method Panel Tabs

There are nine tabs that are used by all of the analytical methods. The Devices
and QC (quality control) tabs have further sub-tabs accessed from within each.
• Timing: Specifies the isotopes and mass ranges that you want to measure
and defines the parameters used to control the acquisition of data from the
mass spectrometer, including the amount of time for measuring each
isotope in the sample and how many times to repeat each measurement.
• Processing: Specifies which detector system will be used in the
determination and defines how the software will manage the processing of
the raw signal data.
• Equation: Defines the equations used to correct for interferences in your
determinations.
• Calibration: Specifies the compositions of the standard solutions,

including any internal standards, and defines the calibration type to be
used for quantitative calculations.
• Sampling: Describes the type of sampling system to be used for sample
introduction and specifies the peristaltic pump speed parameter to
introduce sample solution to the instrument.
• Devices: Specifies the sample introduction control program for various
sampling systems. Each system has its own sub-tabs: for example, the
FIAS™ option specifies the sample introduction control program when
using a flow injection sampling system. Only accessible when specified in
the Sampling field on the Sampling tab.
• QC: Specifies the quality control functionality. The QC parameters are
used to check on the data acquisition quality and to flag out-of-range
results during automated quantitative analysis measurements. See Quality
Control on page 213 for details.
• Report: Specifies the report options template that will be used for creating
reports and defines the destination for the report output (printer, file, or
serial port).
• Notes: Used to enter notes about the analytical method.
Timing Tab
Use this tab to specify the isotopes or range of isotopes to look for in your
samples. You also use this tab to identify the internal standards within the sample,
adjust the analysis time spent on an individual element and to specify the Mass
Calibration and Conditions files to use during determinations. On UCT
instruments, entries on this tab are color-coded: a yellow background indicates
that the element uses a DRC mode acquisition profile; a pale green background
indicates that the element uses a KED mode acquisition profile.
Figure 5-10 Method panel Timing tab

Items on the Timing Tab
• Sweeps/Reading: This entry indicates the number of sweeps through the
mass spectrum that will be averaged to yield each data point or reading.
Method Development
The acceptable range of values is from 1 to 1000. The default value is 1. A

sweep is counted each time that the instrument scans from the lowest to
the highest mass specified in the table on the Timing tab. The software
averages the results of multiple sweeps and saves this average as the
data for one reading. A series of consecutive readings constitute a
replicate. Increasing the number of sweeps/reading is one way to increase
analytical precision. However, with transient signals, you will typically use
one sweep/reading and multiple readings/replicate to measure several
elements in a sample.
• Readings/Replicate: This entry defines how many individual readings will
be acquired during the course of a single sample injection (for a transient
signal) or during the course of a steady-state determination. The
acceptable range of values is from 1 to 25000. The default value is 1. The
Readings/Replicate entry is especially important during determinations
with transient signals. To create an accurate picture of the shape of the
transient profile depends on selecting an appropriate number of readings.
Selecting too few readings will lead to a poorly shaped peak that does not
accurately portray the true data signal. Selecting too many readings
results in excessive total analysis time and very large data files. The
optimum number of Readings/Replicate with transient signals is partially
dependent on the sample technique being employed. With a FIAS
measurement, a 30-second peak might require 25 to 50
Readings/Replicate in peak hop mode. During steady-state
determinations, the signal profile is approximately constant once steady-
state conditions are achieved, and one Reading/Replicate can
satisfactorily define signal intensity.
• Replicates: Indicates the number of times the instrument will repeat a
measurement for an individual sample. This entry is typically set between
1 and 3. When performing a determination with a transient signal, this
value corresponds to the number of repeat sample injections. The
acceptable range of values is between 1 and 1000. The default value is 1.
• Est. Reading Time: Displays an estimate of the time required to complete
each reading, based on the current timing parameters set in the table and
the value entered for the number of Sweeps/Reading. The values in this
field are read-only. The calculation of estimated time is updated whenever
a change is made to the Sweeps/Reading or Dwell Time entry, as soon as
you click in another entry on the tab.
UCT instruments
If the method contains elements defined using multiple profiles and modes
(that is, in more than one of standard, KED, and DRC mode), the estimate
is unavailable due to the delays required for gas flow changes during
mode switching. The delay time between flow rate changes will be
significant — that is, tens of seconds. Short settling times are possible in
single mode methods only.
• Est. Replicate Time: Displays the total time required to measure a single
replicate, based on the timing parameters set in the table and the values
for the Sweeps/Reading and Readings/Replicate. The values in this field
are read-only. The calculation of estimated time is updated whenever a
change is made to the Readings/Replicate, Sweeps/Reading, or Dwell
Time entry, as soon as you click in another entry on the tab.
UCT instruments
If the method contains elements defined using multiple profiles and modes
(that is, in more than one of standard, KED, and DRC mode), the estimate
is unavailable due to the delays required for gas flow changes during
mode switching. The delay time between flow rate changes will be
significant — that is, tens of seconds. Short settling times are possible in
single mode methods only.
• Est. Sample Time: Displays an estimate of the total time to analyze a
single sample based on the current timing parameters set in the table and
the values for the Sweeps/Reading, Readings/Replicate, and Replicates
entries. The values in this field are read-only. The calculation of estimated
time is updated whenever a change is made to the Replicates,
Readings/Replicate, Sweeps/Reading, or Dwell Time as soon as you click
another entry on the tab.
UCT instruments
The calculation of estimated time is also updated whenever a change is
made to the cell gas flow entries.
• MassCal File: Specifies the name of the mass calibration file used to
calibrate the instrument during determinations made with the method.
Every method must have a mass calibration file specified. The default
mass calibration file is named default.tun.
• Enable QC Checking: Starts the quality control functions. The software
includes a comprehensive set of quality control checks for verifying data
integrity when performing quantitative analysis measurements. This option
is available for Quantitative Analysis methods only.
• Conditions File: Specifies the name of the conditions file that will be used
during determinations made with the method. The conditions file contains
important hardware parameters for your instrument, including nebulizer
flow, ICP power, and dual detector calibration information. Every method
must have a conditions file specified. The default conditions file is named
default.dac.
The Timing Table
The Timing table lists the isotopes the software will measure, together with
specifics about the measurement timing conditions. This table must include at
least one analyte (and one Begin Mass/End Mass entry for Data Only and
TotalQuant analyses) and their associated measurement specifications. The
software automatically enters data in some of the table fields when you add an
analyte. These default parameters provide a standard starting point for developing
the method. The conditions yield reasonable data, permitting you to analyze the
results and define the type of modifications required to extract the best possible
data for your specific sample system. On UCT instruments, at the time of analysis,
analytes in the Timing table with the same profile and gas flow settings are
grouped together.
Parameters in the Timing Table
• Internal Standard: (Quantitative Analysis and TotalQuant methods only)
Lists the standard groups and internal standards that have been defined in
the method.
When using internal standards with TotalQuant methods, these entries are
used to calibrate the TotalQuant response table for optimal accuracy
during analytical measurements.
Method Development
• Analyte (*): Specifies the element or isotope that the instrument will
examine in each measurement. The simplest way to specify entries is by
using the Periodic Table Panel. To use this panel, click in any cell in the
Analyte column, and then select the desired element and isotopes on the
Periodic Table panel.
You can also simply click in an analyte cell, and then type an element's
atomic symbol to indicate the intensity for that element in the sample.
Valid entries include the atomic symbols for all naturally occurring
elements, and the atomic symbol followed by “++”, such as Ca++, which
acquires data for the most abundant isotope, but at half the listed mass.
Molecular names for polyatomic species, such as ClO and ArN are also
valid entries. If you enter only the atomic symbol, the system automatically
enters the exact mass for the most abundant isotope (except for Ca, Cd,
Fe, Ni, Se, Sn, Ti, and Zn). For example, if you type Pb, the system will
enter 207.977 in the Mass column. You may also enter the atomic symbol
followed by the specific isotope of interest. For example, if you type
Pb206, the system will enter 205.975 for the mass.
This entry normally does not need to be made, because the system
automatically fills in a mass parameter based on the analyte specified. If
the Scan mode is set to Scanning, this entry represents the center of the
measured peak.
• Begin Mass (amu): (Data Only and TotalQuant methods only) Defines the
start of an atomic mass range for each measurement. The scanning range
and End Mass values set in that specific row. The total mass range that
the instrument will scan during an individual replicate is defined by all the
entries in the table. Valid entries are between 1 and 285 amu. To enter a
Begin Mass value, click in the relevant cell in the table and type a value. In
TotalQuant analyses, detectable isotopes for the naturally occurring
elements range from mass 6 (Li) to mass 238 (U). Because TotalQuant
methods use all the information available in the mass range, you must
gather data over the entire mass range that provides useful information in
your specific samples. The following additional rules should be observed
when parameter Begin Mass and End Mass values:
 Because of the large amount of oxygen present in solution samples,
the measured intensities for the oxygen isotopes (16, 17, 18) are
usually beyond the working range of the instrument. It is generally best
to avoid acquiring data in this mass range, unless you are working with
laser sampling or other techniques that do not introduce water vapor
into the mass spectrometer.
 Exclude masses 40 and 41 from the detection range. These masses
represent 40Ar and 41ArH, both of which are present in concentrations
beyond the working range of the instrument.
 It is not usually necessary to collect data for masses above 209,
except for masses 232 to 238 where thorium and uranium occur,
because no stable element isotopes occur in that range.
 If you specify a mass range that omits all the isotopes for an element,
you will receive no reported concentration for that element. However, if
you include a range that covers at least one isotope of an element,

then concentration results will be reported for that element.
• End Mass (amu): (Data Only and TotalQuant methods only) Defines the
end of an atomic mass range for each measurement. The scanning range
and End Mass values set in that specific row. The total mass range that
your instrument will scan during an individual replicate is defined by all the
entries in the table. Valid entries are between 1 and 285 amu. To enter an
End Mass value, click in the relevant cell in the table and type a value.
• Reference Mass: (Isotope Ratio methods only) Specifies the Reference
Mass to be used in the ratio calculations. When you use Isotope Ratio, you
compare the isotope of interest to a reference isotope of the same
element. For example, the concentration of Pb204 to Pb206. Alternatively,
you can compare more than one isotope or all remaining isotopes of an
element to your reference isotope and obtain a ratio for each.
The formula for the ratio is as follows:
Isotope Ratio = Analyte Isotope/Reference Isotope
where:
Analyte Isotope is set using Analyte and Mass entries
Reference Isotope is set using the Reference Mass
• Scan Mode (*): Specifies whether the system will use either peak hop
data acquisition or peak scanning.Two options are available:
 Peak Hopping: The instrument acquires data at the specified mass
only, then jumps directly to the mass for the next analyte in the method.
Peak hopping causes the software to spend more time at each mass,
reducing the number of readings required to achieve satisfactory
precision.
 Scanning: The instrument acquires data at a number of data points
around the specified mass, based on the value of the MCA Channels
entry.
• MCA Channels: Indicates the number of multichannel analyzer channels
assigned to an analyte when using scanning mode. The MCA Channels
parameter is always 1 when using peak hopping. Valid entries are
between 1 and 20 for scanning. The default value is 1. Spectra are
scanned by rapidly and repetitively sweeping the quadrupole across all of
the channels within the mass range set by the Analyte/Mass entries.
During each sweep, the spectrometer acquires data for a length of time
determined by the dwell time, and the ion count rate is measured and
stored in an MCA channel buffer. The use of a multichannel analyzer
permits enhanced analytical precision by permitting rapid scanning of the
defined mass range, with all elements measured closely to one another in
time.
• Dwell Time per AMU (ms): Indicates the length of time spent measuring
the analyte during a single sweep. The Dwell Time per AMU is the total
time spent at the mass range corresponding to the individual analyte
listed. If more than one MCA channel is being used, this time is divided by
the number of MCA channels to determine the length of time spent at each
MCA channel. The acceptable range of parameters is between 0.1 and 1
800 000 ms. The default value is 50 in both peak hop and scanning
Method Development
modes. The Dwell Time per AMU parameter applies only to the individual
analyte listed in the same row of the table. The optimum dwell time
parameter depends upon your analysis conditions and your sample.
Typical dwell time values for peak hopping are between 20 and 100 ms
using multiple sweeps per reading for a total integration time of 1000 ms. A
longer dwell time measures the analyte more precisely at the expense of
total analysis time. The use of shorter dwell times is recommended only for
transient analysis when determining a large number of analytes. However,
attempting to examine too many analytes using very short dwell times in a
short-duration transient signal will adversely affect accuracy and precision.
In Isotope Ratio determinations, it is important to collect enough analyte
ions of each isotope for an accurate calculation of the true ratio. The dwell
time of a minor isotope should be increased such that an equivalent
number of ions are counted for each isotope.
UCT instruments
For analytes using a DRC mode profile with an RPa value of 0, the
minimum dwell time is automatically raised to 10 ms. If an analyte uses a
DRC mode profile and the RPa value is not 0, the minimum dwell time is
automatically raised to 33 ms. If an analyte's flow rate or RPa value is
changed, putting the analyte in DRC mode, and the dwell time becomes
invalid, the dwell time is automatically changed by the software.
• Integration Time (ms): Displays the total amount of time that the analyte
listed will be measured during one replicate, based on the parameters for
Dwell Time per AMU, Sweeps/Reading, and Readings/Replicate as
follows:
Integration Time = Dwell Time * Sweeps/Reading * Readings/Replicate
This is a read-only entry and is designed to permit a quick assessment of

the time the quadrupole will spend measuring the individual analyte.
• Corrections: This entry is used for all methods except TotalQuant
analyses. Shows that interelement or polyatomic ion corrections are being
applied to this analyte. The interferent species used in the correction is
listed in this entry. See the Equation Tab on page 185 for more information
about corrections.
• Profile: UCT instruments only. Displays the acquisition profile the system
will apply when analyzing this analyte. Each profile consists of a pre-
defined combination of cell gas, physical gas channel, and analytic mode
— Standard, KED, or DRC mode — in which the instrument will work.
When you create a new method, you select profiles that use one or more
modes in which to analyze the analytes. You can mix modes within a
single method to best suit the analytes selected and to work around any
interferences, but, in most cases, you will choose a single mode for
specialized methods, such as Isotope Ratio and Isotope Dilution.
Note: You can create and save methods using one or more unassigned
acquisition profiles (that is, profiles that are not currently assigned to a physical
gas channel), but you can run analyses and optimizations only when all of the
profiles in the methods involved have been assigned to an active channel.
• <Gas> Flow columns: UCT instruments only. These columns display the
gas flow rate for the reaction gases associated with the selected and
assigned profiles. You can also specify multiple gas flows for a single
analyte to mix gases; the cell gas delays of the main gas will be applied.
The default value for each is 0.
• RPa (Rejection Parameter a): UCT instruments only. Displays the RPa
voltage for all the analytes as specified on the Conditions panel Cell
Parameters tab. The default value is 0.
• RPq (Rejection Parameter q): UCT instruments only. Displays the RPq
voltage for all the analytes as specified on the Conditions panel Cell
Parameters tab. The default value is 0.25
Periodic Table Panel
Use this panel to add analytes to your method by selecting them from a graphic
display of the periodic table.
Figure 5-11 Periodic Table panel
Method Development
When you click on an element, it is highlighted in gold and automatically added to

the analyte list in the open method, and the mass and relative abundance of the
element's isotopes appear in the list box below the table. The isotope with the
highest percent abundance is pre-selected. After you have selected all desired
isotopes, a number appears below the element symbol indicating the total number
of isotopes selected.
Processing Tab
Use this tab to specify which detector signals to monitor, and to define the manner
in which raw signal data will be managed by the software. These parameters
include important handling options for both the signal profile and spectral peak
data.
Figure 5-12 Method panel Processing tab

Items on the Processing Tab
• Detector Group: The Detector group is used to specify which detector
signal should be used during a determination. The system incorporates
SimulScan which automatically measures two signals simultaneously from
a single, dual-stage, discrete dynode detector. High-level signals are
measured as an analog current at the midpoint of the detector, while low-
level signals are measured using pulse counting at the base of the
detector. The detector system can also be used in either mode exclusively,
however, in normal operation, you will usually elect to operate in the dual
detector mode. Detector options are as follows:
 Pulse: Specifies use of the detector pulse-counting signal option only.
This option is applicable if you are performing a measurement on a
sample likely to produce a very low signal level.
 Analog: Specifies use of the detector analog signal measurement

option. This option is applicable if you are performing a measurement
on a sample likely to produce a very high signal level.
 Dual: Specifies instrument operation in SimulScan mode, with the
detector measuring both the pulse count and analog signals. This is
the default value for the Detector group.
• Process Spectral Peak: The Process Spectral Peak group defines the
manner in which spectral peak data will be handled during ICP-MS
determinations. The raw spectral data collected during a measurement is
not a smooth curve but rather a series of points, the number of which is
established by a number of acquisition parameters. The system processes
the raw data for each mass according to the method specified in this
group. The available spectral peak processing algorithms are as follows:
 Average: Averages the values of all the MCA channels for each peak.
 Sum: Adds the values of all the MCA channels to create a total ion
count for each peak.
 Maximum: Selects the MCA channel of the maximum value for each
peak.
• QID: You can synchronously scan the QID™ (Quadrupole Ion Deflector)
component with the actual quadrupole mass scan, permitting dynamic
adjustment of the QID voltage for optimum ion throughput. Use the QID
control on the Processing tab to manually turn this function on and off. The
default condition in a new method is for the QID function to be off.
To use the QID feature, you must first perform a QID calibration using the
SmartTune Manual function. For maximum effectiveness, recalibrate the
QID system whenever sample matrices change significantly.
• Isotope Ratio Mode: An Isotope Ratio method is a specialized technique
that you can use to measure the exact ratio of two isotopes of an element
in a sample. This technique is a sensitive indicator of age, reaction, or
metabolism in nuclear, geochemical, and biomedical applications. In
addition to providing an accurate ratio of isotope concentration, these
measurements are also highly precise. The status of the Isotope Ratio
mode is automatically controlled by the type of method applied to a data
acquisition. The Isotope Ratio mode parameters control the operation of
the Axial Field™ technology (AFT) functions during certain types of data
acquisition. You can set the Isotope Ratio mode to on or off when using
Data Only and Quantitative method acquisitions. During all other
acquisition methods, the software automatically controls the Isotope Ratio
mode. To optimize data acquisition, the Isotope Ratio mode is
automatically set to the on position for Isotope Ratio and Isotope Dilution
methods.
• Blank Subtraction: The Blank Subtraction group shows that the
subtraction of the blank signal will occur before or after signal correction
based on your internal standards.
• Process Signal Profile: Signal profile characterization is used primarily
for transient signals. When the instrument has completed the acquisition of
data for a measurement replicate, the data consists of a series of intensity
data points or readings plotted against time. This intensity/time signal
profile can be processed to yield a final intensity value for use in
quantitative calculations. The Process Signal Profile group is used to
Method Development
define the manner in which signal data will be handled during ICP-MS
determinations. The available signal processing algorithms are as follows:
 Average: Calculates the average intensity for all the readings in the
replicate.
 Sum: Adds the total ion counts measured for all readings.
 Amplitude: Indicates the maximum intensity point for all the readings
acquired.
 None: Specifies that no signal processing should be performed on the
acquired data.
You can then set the number of Baseline Readings and a Smoothing
Factor, if applicable. The Baseline Readings entry defines the number of
readings that will be used in baseline correction; it is used to calculate a
baseline intensity value that is subsequently subtracted from all
measurements in the replicate. This baseline count can correct for solvent
effects or other sample induced intensity shifts.
Use the Apply Smoothing function to apply a Savitzky-Golay moving point
average smoothing function to the signal profile data. Smoothing tends to
reduce the effects of measurement noise in low signal-to-noise
measurements. The number of points used in the moving point average
calculation is determined by the value of the Factor entry. The minimum
number of points is five. The larger the value selected, the greater the
smoothing effects.
• Measurement Unit: The Measurement Unit group defines the manner in
which the raw data will be measured:
 cps: Data is displayed using counts per second as the raw data.
 counts: Data is displayed using total counts as the raw data.
Equation Tab
Use this tab to view isotope abundance information, to identify potential
interferences for your analytes, and to define interference corrections for use
during determinations.
Note: The fields that appear on this tab vary, depending on the type of method.
Figure 5-13 Method panel Equation tab

Items on the Equation Tab
• Isotope Information: Displays the mass, natural abundance, and known
interferences for all of the isotopes of the analyte selected in the Equations
table. This listing helps you to develop elemental equations for
interference correction by making important isotopic information readily
available. To display information for a different element, click a different
analyte in the Equations table. If the element you are interested in is not
listed in the table:
 Click in an empty cell in the Analyte column of the Equations table.
 Type in the atomic symbol for the required element, or select the
element from the Periodic Table panel. The information for that
element is displayed in the Isotope Information listing. If you enter an
analyte in this manner, and do not want to include the analyte in your
measurements with the current method, remember to delete the
element from the Equations table.
• Equations Table: The Equations table lists the elements and isotopes
entered on the Timing tab, together with any known potential
interferences. Beside each element is a field for entering the equations
that will be used to correct for interferences during data acquisition. A
series of default equations serve as a starting point, but the specific
equations required are a function of your sample. Before attempting to
develop additional elemental equations, review Interference Correction on
page 200.
 Internal Standard: (Quantitative Analysis methods only) Lists the
standard groups and internal standards defined in the method.
Method Development
 Analyte (*): Defines the atomic mass of the isotope that the instrument
will examine in each measurement. The simplest way to add analytes
is through the Periodic Table panel — click in any cell in the Analyte
column and select the required elements and isotopes. Alternatively,
you can click in a cell and manually type an element's atomic symbol to
determine the intensity for that element in the sample. Valid entries
include the atomic symbols for all naturally occurring elements. You
can also type the atomic symbol followed by “++”, such as Ca++, to
acquire data for the most abundant isotope, but at half the listed mass.
Molecular names for polyatomic species, such as ClO and ArN, are
also valid entries. If you type only the atomic symbol, the system
automatically enters the exact mass for the most abundant isotope
(except for Ca, Cd, Fe, Ni, Se, Sn, Ti, and Zn). For example, if you type
Pb, the system enters 207.977 in the Mass column. You can also type
the atomic symbol followed by the specific isotope of interest. For
example, if you type Pb206, the system shows 205.975 for the Mass.
 Mass (amu): Here you specify the mass at which the isotope will be
measured. This entry normally does not need to be made, because the
system automatically populates the mass parameter based on the
analyte specified. If the Scan mode is set to Scanning, this entry
represents the center of the measured peak.
 End Mass (amu): (Data Only methods only) Specifies the end of an
atomic mass range for each measurement. The scanning range
defined by a single row in the table is the range between the Begin
Mass and End Mass values set in that specific row. The total mass
range that the instrument will scan during an individual replicate is
defined by all the entries in the table. Valid entries are between 1 and
270 amu. To enter an End Mass value, click in the relevant cell in the
table and type a value.
 Reference Mass: (Isotope Ratio methods only) Displays the reference
mass used in the ratio calculations. The Isotope Ratio compares the
isotope of interest to reference isotopes of the same element.
Isotope Ratio = Analyte Isotope/Reference Isotope
 Elemental Equation: (TotalQuant methods only) Lists any
preprogrammed elemental equations included with the software.
 Corrections: This parameter defines the elemental equations to be
used for interference correction. Many quantitation problems produced
by spectral interferences can be compensated for by using an
elemental equation.
 Potential Interferences: This column lists the known interferences,
isotopes and polyatomic ions, for an isotope listed in the Equations
table. The software includes a comprehensive listing of the potential
interferences for a determination, helping you to define problems more
easily and to simplify correction. These standard equations correct for
isotope interferences, not for molecular interferences that may occur.
Calibration Tab
Use this tab to set up a calibration for use in your determinations. Here you can
define the composition of your standards and specify the concentrations of each
analyte in each standard solution. You can define up to 30 standards in a single
calibration. This tab is not available for the Data Only method type.
Figure 5-14 Method panel Calibration tab

Items on the Calibration Tab
• External Std./Std. Addition: Specifies the type of calibration defined:
External Std. or Std. Addition. The solutions listed on this tab are run
whenever the Calibration Action for a sample solution listed in the Sample
panel specifies that the standards should be run. For samples that are not
subject to sample-specific matrix interferences, external standardization is
a simple and effective means of calibrating your instrument. External
standardization involves measurement of a blank solution followed by a
set of standard solutions to create a calibration curve that covers the
concentration range of interest. Typically, two or three standard solutions
are run, each containing different concentrations of all the elements being
examined in the analysis. Increasing the number of points on the
calibration curve — that is, increasing the number of standard solutions —
may improve accuracy in circumstances where the calibration range is
very broad. Standard addition calibration provides an effective means of
minimizing sample-specific matrix effects through the use of spiked
samples.
In standard addition calibration, you start by measuring a blank solution.
Next, you measure the sample solution spiked with a known concentration
of each element that you are determining. You may perform the spike
Method Development
measurements at one or more spike concentrations, depending on the

accuracy required in your determinations. You then measure the unspiked
sample solution. The software measures the responses for the spiked
samples, and creates a calibration curve for each element for which a
spike has been added, based on the known concentration values which
you have entered. Based on the slope of the calibration curves, the
software calculates the unspiked concentrations of the analytes in the
unknown.
• Concentration Unit: The concentration of the sample or standard in
selectable units — for example, ppm or mg/L. This is available for
TotalQuant methods only.
• Conversion Factor: All units are calculated internally using ppm. The
conversion factor is used to create the displayed value from the internal
value. This is available for TotalQuant methods only. For example, the
conversion factor for ppm is 1; the conversion factor for ppb is 1e-3.
Parameters in the Calibration Table
The Calibration tab includes a table where you can enter information to specify the
composition of your standard solutions. Each element or isotope and any internal
standards listed on the Timing tab are automatically added to the table. Here, you
can also use the Int. Std. field to specify an internal standard.
The following entries appear in the Calibration table:
• Internal Standard: Lists the standard groups and internal standards
defined in the method.
• Analyte (*): Defines the atomic mass of the isotope that the instrument will
examine in each measurement. This entry lists all the isotopes entered in
the Analyte column on the Timing tab. You may specify additional isotopes
on this tab; however, it is preferable to enter new isotopes on the Timing
tab, because the timing parameters may need to be adjusted from their
default values. The simplest way to specify entries is by using the Periodic
Table panel; click in a cell in the Analyte column and select the required
elements and isotopes from the dialog box that appears.You can also click
in the appropriate cell and type an element's atomic symbol to indicate the
intensity for that element in the sample. Valid entries include the atomic
symbols for all naturally occurring elements. You may also type the atomic
symbol followed by “++”, for example Ca++, to acquire data for the most
abundant isotope, but at half the listed mass. Molecular names for
polyatomic species, such as ClO and ArN are also valid entries. If you
enter only the atomic symbol, the system automatically enters the exact
mass for the most abundant isotope (except for Ca, Cd, Fe, Ni, Se, Sn, Ti,
and Zn). For example, if you type Pb, the system enters 207.977 in the
Mass column. You can also enter the atomic symbol followed by the
specific isotope of interest. For example, if you type Pb206, the system
enters 205.975 for the mass.
This entry normally does not need to be made, because the system
automatically fills in a mass parameter, based on the analyte that you
specified. To set a mass value, click in the relevant cell in the table, then
type a value. To modify the mass parameter, click in the appropriate cell
and type the exact mass at which the isotope should be measured, to a
maximum of four decimal places. If the Scan mode is set to Scanning, this
parameter represents the center of the measured peak.
• Curve Type (*): Specifies the type of calibration curve that will be
constructed from the calibration information for the specific analyte listed
on the same row of the Calibration table. To select a curve type, right-click
in the Curve Type field and then click a type. The following options are
available:
 Simple Linear: Uses standard linear regression for curve calculation,
with equal weighting applied to all calibration solutions
 Linear Thru Zero: Uses linear regression with a forced zero, that is, the
curve includes a point at the origin of the calibration graph
 Weighted Linear: Uses a linear regression algorithm that incorporates
a standard, concentration-dependent weighting factor to emphasize
measurements in the low concentration region of the calibration curve.
The weighting factor (w) equals the inverse of the square of the
concentration of the standard.
• Sample Units (*): Specifies the concentration units for the sample
solutions. The following concentration units are available:
 ppm: parts per million
 ppb: parts per billion
 ppt: parts per trillion
 mg/L: milligrams per liter
 µg/L: micrograms per liter
 ng/L: nanograms per liter
 µg/g: micrograms per gram
 ng/g: nanograms per gram
 mg/dL: milligrams per deciliter
 µg/dL: micrograms per deciliter
 ng/dL: nanograms per deciliter
 µg/mL: micrograms per milliliter
 ng/mL: nanograms per milliliter
 pg/mL: picograms per milliliter
Method Development
Sampling Tab
Use this tab to define the sampling device parameters for all analytic solutions
within the method. The information entered here includes general information
about the type of autosampler, plus information about pumping rates and times.
Note: Only one sampling device can be active in addition to the peristaltic pump.
Figure 5-15 Method panel Sampling tab

Items on the Sampling Tab
• Peristaltic Pump: This table provides peristaltic pump parameters derived
from the parameters defined on the Syngistix Options dialog box
Peristaltic Pump Defaults tab. Change these to override the default
parameters for this method:
and 99 999
(300/350 series instruments) is valid
between 0 and 99 999

indicates clockwise rotation
 Analysis Speed: Read only. Displays the pump rate in rpm used during
the determination. A negative value indicates counter-clockwise
rotation of the pump head and a positive value indicates clockwise
rotation
acquisition. Type a value between 0 and 99 999
tubing
• Auto Diluter Controls: When an autodiluter (such as the ESI prepFast or
the Cetac ADX-500) is selected as the sampling device, one or more of the
following fields become available:
 Dil. Factor: Controls dilution factors ranging from 2 to 1 000, with a
default value of 10. A dilution factor of N should lower the measured
intensity by a factor of N.
Note: The Dilution Factor acts as a multiplier of the Diluted to Volume
field on the Sample panel Batch tab. To maintain the dilution factor
entered on the Sampling tab, enter 1 in the Diluted to Volume field.
 Dil. To Vol.: Here you can specify the volume of the diluted samples
the autodiluter will create. This volume ranges from 2 mL to 50 mL,
with a default value of 10 mL.
 1st. Dilution Pos.: Here you can specify which tubes should be used
when diluted samples are created. The first diluted sample is created
in the 1st. Dilution Pos. tube, the second in the next higher numbered
tube and so on.
 Probe Purge Pos.: Here you can specify the tube to be used for the
autodiluter initialization. In order to accurately measure the volumes of
liquid involved in each dilution, the probe and associated tubing must
be full of diluent before any dilutions are done. Ten milliliters of diluent
are therefore pumped into the probe, and the tube at the Probe Purge
Pos. is used to collect any spillage. The default position for this probe
is 10.
• Sampling Device: Specifies the use of an optional sampling device such
as a FIAS™ system or a liquid chromatograph.
 If you select the FIAS option, the Devices tab becomes active and
available. Define the parameters on the Devices tab; then use the
Control screen Devices panel FIAS tab to configure the device.
 If you select the External option, you can attach an external sampling
device, such as a liquid or ion chromatograph or laser ablation tool, to
the instrument.
When you select External, the External Read Trigger dialog box
Method Development
appears. The external sampling device must effect a contact closure or

opening in conjunction with the instrument before it starts its
measurements. Here you can select the type of external read trigger
needed. You can configure the system to respond to an external trigger
by either running all replicates in the method in sequence, or running
just the next replicate in the method. Note that external devices also
require a connector cable to communicate between the external
sampling device and the instrument.
Parameters in the External Read Trigger dialog box

 Timing and Read Delay fields: Enter the desired contact and delay
parameters, and then, in the and trigger drop-down list, select either
just one replicate or the entire method, as required.
 Action if no contact received after wait period: Select the action
you want the system to take if no contact is achieved — you can
choose to have the system Idle or to Stop the plasma / device.
 Complete cell gas transitions: UCT instruments only. Select the
Before responding to trigger check box if you want any cell gas
changes to take place before the system responds to the trigger. This
ensures that the system is completely primed to go before any trigger
response actions are activated. If you are using an ESI FASTFIAS
sampling system, ensure that you check this box for the most efficient
operation of your system.
• Autosampler and Tray: Displays the autosampler and tray selected on
the Control screen Devices panel Autosampler tab.
• Peristaltic Pump Under Computer Control: Select this check box if you
want the peristaltic pump speeds to be automatically controlled by the
software. If this check box is cleared, you must control pump speeds
manually.
Parameters in the Sampling Table

These entries contain information for the blank and standards.
• Solution ID: Here you can specify the Solution ID for Calibration
Standards and Blanks. The contents are stored in the Method file, and are
displayed as the Sample ID in reports if specified, during acquisition in the
Measurement Status dialog box, run list, and in the dataset. If you do not
have a solution ID specified, the instrument uses default sample IDs.
• A/S (Autosampler) Location: Lists the autosampler location for the blank
or standard. This is the location that the solution occupies in the
autosampler tray. For standard additions calibration, enter the autosampler
locations for the blank and the two standards here. Use negative numbers,
indicating the location of the blank and standards relative to the sample
location. This entry is ignored if a manual analysis with no autosampler is
being performed.
• Wash Override (sec): Specifies the time in seconds that the autosampler
probe is in the wash solution before it moves to the next solution to be
analyzed. Any positive value is valid, including zero. Use this function to
provide a longer wash time than specified in the peristaltic pump
parameters for specific solutions.
Report Tab
Use the Report tab to specify the type of report you want to produce and the
report template to be used. You can also specify the creation of a results file in tab
or comma delimited ASCII format.
Figure 5-16 Method panel Report tab
Method Development
Items on the Report Tab

• Report View group: The Report View group lists the name of the Report
Options template that will be used to format the results from your
determinations
• NetCDF group: NetCDF files are used to export data to chromatographic
data handling software, such as the TotalChrom® software. The software
automatically creates the NetCDF file after each sample is run.
• Report Concentration group: These controls apply to TotalQuant
methods only.
 Concentration Unit: The concentration of the sample or standard in
selectable units — for example, ppm or mg/L.
 Conversion Factor: All units are calculated internally using ppm. The
conversion factor is used to create the reported value from the internal
value. For example, the conversion factor for ppm is 1; the conversion
factor for ppb is 1e-3.
• Report to File group: Select the file where you want to store the data
from the determination, send the file to a serial port, or export the file in
PKI LabWorks format.
• Report Format group: The following options are available in the Report
Format group:
 Include Titles adds section and control titles to the report.
 Use Delimiter causes a tab-delimited format to be used for the report.
This means that a tab character is inserted between each field.
 Use Separator causes a comma-separated variable format to be used
for the report. This means that a comma is inserted between each
field.
 Use International Character Set enables international characters to be
displayed and printed on the report.
• File Write Option group: The following options are available in the File
Write Option group:
 Append adds the data to the end of the existing file.
 Overwrite causes all current data in the file to be erased and replaced
with the new data.
 New Per Sample sends the data to a new file for each sample.
Notes Tab
Use the Notes tab to record notes about the method or about specific procedures
that may be required when using the method.
Figure 5-17 Method panel Notes tab
Chapter 6
Interference Correction
This section provides information on interferences that can affect your ICP-MS
results; how to identify these problems in your data; and procedures for correcting
for these defects.
• Interferences in ICP-MS on page 197
• Interference Identification on page 200
Interferences in ICP-MS
The ICP-MS technique offers numerous analytical benefits. However, during
method development, it is necessary to understand the influence of spectral
interferences that can affect your final results. An interference is anything that
causes the signal from an analyte to be different from the same signal for the
same concentration of that analyte in a calibration solution.
As with all other atomic spectrometric analytical techniques, interferences of
various types can occur during routine ICP-MS determinations. Interferences
associated with sample introduction using a nebulizer or spray chamber are
common to atomic absorption, optical emission ICP, and ICP-MS. These are
termed transport interferences. In addition, interferences can occur from the
presence of other isotopes or elements with the same atomic weight or mass
number as an analyte of interest. These are termed spectral interferences.
Matrix Interferences
Sample introduction effects when using a nebulizer or spray chamber system are
common in ICP-MS determinations. These interferences are generally the result
of either sample matrix effects that influence aerosol formation or the formation of
ions in the plasma (surface tension, viscosity). Complex sample matrices may
interfere with focusing ions into the sample and skimmer cone orifices, and
focusing and transporting ions through the ion lenses and quadrupole.
Matrix interferences can be identified by:
• Observing the intensity of the argon dimer, (Ar 40)(Ar 40), versus the
blank. The argon dimer peak and analyte element signals are usually
affected similarly by matrix interferences
• Determining if response is linear with dilution. Response dependence on
the absolute concentrations of analyte and matrix is an indicator of a
matrix interference
• Analyzing at low and high nebulizer argon flow rates
Note: A sample with an interference and a standard solution will respond

differently.
The most commonly observed result of matrix interference is the ion intensity if an
analyte element becomes dependent upon the total composition of the sample.
Typical signal suppression is observed. For example, a given concentration of
197
selenium will exhibit a signal approximately 25% lower in a 1 000 mg/L NaCl
solution than the same concentration of selenium in water. This signal attenuation
is mass dependent. Light analytes in a predominantly high mass matrix (for
example, 1000 mg/L U) are more prone to signal attenuation than a heavy analyte
in the presence of a light mass matrix (for example, 1 000 mg/L Li).
Several methods can be used to compensate for matrix-induced signal
suppression. For a well-defined matrix, it is simple to match the composition of the
standard solutions with the sample solutions, and thus obtain the necessary
analytical accuracy. For a matrix of unknown composition, standard addition
calibration, in which known concentration standards are added directly to a
sample solution, provides a method for compensating for the sensitivity difference
between samples and standards.
Spectral Interferences
Spectral interferences are the result of other chemical species, such as isotopes
or ions, which are present at the same atomic mass as the analyte of interest.
Spectral interferences generally occur from the sources listed in the following
sections.
Isobaric Overlaps
Because most elements have more than one naturally occurring isotope, it is
possible for the mass spectrum of an isotope of one element to directly overlap
that of an isotope of another element. These interferences are termed isobaric
overlaps. All elements, except indium, have at least one isotope free from overlap.
Therefore, you can overcome this problem by selecting of isotopes carefully when
developing your methods.
Minor overlaps are corrected by measuring the intensity of the interfering element
at one of its major isotopes. Then, using published isotope ratios, it is possible to
subtract the intensity of the interfering isotope that is contributing to the analyte
signal. Using this principle, the software uses built-in calculation routines to
automatically correct for known isobaric overlaps when calculating analyte
concentrations in samples. In general, you do not need to make any further
adjustments to the system, assuming that the default calculations are not
modified.
Plasma-Induced Polyatomic Ions
The presence of atmospheric gases or the argon carrier are sources of potential
interfering ions as the result of reaction with other analyte or matrix components.
These interfering ions occur as polyatomic molecular ions. The following table lists
the most severe of the commonly occurring overlaps:
Analyte % Abundance of isotope Interfering ion

S 32+ 95.0 (O 16)(O 16)+
K 39+ 93.3 (Ar 38)(H)+
Ca 40+ 96.9 Ar 40+
Fe 56+ 91.7 (Ar 40)(O 16)+
Se 80+ 49.6 (Ar 40)(Ar 40)+
Of these, only the overlap of the most abundant isotope of argon with calcium
precludes analysis at the preferred isotope. In the case of calcium, determinations
using a basic quadrupole instrument are generally performed at Ca44, which is

approximately 2% abundant.
Note: On UCT instruments, the interference reduction capabilities of the DRC mode
mean that you can use the most abundant isotopes for K, Ca, Fe, and Se.
Sulfur detection limits are affected both by poor ionization in the ICP (14%),
resulting in low ion intensity, and by the overlap of the primary sulfur ion by
diatomic oxygen. Unless the oxygen entering the plasma can be reduced to trace
levels, the overlap forces the use of a less abundant sulfur isotope S34 for
determinations.
Matrix Solvent-Induced Polyatomic Ions
The solvent or acid in which the sample is dissolved can also be a source of
interfering polyatomic ions. Chlorine from hydrochloric or perchloric acid and
sulfur from sulfuric acid all form polyatomic ions with argon and other plasma
gases. For organic solvents, carbon and oxygen can form polyatomic ions. The
most severe solvent-induced interference is from CO on silicon. All three silicon
isotopes are overlapped by carbon species, precluding the determination of
silicon in organic matrices. The major solvent-induced overlaps are listed in the
following table:
Analyte % Abundance of isotope Interfering ion

Si 28+ 92.2 (C 12)(O 16)+
Ca 44+ 2.0 (C 12)(O 16)(O 16)+
Ti 48+ 73.8 (S 32)(O 16)+
V 51+ 99.7 (Cl 35)(O 16)+
Zn 64+ 48.6 (S 32)(O 16)(O 16)+, (S
32)(S32)+
As 75+ 100.0 (Ar 40)(Cl 35)+
Matrix-Induced Polyatomic Ions

Polyatomic ions may also be generated by sample constituents, usually in
combination with oxygen. Oxides of some heavier elements can be formed in the
plasma/spectrometer interface. Typically, oxides are formed in relatively low
concentrations, with the worst cases only a few percent of the parent isotope. In
sufficient concentrations, however, oxide-forming elements can interfere with
determinations of analytes at higher masses. An example is the formation of
molybdenum oxide which overlaps all the major isotopes of cadmium.
In most cases, you can compensate for these interferences with a knowledge of
the intensities of the oxide and parent ion. Then, by measuring the intensity of
parent interfering ion, you can subtract the calculated interfering oxide intensity
from the analyte intensity.
Dissolved Solids Limitations

In ICP-MS, the physical design of the ICP-mass spectrometer interface limits the
concentration of dissolved solids to approximately 0.25%. At higher
concentrations, the sampler cone orifice may become plugged when performing
steady-state determinations. While this seems like a limitation, the extremely low
detection limits of the instrument usually offset the problem, because you rarely
need to run a solution at a high-enough concentration to cross the dissolved

solids limit. In fact, it is routinely necessary to dilute samples 50100 before
introducing them to the spectrometer, in order to not exceed the signal range of
the detection system and to avoid coating the ion optics.
Interference Identification
Whenever samples of unknown composition are received by an ICP-MS
laboratory, the method development and selection process involves a careful,
stepwise approach to determining potential interference problems and to defining
a solution to these interferences. This approach begins by performing a
TotalQuant™ analysis on the solution to determine the following:
• Elements present at measurable concentrations
• The concentration ranges for the elements of interest
• Interfering molecular ions
•Masses at which no elements are present, where internal standards could
be defined
This same information could also be determined by performing a full mass scan
and manually reviewing the spectral results in the Interactive panel. However, the
TotalQuant approach provides a fully automated means of gathering both spectral
and semi-quantitative data.
Using this information, you can determine which element isotopes to use to best
avoid potential interference problems, plus you can determine the best mass
ranges for internal standards.
This section describes various interference correction strategies, and provides
relevant examples.
Operating Modes and Interference Correction

The NexION® 300q/350q instrument operates in a single mode to perform typical
ICP-MS analyses of samples having no significant interferences. NexION
instruments with UCT™ functionality (all 2000 instruments, and the 300/350 X, D,
and S models) have three available operating modes — standard mode, DRC™
mode, and KED mode. The mode you choose depends on the samples you will be
analyzing and the types of interference you expect to encounter.
• Standard mode: Standard mode provides excellent ICP-MS analysis for
most of the isotopes in the periodic table where complex polyatomic
interferences are not an issue, or where it is not critical that you use the
most abundant isotope of each element.
• KED mode: This mode uses collisions with an inert gas and kinetic energy
discrimination to reduce polyatomic interferences. While not as sensitive
as DRC mode, this method can be applied to all polyatomic interferences
equally, and does not require an in-depth knowledge of the sample prior to
analysis.
• DRC™ mode: DRC mode provides for high-sensitivity elemental analyses
for complex spectral interferences. The DRC technology uses ion-
molecular reactions and band-pass tuning to chemically correct for
interferences.
For example, if you want to examine the isotopes 56Fe and Ar40O16, you will
encounter an isotopic interference, as the mass of the two isotopes is identical. To
deal with this:
• In standard mode, select a less abundant isotope, such as 54Fe rather
than 56Fe, to avoid the interference
• In KED mode, helium gas introduced into the cell reduces the interferent
isotopes through collision and kinetic energy discrimination
• In DRC mode, the cell gas triggers an ion-molecule reaction that obviates
the interference, without affecting the isotope of interest:
NH3 + 56ArO+xxxxxNH3+ + 56Ar O
NH3 + 56Fe+xxxxxx no reaction
Corrections in Quantitative Analysis, Isotope Ratio, and Isotope

Dilution Methods
Sample specific matrix effects and spectral interferences require two different
approaches for correction. The use of internal standards and standard addition
calibration are the primary means of correcting for matrix interferences in sample
solutions.
For spectral interferences, your system uses elemental equations to correct for
the spectral overlaps that can affect your results. Corrections for isobaric overlaps
and many known polyatomic ion overlaps are programmed into the software, and
the standard equations are automatically listed on the Method panel Equation tab.
These standard equations correct for known isotope interference, but do not
correct for interferences due to molecular species. Using the Equation tab, you
can modify the standard equations or construct new equations to suit your
requirements.
Corrections in TotalQuant™ Analyses
Elemental equations are also used to correct for sample-specific molecular or
polyatomic ion interferences in TotalQuant analyses. The TotalQuant software not
only incorporates standard isotopic interference equations, but also uses a
polyatomic species table to correct for common polyatomic interferences.
However, it is still often necessary to manually alter measurement calculations for
certain elements due to sample-specific interferences.
The Method panel Equation tab permits you to specify the isotope you want to
measure, and then specify any corrections needed to accurately measure the
element of interest. By selecting your isotope carefully, you can minimize the
number of corrections necessary. Note that the Equation tab is used to program
the isotope to be used for element concentration calculations, and to program
corrections for interferences. This is different from the correction protocol in other
analytical methods, where you specify corrections only. When you enter an
elemental equation in a TotalQuant method, it overrides all the heuristics normally
associated with that element. As a result, it is normally not necessary to program
corrections for polyatomics. However, if your sample solution is an especially
complex matrix, you can also specify polyatomic corrections on the TotalQuant
Equation tab.
Interference Correction: Examples

You can quickly and easily perform interference correction using the Method panel
Equation tab. The following examples demonstrate the use of elemental
equations for Quantitative Analysis/Isotope Ratio/Isotope Dilution measurements
and TotalQuant measurements.
Correcting for Spectral Overlap (Quantitative)
The following example explains how the software uses elemental equations to
correct for simple elemental overlap.
The instrument measures the intensity of an isotope at the indicated mass. This
measurement represents the total intensity at the mass value, including
contributions from the analytes and any other element or polyatomic species that
might occur at that mass. For example, to determine the amount of Zr 94 present
in a sample, the system measures signal intensity at mass 93.906. Imagine a
sample in which the system measures 100,000 counts at mass 93.906. This
measurement includes contributions from Zr 94 and Mo 94.
During the determination, the system measures the intensity of an isotope of the
interfering element (Mo) that does not overlap with the analyte. For our example,
the instrument measures the intensity of molybdenum at mass 94.906, equalling
5,000 counts.
The software calculates the proportion of the interfering isotope present in the
sample based on the intensity of the non-interfering isotope and the ratio of the
naturally occurring abundances of the interfering and non-interfering isotopes. For
example, the natural abundance ratio of Mo 94 to Mo 95 is 0.581030. So, if the
system measures 5,000 counts for Mo 95, there must be (0.581030 * 5000)
counts of Mo 94 present that are interfering with Zr 94.
The software can now calculate the intensity of the analyte by subtracting the
intensity of the interfering isotope from the total intensity at the atomic mass of the
analyte.
In this example, we know that 2,905 (that is, 0.581030 * 5000) of the counts at
mass 94 are due to Mo 94. We also know that the remainder of the counts at
mass 94 are likely due to Zr 94. As a result, the elemental equation calculation for
this example is:
(Zr 94) = I (94)  [I (95) * (abundance (Mo 94) / abundance (Mo 95))]
where:
I = intensity of the specified mass
abundance = natural abundance of the isotope
You would make the following entry on the Equation tab to perform this
calculation:
0.581030 * Mo 95
Detector Shutdown
The pulse shutdown threshold is two million count per second (cps). This means
that when acquiring data in pulse mode, if the measured intensity of an analyte
goes beyond 2 million cps, the analyte goes into pulse shutdown.
Shutdown values are denoted by the letter S. To convert the S to a cps value,
reprocess the data with a method that uses a dual detector calibration. For
quantitative accuracy, you must perform a dual detector calibration for every mass
that you want to measure above two million cps. You can view and determine
intensities above two million cps using the analog or dual modes of the detector.
However, if the analyte intensity exceeds the dynamic range of the detector
(typically 1e9 cps), then the analyte goes into analog shutdown. Analog shutdown
values are also denoted by an S. In this case, the true value cannot be
determined unless the solution is diluted and reanalyzed. When the analyte
intensity cannot be accurately determined because a correction mass is in
shutdown, the intensity is denoted by an E on the plot to signal an elemental
equation error. This E point is included in the regression automatically.
When acquiring data in pulse mode, analytes whose correction equation has
some terms in shutdown are calculated by substituting the value of 2e6 for those
terms. The resulting value is displayed in brackets; for example:
.
Analyte Intensity Std. dev %RSD Concentration Conc. std. dev

V 51 [623000] 9898 N/A [40] ppb 4.2 ppb
The intensity value is displayed in brackets to denote that an interelement or

polyatomic correction has gone into shutdown and an accurate determination of
the vanadium intensity was not possible.
Corrections for Polyatomic Species (Quantitative)
You can use elemental equations to correct for the effect of polyatomic species
interference on an analyte isotope. For example, arsenic has a single isotope,
As 75, which is overlapped by a peak from (Ar 40)(Cl 35). While this interference
is normally quite small, you may want to correct for it in samples with a high
chloride concentration. Because chlorine has isotopes at both masses 35 and 37,
(Ar 40)(Cl 37) can be measured at mass 77 and this information used to calculate
and correct for the interference at mass 75.
The following equations are used:
I (As 75) = I (75)  I (Ar 40 Cl 35)
I (Ar 40 Cl 35) = I (75)  [abundance (Cl 35) / abundance (Cl 37) * I (77)]
where:
By combining these two equations and rearranging, we get:
I (As75) = I (75)  [abundance (Cl 35) / abundance (Cl37) * I (77)]
Substituting the abundances for the chlorine isotopes yields the following
result:
I (As75) = I (75)  [(0.7577 / 0.2423) * I (77)] = I (75)  3.127 * I (77)
As a result, you would enter the following on the Equation tab:
 3.127 * mass 77
Corrections for Spectral Overlap and Polyatomic Interferences

(Quantitative)
In certain cases, you must account for interferences resulting from both spectral
overlap and polyatomics. For example, when determining arsenic concentration in
the presence of high chloride concentrations, you can use the (Ar 40)(Cl 37)
intensity at mass 77 to calculate a correction for the presence of (Ar 40)(Cl 35) at
mass 75 (as demonstrated in the previous example). That example assumed that
no additional isotope other than Ar Cl occurred at mass 77. In actual practice,
selenium has an isotope at mass 77 and, therefore, displays an ion intensity if
present. So, to accurately determine the amount of (Ar 40)(Cl 37) present, you
must perform an additional correction for selenium. The selenium isotope at mass
82 is subject to very few interferences, and can be used to determine the
selenium concentration.
The following equations are used:
I (As 75) = I (75)  I (Ar 40 Cl 35)
I (Ar 40 Cl 35) = I (75)  [abundance (Cl 35) / abundance (Cl 37) * I (77)]
I (Se 77) = (abundance (Se 77) / abundance (Se 82)) * I (82)
where:
By combining these equations and rearranging, we get:
I (As 75) = I (75)  [abundance (Cl 35) / abundance (Cl 37)]
* {I (77)  [abundance (Se 77) / abundance (Se 82) * I (82)]}
Substituting the abundances for the chlorine and selenium isotopes yields
the following result:
I (As 75) = I (75)  3.127 * [I (77) - (0.874 * I (82))]
As a result, you would enter the following on the Equation tab:
 3.127 * (mass 77 - (0.874 * mass 82))
Isotope Selection (TotalQuant™ Methods)
When using elemental equations in TotalQuant methods, the first step is
specification of the measurement isotope that you want to use. This can be either
the actual isotope (that is, Se 77 to measure selenium at mass 77) or it can be an
alternate isotope. For example, the major isotope of sulfur occurs at mass 32.
However, this mass is also subject to interference from a plasma-induced
molecular ion overlap caused by (O 16)(O 16)+ ions. For more accurate data in
the presence of a high oxygen concentration, it is helpful to identify an alternate
isotope, such as S 34, which is subject to fewer interferences.
To specify S 34 as the measurement isotope for sulfur, we first determine
the natural abundance (4.21), then calculate its inverse * 100.
[(1 / 4.21) * 100] = 23.75
You would make the following entry in the Corrections column of the
Equation tab:
23.75 * mass 34
Spectral Overlap (TotalQuant™ Analyses) Corrections
TotalQuant elemental equations retain all of the correction functionality of the
elemental equations in other analytical techniques. The primary difference in their
use is the requirement to first specify the measurement isotope. After you have
specified the isotope to use as the base intensity measurement, you can enter
additional corrections as required by your sample.
For example, the major isotope of selenium occurs at mass 80. This mass is also
subject to interference from a plasma-induced molecular ion overlap caused by
(Ar 40)(Ar 40)+ ions. The argon intensity is generally much greater than the
selenium signal, so you would usually select an alternate isotope. For this
example, we will select Se 82, which has a relative abundance of 8.73.
First, we set the abundance factor by calculating the inverse of the normal natural
abundance, multiplying the quotient by 100.
[(1 / 8.73) * 100] = 11.45
Next, we set the determination mass to 82. However, the signal at mass 82 is also
subject to contribution from Kr 82, so a correction must be programmed.
To correct for Kr 82, we must find a non-interfering Kr signal. Here, we will use
Kr 83. Because the ratio of the natural abundance of Kr at mass 82 and mass 83
is nearly identical, the abundance factor is 1.00. And, because we must subtract
the contribution from Kr, we will set the factor to 1.00. Thus, our equation for the
calculations is:
I (Se) = 11.45 * [I (82)  (abundance (Kr 82) / abundance (Kr 83) *I (83))]
where:
The entries to be made in the Corrections column of the Equation tab are:
11.45 * (mass 82 1.00 * mass 83)
In practice, you would compensate for the Kr overlap by performing a blank
subtraction before analyzing the sample. The assumption is that the Kr comes
from the argon gas supply, and is the same for both samples and blanks.
Chapter 7
Sampling Systems
In addition to pneumatic nebulization, the software incorporates control
parameters for different sample preparation and delivery options.
• FIAS™ Sampling Systems on page 207
FIAS™ Sampling Systems

Flow injection analysis (using a FIAS system) differs from conventional ICP-MS
solution sampling with a nebulizer in that small, discrete volumes of sample are
introduced into the ICP-MS in a timed sequence. When analyzing samples via FI-
ICP-MS, you can use any method type.
Before proceeding with an analysis on the FIAS system, you should carefully
review your analytical requirements. To define an effective FI-ICP-MS analysis,
you must be familiar with the chemical characteristics of your sample analytes and
the matrix. These chemical properties will determine the optimal FIAS program to
use.
FIAS™ Program Example

Follow this example for a better understanding of how the FIAS program
functions:
• Pre-Sample step: We entered 10 seconds for the duration and a speed of
120 rpm for pump 1 and 60 rpm for pump 2. Pump 1 delivers the sample
from the autosampler to the injection valve for loading the sample loop.
Pump 2 directs the carrier solution through the bypass to the system.
• Step 1 (Load): We used a 10 second duration for pump 1 at 120 rpm and
pump 2 at 60 rpm, and set the FIA valve to position 1. This acts as a loop-
filling step for additional replicates.
• Step 2 (Sample Injection and Read): We set pump 2 to 120 rpm and the
FIA valve to position 2 to deliver the sample to the instrument at
approximately 6 mL/min. The duration is set to 20 seconds. This value
corresponds to the estimated replicate time on the Method panel Timing
tab. This should not exceed the total time for the signal peak to appear,
maximize, and return to baseline. Step 2 also contains the read; note the x
in the Read column.
• Post-Run step: We set the pumping time to continuous operation (“-”) and
set both pump speeds to 60 rpm. An appropriate post-run A/S location
must be entered, or it will remain at the last sample tube position. If the
post-run step is wash, enter “0” for the wash station.
207
Method Panel Devices FIAS Tab

Use the Devices FIAS tab to set FIAS program parameters, including pumping
time, pump speed, FIA valve position, and autosampler location.
Figure 7-1 Method panel Devices FIAS tab

Items on the Devices FIAS Tab
• Repeat Steps: Indicates that a continuous set of program steps (for
example, 1 through 3) will be repeated an additional number of times. Note
that these iterations are in addition to the number of times the steps repeat
automatically due to multiple replicates in the parameter set. For example,
a value of zero (0) times entered here means that the program steps will
be executed once and repeated zero times, unless multiple replicates are
specified.
• Step Number: Defines the sequence in which the FIAS program
parameters will be executed. The pre-sample step is used before each
sample. For example, it can be used to set up the FIAS program by
pumping sample from the autosampler to the sample loop. This step will
not be repeated for multiple replicates of an individual sample. The post-
run step defines the stand-by status of the FIAS device at the end of an
analysis of samples. To return the autosampler to the wash position after
an analysis set the A/S position to “0” in the post-run step; otherwise it will
stay in the last sample position.
• Read: The step that includes the Read defines when the system starts to
acquire data from the FIAS injection. The instrument starts its read cycle at
the beginning of this step. To select the step in which the Read occurs,
click in the Read column of the appropriate step, press any key and press
Enter. Only one Read may be included in any FIAS program; therefore a
Read cannot be specified in a repeated step. The instrument will read for
as long a time as is specified in the active method, whether this is a shorter
or longer time than specified in the FIAS program.
Sampling Systems
• Duration: Specifies the length of time for a step in the FIAS program. One
or both pumps may be utilized in any single program step. The acceptable
range is 0 - 99 seconds. A value of “-” specifies continuous operation.
• Pump 1 / Pump 2: Defines the rotation rate in rpm at which the FIAS
pumps will operate. A positive entry indicates clockwise rotation of the
pump, while a negative entry specifies counterclockwise rotation. The
acceptable range is -10 to -120, 0, and 10 to 120. The actual flow rate
depends on the inner diameter of the tubing used and the speed of
rotation of the pump. You should calibrate this rate every day.
• Valve: This is the position of the FIAS valve. Use Position 1 for filling the
sampling valve, and Position 2 to inject the sample into the ICP-MS.
• A/S (Autosampler) Location: In this column you will enter the rack
location to which the autosampler probe should move before the
corresponding row or step is executed. This location is the “start point” of
sampling and is available to all rows including the Pre-sample and Post-
run steps. An autosampler must be used in conjunction with the FIAS
sampling device. There are three ways to specify the autosampler location
in this column:
 As an absolute number, such as 10 (indicates an actual rack location)
 As a relative number, such as +5 or -5 (indicates a location relative to a
reference A/S location)
 As a blank entry (the reference A/S location).
No pre-run error checking on the validity of the A/S location entered is
done by the software. If an incorrect A/S location is entered, the error
message Autosampler position is out of range appears during the run and
the FIAS program stops. Any partial data collected is not saved to the
dataset. The Reference A/S Location depends on the context in which the
FIAS program is executed:
 If the FIAS program is applied to a manual or batch sample analysis,
the Reference A/S Location is the A/S Loc. entry in the Details dialog
box on the Sample panel Manual tab or Batch tab
 If the FIAS program is applied to a Blank or Standard, the Reference
A/S Location is the net resultant location specified by the A/S Loc.
entry in the Method panel Sampling tab
 If the FIAS program is applied to a QC Standard, the Reference A/S
Location is the A/S Loc. entry in the Method panel QC/Autosampler tab
Based on these rules, a net A/S location is calculated for each step of the
FIAS program. The A/S probe is moved to the net A/S location prior to the
execution of the corresponding FIAS step. If the net A/S location is the
same for two consecutive FIAS steps, the A/S probe is not moved
between the FIAS steps. You can also define the Reference A/S Location
in the Reference Autosampler Location field in the FIAS tab of the Device
Control panel. When Run Current Step or Run Current Program are
selected, this A/S location is used as the Reference Location for blank or
relative autosampler location entries on the Method panel Devices/FIAS
tab. You must fill in this field prior to selecting Run Current Step/Program
or an error message appears.
• Switches (2, 3, 4): Activates switch closures 2, 3 and 4 on the back of the
FIAS device at the beginning of the program step in which the action is
programmed. These switches constitute contacts for outputs to external

controls and remote devices. Remotes are programmed by setting the
cursor to the required position, and then pressing any keyboard character,
followed by Enter.
Control screen Devices panel FIAS tab

This tab is displayed only if a FIAS system is installed and enabled, and selected
in an active method. Use this tab to establish communication with and manually
run the FIAS™ program without making measurements. Note that these controls
cannot execute a Read command, even if the FIAS step contains the Read.
Figure 7-2 Control screen Devices panel FIAS tab

Items on the FIAS tab
• Status: Indicates the status of communication and the current step in the
FIAS program.
• Reference A/S (Auto Sampler) Location: Displays an autosampler
location. This location is used as the Reference Location for blank or
relative autosampler location entries in the FIAS tab. If a location is not
Sampling Systems
entered prior to selecting Run Current Step/Program, an error message is

displayed.
• Initialize: Initializes communication with the FIAS device. A message
appears in the Status field.
• Run Current Step: Runs the step. The software performs the step where
the cursor is located. There must be an entry in the Reference A/S
Location field to run this step.
• Run Current Program: Performs the FIAS program in the active method.
This will not execute a Read command. There must be an entry in the
Reference A/S Location field to run this program.
Chapter 8
Quality Control
This section describes the software quality control (QC) functions for quantitative
measurements.
• Quality Control Overview on page 213
• Instrument Actions and Quality Control Functions on page 214
• Quality Control Software Reference on page 216
Quality Control Overview

The software incorporates a series of sophisticated routines for monitoring your
data integrity during unattended operation. Quality control software routines are
not invoked during a manual analysis; they are run only during an automated
batch analysis.
Quality Control Workflow

This is the workflow that the instrument typically follows when running a QC
analysis:
The instrument is calibrated according to the method being used

The calibration is verified by running a quality control sample

Samples are run. For example, a batch of ten samples is run

Every ten samples, a calibration check standard and blank are run

Matrix spikes, diluted samples, and duplicate samples are run for each type of
sample, such as water samples and then soil samples

At the end of the batch, final QC samples are run. These consist of the
calibration check standard and the calibration blank
213
Table 8-1 Instrument Actions and Quality Control Functions
Instrument action Quality control function Quality control action

Calibrate instrument Calibration results (for
Upon failure of checked
according to method example, correlation limit (for example,
being used coefficient) checked correlation coefficient is <
against limits set up in
0.995), the message
method entered by the user is
printed and the specified
For example, correlation actions are taken
coefficient >0.995
For example, recalibrate
The calibration is verified The results of the QC Upon failure (for example,
by running a quality analysis are compared to Analysis shows measured
control sample. The the true value and values not within limits),
software names it acceptance limits entered the message entered by
QC Std N in the QC/ QC Standards the user in the Message
tab of the Method panel. column of actions section
Percent recoveries as is printed (for example, QC
compared to the true standard is out of limits)
value are printed in the and the specified actions
QC Calculated Values are carried out
section of the report
For example, recalibrate
For example, true value = and rerun
50 ppb * 10%
Samples are run. For Samples are checked Upon failure of any limit
example, a batch of 10 against sample limits. For checked, either upper or
samples are run example, sample result lower sample
between detection limit concentration limits or
and upper linear range internal standard limits
the action selected in the
QC tab for that limit is
Internal Standard
recoveries are monitored carried out and the
message entered by the
and checked against
user is printed on the QC
limits. For example,
Internal Standard Percent Out of Limits summary in
the report
Recoveries must be
between 60‐120% of that
in the blank for the For example, rerun or
selected method recalibrate
Quality Control
Table 8-1 Instrument Actions and Quality Control Functions
Instrument action Quality control function Quality control action

At a frequency of every The results for the check
The appropriate message
10 samples a calibration standard and check blank
is printed upon failure of
check standard and blank are compared against the
either or both calibration
are analyzed limits check or blank checks and
the appropriate action is
carried out
For example, calibration
check standard limits are
*10% of the true value. For example, the
Blank limits are set at 3 calibration check is out of
times the instrument limits and the recalibrate
detection limit action is carried out
Matrix spikes, dilutions The spiked sample results If the spike recoveries are
and duplicates are or dilution or duplicate not within the stated
performed on one out of results are compared to limits, the message “Spike
every ten samples, an aliquot of the recovery is out of limits”
diluted samples and unspiked sample and the or other
duplicates spike recovery is user‐entered message is
calculated. The spike printed and the
recoveries are compared designated action is
to the limits set in the carried out
Spike tab
For example, rerun
For example, spike original sample and spiked
recovery limits are sample
required to be within *
30% of the spiked value
At the end of the batch, The results for the check The appropriate message
final QC samples standard and check blank is printed upon failure of
consisting of the are compared against the either or both calibration
calibration check limits. Internal Standard check or blank checks and
standard and the recoveries are monitored the appropriate action is
calibration blank are run and checked against carried out
limits
For example, the
For example, Internal “calibration check—out of
Standard Percent limits” rerun action is
Recoveries must be carried out
between 60‐120% of that
in the blank for the
selected method
Basic QC parameters
You can set up the software to automatically perform a variety of QC functions. In
order to take advantage of these functions, you must first configure several areas
of the software:
• The QC checking algorithms are active only during a batch analysis. The
sample batch file, which controls the autosampler for samples, must be
configured correctly.
• The QC Checking Enable check box on the Method panel Timing tab must
be selected.
• All true values and limits must be entered into the various screens in the
software for which QC checking is needed. It is important to note that the
QC checks are embedded in the individual methods, and not stored in a
separate file. This means that for each different set of QC standards or
limits, a new method must be created.
• The report options file must have the QC functions and the necessary
fields selected in order for you to actually see the results from the QC
checking calculations.
QC Software Conventions
The software employs several conventions regarding the QC functions:
• When a control label has a star in parentheses (*) in it, this indicates that
there are additional options available through a right-click menu. This
function also appears in other areas of the software.
• You must complete the calibration and blank information in the Method
panel for the standards used to calibrate the instrument; the QC
Autosampler tab provides the location for the calibration blank and
standards only. Note that, for QC purposes, it is not sufficient to simply
complete the calibration, blank, and standard locations on the Sample
panel Batch tab.
• For flagged QC samples (QC spike, QC duplicate, QC dilution, and so
forth), a detailed name or description may be entered in the Description
column of the Sample panel Batch tab. Also, if dilution factors are entered
using the Aliquot and Diluted to Volume columns on the Sample panel
Batch tab, the dilution factors for the reference sample and the flagged QC
sample must be the same.
Quality Control Software Reference

The software incorporates a comprehensive series of quality control functions as
part of the method. These functions are available only when using a Quantitative
Analysis method and only when the Enable QC Checking check box has been
selected on the Method panel Timing tab. When this option is selected, the QC tab
becomes active. The QC tab contains a series of additional sub-tabs with the
following functions:
• Calibration tab: Used to monitor calibration curve statistics, including the
slopes, intercepts and correlation coefficients of the calibration curves for
each of the analytes in your method. The slope of the calibration curve is
one measure of the system's sensitivity, and by monitoring it over time,
Quality Control
you can measure when the system's overall sensitivity has degraded
significantly. Intercepts can be monitored so that the zero point in the
calibration curve is never too far from the original value obtained. The
correlation coefficient can be monitored to assure those calibration
standard data are well correlated to the calibration algorithm chosen.
• QC Standards tab: Used to set concentration limits for the QC standards
to measure if the system continues to provide accurate answers for
solutions of known concentrations.
• QC Measurement Frequency tab: Used to specify the frequency with
which QC measurements are made.
• QC Standard Internal Standards tab: Used to set up the parameters for
measuring an internal standard element within the QC standards. This
feature enables the definition of limits on the Internal Standard Intensity
drift for QC standards.
• Calibration Standards tab: Used when calibration standards are
measuring how well the system is performing. The standard deviation of
the blank or RSD of the standards can both be monitored. If either the
standard deviation or RSD of the standards is too high, the system may
not provide sufficient precision for your determinations. This may indicate
a problem with the sample introduction system or other hardware
components.
• Sample Internal Standards tab: Used to set up the measurement of the
internal standard element that can be monitored for drift of the sample.
This feature enables the setup of limits on the Internal Standard Intensity
drift for samples.
• Sample tab: While samples are being measured, you can monitor the
sample concentration, sample standard deviation, and sample RSD.
Sample concentrations can be monitored to determine when the results
are below or above a default measurement limit. As a result of this
monitoring, certain actions can be automatically executed when a sample
is out of range. Monitoring the sample standard deviation is especially
useful for estimating a detection limit on samples with no concentrations.
Sample RSDs can be monitored to see if the instrument system is
providing satisfactory precision, a measure of the performance of the
sample introduction system and other hardware components.
• Spike tab: Used to set spike recovery limits for a determination. Spike
recovery is performed by spiking samples with a known concentration of
an analyte, then measuring how accurately the system determines this
spike concentration.
• Dilution tab: Used to monitor dilution measurements on sample solutions.
The percent difference between a sample and a dilution of that sample can
be measured during determinations. You can then set a maximum percent
difference and have out-of-range samples identified.
• Duplicate tab: Used to measure the relative percent difference between
two aliquots of the same sample solution.
• Spike Tables tab: Used to set up spiking tables. A spike table contains the
spike concentrations. Spike concentrations are set in up to 20 tables for
use during the QC measurements.
• QC Action Controls tab: Used to specify how often Action 1 is to be done

before proceeding to Action 2, and how often Action 2 is to be done before
the analysis is stopped or continued.
• Autosampler tab: Used to identify the location in the autosampler for
each of the QC standards.
Common Information and Controls

The following information parameters and controls are found on multiple QC tabs.
Details about parameters specific to a particular tab can be found later in this
section.
Control Description
Analyte Specifies the element that the instrument will determine
in each measurement. Read‐only. To add or delete an
analyte, go to the Method panel Timing tab
Mass (amu) Specifies the mass at which the element will be
measured. Read‐only. The system sets the mass based on
the analyte specified. To change the mass, go to the
Method panel Timing tab
Action 1 (*) / Action 2 Specifies what action the system should take if the
(*) corresponding measurement is out of limits. Action 1 is
executed first, and is repeated as often as indicated on
the QC Action Controls tab if results are beyond the
specified limits. Action 2 is then performed, and is also
executed as often as indicated if results are beyond the
specified limits. If the results are still out of limits, the
analysis is either continued or stopped, depending on
the QC Action Control parameters
When a measurement is out of limits, the text is entered
in the Message to Print column for all the elements out
of limits. Select one of the following from the list. Note
that some tabs will have a sub‐set of the options listed
here:
• Continue: The out‐of‐limits message is printed, and
the analysis continues. This is the default action.
• Stop: The out‐of‐limits message is printed, and the
analysis stops
• Wash for X and Recalibrate: The out‐of‐limits
message is printed. The autosampler probe returns
to the wash position for X seconds. For X enter any
positive number. Then, all elements are recalibrated
by analyzing from the blank solution again
Quality Control
Control Description
• Wash for X, Recalibrate and Rerun Current: The
autosampler probe returns to the wash position for X
seconds. For X enter any positive number. If zero is
entered, a wash is not done and only a recalibration
and rerun of the current standard will occur. The
failed item is recalibrated and rerun
• Wash for X, Recalibrate and Rerun Samples: The
seconds. For X enter any positive number. If zero is
entered, a wash is not done and only a recalibration
and rerun of the samples occurs. All the elements are
recalibrated. Recalibration is performed by analyzing
from the Blank solution again. For the Rerun Samples
portion of this action, the analysis resumes with the
first sample between the last passed QC and the
failed QC. For example, if you ran a blank, Standard 1,
Standard 2, QC1, samples 1 through 10, QC1 again,
samples 11 through 20 and QC1. If this QC1 now fails
the instrument recalibrates and resumes at sample
11
• Wash for X and Continue: The autosampler probe
returns to the wash position for X seconds. For X
enter any positive number. If zero is entered, a wash
is not done and the analysis continues. For the
Continued portion of this action, the analysis
continues with the next determined solution type
• Wash for X and Rerun Current: The autosampler
probe returns to the wash position for X seconds. For
X enter any positive number. If zero is entered, a
wash is not done and only a rerun of the current
blank or standard occurs. For the Rerun Current
portion of this action, the failed QC is rerun
• Wash for X and Rerun from Original: The
seconds. For X, enter any positive number. If zero is
entered, a wash is not done and only a rerun of the
original sample occurs. For the Rerun from Original
portion of this action, the analysis starts with the
original sample
Control Description
• Wash for X, and Continue from Sample: The
seconds. For X, enter any positive number. If zero is
entered, a wash is not done and only a rerun of the
current blank or standard occurs. The analysis
continues with the sample specified. Select a sample
from where the analysis should resume
Action 1 Data / Action Displays any variable associated with Action 1 or Action
2 Data 2, such as the number of seconds specified to wash and
recalibrate
Message To Print Type a message to be printed in the summary section of
the report to warn that the element on that line is out of
limits. The message can be up to 78 characters in length.
For example, “Slope not within set limits”
QC Action Criteria (*) Specifies the conditions required for an action to be
taken. You can specify how many or which elements in
your QC standards must be out of limits before an action
is taken. For each element, right‐click and select one of
the following options from the list:
• Must Act: The action designated for that QC
standard will be carried out if that one element is out
of limits
Quality Control
Control Description
• Do Not Act: The action designated for the QC
standard will not be carried out regardless of
whether it is out of limits. Any message specified in
the Message To Print column is printed so you can
monitor the element
• Act if X Elements Out: The action designated for
that QC standard will be carried out only if a specified
number of elements are out of limits. Any number
from 1 to the total number of elements can be
specified (this number must be the same for all
elements for which you specify this option)
QC Action Priority (*) Specify the relative priority of each analyte. The value
entered can be from 0 to 500. Enter a value of zero,
indicating Do Not Act, if the analyte is to be monitored
for information purposes only. Values from 1 to 500
indicate a Must Act priority. A value of 1 has the highest
priority and its actions are performed if that analyte is
out of limits. If no value is entered, the analyte is
assigned the default priority. The default sequence of
values starts from 1
The QC Action Priority column is used to tell the software
the priority of checking for the individual isotopes in the
checking routine. Only the action for the element out of
limits with the highest priority (lowest number) is carried
out to avoid multiple actions. In the event that multiple
isotopes have the same level of priority, action is taken
only if all are out of limits
Calibration Tab
Use this tab to monitor calibration curve statistics, including the slopes, intercepts,
and correlation coefficients of the calibration curves for each analyte in your
method. The slope of the calibration curve is one measure of system sensitivity
and, by monitoring it over time, you can detect when the overall sensitivity has
degraded significantly. Monitor the intercepts to keep the zero point in the
calibration curve close to its original value. Track the correlation coefficient to
ensure calibration standards remain well-correlated to the calibration algorithm
chosen.
Figure 8-1 Calibration tab

Items on the Calibration Tab
This section of the software contains the following information and controls. For
more information about common QC controls, see Common Information and
Controls on page 218.
• Slope Lower: Enter the lower slope limit for each analyte except internal
standards. The lower and upper slope limits determine the out-of-limit
conditions. Any positive or negative value is valid. Either an upper or lower
slope value can be entered for limit checking to be performed for that
analyte.
• Slope Upper: Enter the upper slope limit for each analyte except internal
standards. The upper and lower slope limits determine the out-of-limit
conditions. Any positive or negative value is valid. Either an upper or lower
slope value can be entered for limit checking to be performed for that
analyte.
• Intercept Lower: Enter the lower intercept limit for each analyte except
internal standards. The lower and upper intercept limits determine the out-
of-limit conditions. Any positive or negative value is valid. Either an upper
Quality Control
or lower intercept can be entered for limit checking to be performed for that
analyte.
• Intercept Upper: Enter the upper intercept limit for each analyte except
internal standards. The upper and lower intercept limits determine the out-
of-limit conditions. Any positive or negative value is valid. Either an upper
or lower intercept can be entered for limit checking to be performed for that
analyte.
• Corr. Coef. (min): This limit determines the minimum acceptable
correlation coefficient for each analyte, except internal standards. Values
from 0.0000 to 1.0000 are valid. If no value is entered, limit checking is not
performed for that analyte.
• Measurement: Lists the types of measurement available, such as slope,
intercept, and correlation coefficient. Read-only.
QC Standards Tab
Use this tab to set concentration limits for the QC standards in order to track
system accuracy for solutions with known concentrations.
Figure 8-2 QC Stds tab

Items on the QC Standards Tab
• QC Std 1 (Conc.) to QC Std 50 (Conc.): For each QC standard used (up
to 50), enter a concentration value for each analyte. Zero or any positive
value is valid.
• QC Std 1 Lower to QC Std 50 Lower: The upper and lower concentration

limits for each analyte determine the out-of-limit parameters. These limits
can be expressed as a percent or as a concentration value. To access the
dialog box, right-click in a cell in the QC Std Lower (Conc. or %) column.
Select Absolute Concentration Value, Absolute Percent Value, or Relative
Percent Value option from the dialog box that appears. Type the lower
value. If you selected Absolute Concentration Value the lower value can
be a positive or negative value. This number will appear in this column. If
you selected Absolute Percent Value, the lower integer value shown in this
column will be followed by a % sign. If you selected Relative Percent Value
the lower integer value shown in this column will be shown as a + or -
value with a percent. If a value is not entered for a limit, limit checking is
not performed for that limit for that analyte. Up to 50 QC standards are
available. QC limit checking will be performed for each QC standard.
• QC Std 1 Upper to QC Std 50 Upper: The upper and lower concentration
limits for each analyte determine the out-of-limit parameters. These limits
can be expressed as a percent or as a concentration value. To access the
dialog box, right-click in a cell in the QC Std Upper (Conc. or %) column.
Select Absolute Concentration Value, Absolute Percent Value, or Relative
Value option from the dialog box that appears. Type the upper value. If you
select Absolute Concentration Value, the upper value is positive. If you
select Absolute Percent Value, the upper integer value shown is followed
by a % sign. If you select Relative Percent Value, the upper integer value
can be either a positive or negative value. If a value is not entered, limit
checking is not performed for that limit. Up to 50 QC standards are
available. QC limit checking will be performed for each QC standard.
• QC Std 1 Conc. RSD to QC Std 50 Conc. RSD: For each QC standard
Concentration RSD used (up to 50) enter a maximum value for each
analyte. Any positive value is valid.
• Measurement: Lists up to 50 QC standards. Read-only.
• Solution ID: Here you can enter specific solution identifiers for QC
Standards. You can use these identifiers to reference a standard rather
than using the default labels (QC Std 1, QC Std 2, and so forth) from the
Measurement field.
Quality Control
QC Measurement Frequency Tab

Use this tab to specify the frequency with which QC measurements should be
made.
Figure 8-3 QC Measurement Frequency tab

Items on the QC Measurement Frequency Tab
• Measurement: Lists the calibration and all QC standards (up to 50
available) entered on previous method tabs. Read-only.
• Count as Sample: An X entry indicates that this QC standard is counted
as a sample for the purpose of determining when subsequent QC
standards are run. To enter an X, click in a field, press any key, and then
press Enter. When a QC standard designated as a sample is run, the
sample count goes up by one. When the sample count reaches the
number entered in the Every # Sample column, the system performs the
corresponding measurement.
• Initial: An X entry indicates that this QC standard will be run at the
beginning of the analysis, following the initial calibration. To enter an X,
click in a field, press any key, and then press Enter.
• Final: An X entry indicates that this QC standard will be run at the end of
the analysis, following the last sample. To enter an X, click in a field, press
any key, and then press Enter.
• After Recalib: An X entry indicates that this QC standard will be run
immediately following a recalibration. To enter an X, click in a field, press
any key, and then press Enter.
• Every # Samples: Specifies when the QC standards will be run during the
analysis by defining how many samples should be run between QC
standards. Type a number representing the number of samples to be run
between each QC standard.
Note: If the final QC Standard in this grouping happens to occur at the end of
your batch as the last sample, it will not be run. In order to run a QC Standard as
the final sample in a batch, you must explicitly designate it as the final sample, by
placing an X in the Final column on this tab.
• Before A/S Loc.: Specifies when the QC standards are run in relation to
the autosampler positions. For example, you can set a QC standard to run
before autosampler position 10. This tab has fifty Before A/S Location
columns. Use this to space the QC standards as best suits your analyses,
rather than in a fixed pattern like the Every # Samples column.
Note: When multiple QC standards are run (for example, QC Std 1, QC Std 2,
QC Std 3, and QC Std 4 have the Initial option selected), the QC Standards run in
numerical order: QC Std 1 then QC Std 2 then QC Std 3 and then QC Std 4.
QC Std Internal Standards Tab

Use this tab to set limits for intensity drift of internal standards within the QC
standards. For example, Cu can drift to a negative 60% or to a positive 25%.
Figure 8-4 QC Std Int Stds tab
Quality Control
Items on the QC Standard Internal Standards Tab

• QC Stds Int Std Lower %: Right-click to display the Enter Percent Limit
Value dialog box. To enter an absolute value, select the Absolute Value
option and type a value (for example, 90). To enter a relative value, select
the Relative Value option and type a negative value in the Lower field (for
example, -10). Only numerical entries are accepted. After the entry is
accepted, the units appear on the QC Stds Int. Std tab as a percentage.
• QC Stds Int. Std Upper %: Right-click to display the Enter Percent Limit
the Relative Value option and type a positive value in the Upper field (for
example, 10). Only numerical entries are accepted. After the entry is
accepted, the units appear on the QC Stds Int. Std tab as a percentage.
• Measurement: The list shown is based on the number of internal
standards. Read-only. To add or change an entry, go to the tab on which it
was made.
Calibration Standards Tab

You can run calibration standards to gain information about how well your
instrument is performing. The standard deviation of the blank or RSD of the
standards can both be monitored. If either the standard deviation or RSD of the
standards are too high, then the system may not be providing sufficient precision
for your determinations. This may indicate a problem with the sample introduction
system or other hardware components.
Figure 8-5 Calibration Stds tab
Items on the QC Calibration Standards Tab

• Blank Intensity SD: For the blank an SD (standard deviation) value for
the net intensity can be entered to determine the maximum acceptable
value for each analyte. Any positive value is valid. If no value is entered,
limit checking is not performed.
• Std 1 Intensity RSD to Std 30 Intensity RSD: For each standard (to a
maximum of 30 standards) an RSD (relative standard deviation) value for
the net intensity can be entered to determine the maximum acceptable
value for each analyte. Any positive value is valid. If no value is entered,
limit checking is not performed.
• Measurement: Lists the blank and up to 30 standards. Read-only.
Sample Internal Standards Tab

Use this tab to set up the measurement of the internal standard element which
can be monitored for drift throughout the course of the determinations.
Figure 8-6 Sample Int Stds tab

Items on the Sample Internal Standards Tab
• Sample Int. Std Lower %: Right-click to display the Enter Percent Limit
Quality Control
the Relative Value option and type a negative value in the Lower field (for
example, -10). Only numerical entries are accepted. After the entry is
accepted, the units appear on the Sample Int. Std tab as a percentage.
• Sample Int. Std Upper %: Right-click to display the Enter Percent Limit
the Relative Value option and type a positive value in the Upper field (for
example, 10). Only numerical entries are accepted. After the entry is
accepted, the units appear on the Sample Int. Std tab as a percentage.
• Measurement: The list shown is determined by the internal standard
elements specified on the Timing tab. Read-only. To add or change an
entry, go to the tab on which it was made.
Sample Tab
You can monitor the sample concentration, sample standard deviation, and
sample RSD during a determination. Sample concentrations are monitored to
determine when the results are outside a default measurement limit. As a result of
this monitoring, certain actions can be automatically executed when a sample is
out of range. Monitoring the sample standard deviation is especially useful for
estimating a detection limit on samples with no concentrations. Sample RSDs are
monitored to determine if the system is providing satisfactory precision, which is a
measure of the performance of the sample introduction system and other
hardware components.
Figure 8-7 Sample tab
Items on the Sample Tab

• Sample Lower (conc.): For each analyte, enter a sample lower
concentration limit. This number will determine the acceptable lower limit
for the sample concentration value. Any value entered is valid. The lower
limit must be a smaller value than the upper value.
• Sample Upper (conc.): For each analyte, enter a sample upper
concentration limit. This number will determine the acceptable upper limit
for the sample concentration value. If a measurement exceeds the value
entered, it will trigger the prescribed action (for example, Wash for X,
Dilute and Rerun Current).
Any value is valid. The upper limit must be a larger value than the lower
limit. If the upper limit is exceeded the software will indicate either S for
shutdown, or EEE for elemental equation error.
Note: This option is available only if an autodiluter has been installed.
• Sample Conc SD: Type an SD (standard deviation) value for the net
intensity. This determines the maximum acceptable value for each analyte.
Any positive value is valid. If a value is not entered, limit checking is not
performed.
• Sample Conc RSD: Type an RSD (relative standard deviation) value for
the net intensity. This determines the maximum acceptable value for each
analyte. Any positive value is valid. If a value is not entered, limit checking
is not performed.
• Measurement: Each element has four lines, listing the upper
concentration, lower concentration, SD and RSD. Read-only. To add or
change an entry, go to the tab on which it was made.
Quality Control
Spike Tab
Use this tab to set spike recovery limits for a determination. Spike recovery
involves spiking samples with a known concentration of an analyte, then
measuring how accurately the system determines this spike concentration.
Figure 8-8 Spike tab

Items on the Spike Tab
• Spike % Rec (lower) (*): To enter a spike recovery limit, right-click to
display the Enter Percent Limit Value dialog box. To enter an absolute
value, select the Absolute Value option and type a value (for example, 90).
To enter a relative value, select the Relative Value option and type a
negative value in the Lower field (for example, -10). Only numerical entries
are accepted. After the entry is accepted, the units appear on the Spike tab
as a percentage.
Note: If the spike recovery calculated for any spiked sample is below the lower
limit, a corresponding message is printed. To set a limit, type any positive value.
Spike % recovery is calculated as:
Spike % Recovery = [(SS - US) / SA] x 100
where:
US = unspiked sample result
SA = spike added
SS = spiked sample result.
If the original sample result is smaller than the detection limits specified in
the Spike Table used, zero is used in this equation instead of the original
result. This avoids subtracting negative sample results. Specifying the
detection limit is optional. If this field is empty, the original sample results
are used.
• Spike % Rec (upper) (*): To enter a spike recovery limit, right-click to
display the Enter Percent Limit Value dialog box. To enter an absolute
value, select the Absolute Value option and type a value (for example,
110). To enter a relative value, select the Relative Value option and type a
positive value in the Upper field (for example, 10). Only numerical entries
are accepted. After the entry is accepted, the units appear on the Spike tab
as a percentage.
Note: If the spike recovery calculated for any spiked sample is above the lower
limit a corresponding message is entered. To set a limit, type any positive value.
Spike % recovery is calculated as:
Spike % Recovery = [(SS  US) / SA] x 100
where:
SA = spike added
SS = spiked sample result
If the original sample result is smaller than the detection limits specified in
the Spike Table used, zero is used in this equation instead of the original
result. The defining detection limits are optional. If this field is empty, the
original sample results are used.
• Measurement: Lists the spikes for the elements specified on the Timing
tab. You cannot edit entries in this column. If you want to change an entry,
or add another measurement to monitor, you must change the entry on the
tab on which it was made, and then return.
Quality Control
Dilution Tab
Use this tab to monitor dilution measurements on sample solutions. The percent
difference between a sample and a dilution of that sample can be measured
during determinations. You can then set a maximum percent difference to identify
out-of-range samples.
Figure 8-9 Dilution tab

Items on the Dilution Tab
• % Difference (max): Sets the limit for the percent difference between a
sample and its dilution. If the percent difference calculated for any solution
identified exceeds the limit a corresponding message is entered. To set a
limit, type a number between 0 and 100. The default system parameter is
10%. Percent difference is calculated as follows:
% Diff. = [|OS  (DS x DF)| ÷ OS] x 100
where:
OS = original undiluted sample result
DS = diluted sample result
DF = dilution factor
OS = original sample result (same name as dilution)
• Measurement: Lists dilutions for the elements specified on the Timing tab.
This column is read-only—to change an entry or add another
measurement to monitor, you must change the entry on the tab on which it
was made.
Duplicate Tab
Use this tab to measure the relative percent difference between two aliquots of the
same sample solution.
Figure 8-10 Duplicate tab

Items on the Duplicate Tab
• % Rel % Diff (max): Sets a limit for the relative percent difference
between a sample and its duplicate. If the relative percent difference
calculated for any solution identified as a duplication exceeds the limit, a
corresponding message is entered. To set a limit, type a number between
0 and 100. Relative percent difference is calculated as follows:
%D = | o - d | x 100
½ ( o + d)
where:
o = original sample result (result of sample with same name as duplicate)
d = duplicate sample result
• Measurement: Lists duplicates for the elements which were specified on
the Timing tab. This column is read-only—to change an entry or add
another measurement to monitor, you must change the entry on the tab on
which it was made.
Quality Control
Spike Tables Tab

Use this tab to set up spiking tables. Spike concentrations are set up in up to 20
tables for use during the QC measurements.
Figure 8-11 Spike Tables tab

Items on the Spike Tables Tab
• Spike Table 1 (Conc.) to Spike Table 20 (Conc.): Displays the
concentrations for each element in the current spike table. The units are
assumed to be those of the standard units, as specified on the Calibration
tab.
• Spike Table 1 Det. Limit (Conc.) to Spike Table 20 Det. Limit (Conc.):
Optional. Specifies the detection limits for the elements in the current spike
table. If the original sample result is smaller than the detection limits
specified in the Spike Table used, zero is used in this equation instead of
the unspiked sample result. The defining detection limits are optional. If
this field is empty the original sample results are used. The equation used
to perform unspiked recovery is as follows:
Spike % Recovery = [(SS  US) / SA] x 100
where:
SS = spiked sample result
SA = spike added
QC Action Controls Tab

Use this tab to specify how actions are taken and how often they are repeated.
Figure 8-12 QC Action Controls tab

Items on the QC Action Controls Tab
• Number of Retries: Denotes the number of times each action will be re-
tried before proceeding to the next action. Any positive integer value is
valid. For example, if the number of retries for Action 1 is zero then Action
1 is performed only once. If retries equal 1, then Action 1 is tried again. If
the condition is still not satisfied, then Action 2 is performed.
• Action When All Retries Are Exceeded: Determines what happens to
the analysis if both actions fail to remedy the QC condition. Stop stops the
analysis (the plasma will not turn off). Continue permits the analysis to
continue, and the QC criteria to be applied to subsequent samples in the
analysis.
• Limits Priority Table: This table shows the priority of the QC Limits in the
method. A value of 1 indicates that this limit has the highest priority, if more
than one of the QC Limits have been exceeded. In the event that QC
Limits are exceeded in one sample, the software will perform only the
action with the higher priority. For example, when the sample
concentration and the internal standard intensity are both out of limits, the
software performs the corrective action for the Internal Standard because
it has a higher priority. We recommend that you not change the priorities
that appear in the pre-defined Quantitative Analysis method.
Quality Control
QC actions Priority
Calibration limits: Correlation coefficient 1
Intercept 2
Slope 3
Sample limits: Lower concentration 2
Upper concentration 3
SD 4
RSD 5
Internal standard intensity 1
QC standard limits: Concentration or RSD 2
Flagged sample Flagged calc. (Spike Rec. %Diff, 2
limits: Rel.%Diff.)
Note: Some solution limit types in the QC Action Controls tab are further
prioritized internally by the software. When multiple limit conditions are exceeded
within a solution type, the action for the limit with the highest priority is executed.
You cannot modify these internal priorities.
• No QC Action Taken Message: This message is automatically printed

when all QC measurements are found to be within proper limits. If
required, you can type in a different message.
Autosampler Tab
Use this tab to identify the location in the autosampler for each of the QC
standards.
Figure 8-13 Autosampler tab

Items on the Autosampler Tab
• QC Std.: 50 QC standards are listed in this column.
• A/S Loc.: Specifies at what autosampler position the QC standard is
located. Any positive value is valid. Positions can be reused if it is the
same solution. For example, QC Std 1 and QC Std 3 are the same
solution.
• Wash Override (sec): Overrides the Wash time specified on the Method
panel Sampling tab. Specifies the time in seconds that the autosampler
provide a longer than usual wash cycle for samples where carry-over is a
concern.
Chapter 9
Sample Preparation and Analysis

This section presents information about performing manual and batch analyses
using a method file you have already created and configured.
• Sample Analysis on page 239
• Analysis Order for UCT™ Instruments on page 241
• Sample Files Created using a Text Editor on page 241
• Sample Panel Software Reference on page 244
Sample Analysis
Virtually all the parameters required for controlling a determination are contained
within the analytical method file. After selecting the method you want to use for a
determination, you set up and optimize the instrument. Next, you use the Sample
screen to identify samples, control the order in which they are measured, and
initiate the determination.
The main Sample screen consists of a single Sample panel divided into two tabs
to facilitate two different types of sample introduction:
• Manual: You introduce individual sample solutions into the spectrometer
• Batch: You group blanks, standards, and samples into batches to feed
them automatically into the spectrometer
The Sample screen is accessed via the Sample icon on the ribbon. It contains the
Sample panel, as well as instances of the Report View and Realtime panels,
allowing you to monitor your results in graphic and tabular form as they are run
(see Reporter™ Panels on page 261 and Realtime Panel on page 291 for details).
Following a determination, you can generate a report on the results of the
measurement, review and analyze the results in graphic form, reprocess the data,
and export the results.
239
Figure 9-1 Sample screen
Files Required During an Analysis

During a determination, a number of files must be open for data acquisition and
processing to occur properly. These files include:
• An analytical Method file
• A Calibration file, if you are not acquiring new calibration data as part of
the current determination (except in TotalQuant™ analyses, where you
use a Response file instead)
• A Dataset for storing the results from the determination
• A Mass Calibration .tun file is specified in the method and needs to be
changed only if you want to use a different file from the one associated
with the method
• A Conditions .dac file is specified in the method and needs to be changed
only if you want to use a different file from the one associated with the
method
• A Sample file containing the names of your solutions and specific
instructions for performing the determination
You can open these files individually or use a workspace, which provides quick
access to all the files used during an analysis. Use the default Quantitative
Analysis and TotalQuant workspaces as guides to create your own application-
specific workspaces.
Analysis Order for UCT™ Instruments

In UCT™ instruments, all analyses follow a strict order when multiple profiles,
modes, and cell gases are involved. This is helpful to remember when reviewing
graphic or raw data from any analysis featuring multiple modes, particularly those
having multiple modes attached to the same base element. See Acquisition order
on page 32 for more information.
Sample Files Created using a Text Editor

You can use the following information to manually create a software sample file.
After you create a sample file, open it in the instrument software, and save it
before running your analyses.
Sample file format

The sample information file (*.sam) is a comma-delimited ASCII text file. You
create the sample file using any word processor, barcode reader, or text editor;
save it in ASCII format; and then load it into the software.
A sample information file has three sections: header, body, and footer. Each
section must be separated from the others by a carriage return (blank line). The
header and footer format must be the same for all sample files. The body consists
of multiple columns of information for each sample, entered in successive rows.
Header Section:
[Begin SampleFile]
FileType=ElanSample
FileVersion=3
Body Section:
[Begin sample]
]
Table 9-1 Sample file field descriptions
Column number Information Entry format

1 Row number (batch An integer value, starting at zero,
index) incremented by one
2 Batch ID Text in double quotes
3 Sample ID Text in double quotes
4 Autosampler position Positive integer
5 Sample type Select one of the following:
0 = Sample
1 = QC Spike
2 = QC Dilution
3 = QC Duplicate
4 = QC Reagent Blank
5 = TotalQuant Addition
6 = QC Duplicate Spike
Table 9-1 Sample file field descriptions
Column number Information Entry format

6 Spike table number When column 5 = 1, then a
positive integer indicating the
spike table for this sample.
Otherwise = 0
7 Dilution factor Positive integer or zero
8 Initial sample quantity Positive, floating point number. If
(mg) the box is to be left blank, use n/a
9 Sample prep volume Positive, floating point number. If
the box is to be left blank, use n/a
10 Aliquot volume (ml) Positive, floating point number. If
11 Diluted to volume (ml) Positive, floating point number. If
12 Solids ratio Positive, floating point number. If
13 Description Text in double quotes
14 Method name Text in double quotes
15 Calibration/measurement Select one of the following:
action 0 = Run Sample
1 = Run Blank, Standards, and
Sample
2 = Run Blank and Sample
3 = Run Standards and Sample
4 = Run diluted Sample
5 = Run Blank and diluted Sample
6 = Run Standards and diluted
Sample
7 = Run Blank, Standards, and
diluted Sample
16 QC parent row number Positive integer. Applicable to QC
(batch index) Dilution, Spike, Duplicate, and
Duplicate Spike samples only. For
other samples, use n/a
17 Wash override time (sec) Positive integer or zero. If box is to
be left blank, use n/a
Footer Section:
[End Samples]
[End SampleFile]
Sample Text File

[Begin SampleFile]
FileType=ElanSample
FileVersion=3
[Begin Samples]
0, "stability", "stab001", 1, 0, 0, 0, 0.1, 10, 100, 1000, 0.11, "Stability test",
"stability.mth", 0, n/a, 2
"stability.mth", 1, 0, 4
"stability.mth", 2, 1, n/a
3, "stability", "stab004", 4, 5, 0, 0, n/a, n/a, n/a, n/a, n/a, "Stability test",
"stability.mth", 5, 2, n/a
"stability.mth", 6, 3, 14
[End Samples]
[End SampleFile]
Sample Panel Software Reference

Use the Sample panel to identify the samples in a determination, control the order
in which samples are analyzed, and initiate measurements.
Sample Panel Manual Tab

Use the Manual tab to individually identify samples for manual control of a
determination. This tab is the main measurement control interface on instruments
configured without an autosampler. You can also use this tab to control individual
sample measurements on systems that have an autosampler attached.
Figure 9-2 Sample panel Manual tab

Items on the Sample Panel Manual Tab
• Standard Number: Identifies the number of the standard solution to be
measured when Analyze Standard is clicked. Use the arrow controls to
change the value. Valid values correspond to the number of standards
defined in the active method; for example, you cannot enter “5” if there are
only three standards defined in the method.
• Standard Type: Identifies the type of standard solution to be measured.
The following options are available:
 Standard: Use this option with a normal standard solution
 QC Standard: Use this option if your solution is a QC standard used in
QC checking
• Analyze Blank: Initiates a measurement on the blank solution listed in the
active method — the method open in the Method panel. The measurement
parameters are also established by the active method.
• Analyze Standard: Initiates a measurement on a standard solution. The
standards are defined in the active method. The number of the standard to
be measured is determined by the Standard No. entry on this tab. The

measurement parameters are determined by the active method.
• Analyze Sample: Initiates a measurement on the sample solution. The
sample is described by the Sample ID entry on this tab, and by any
information entered in the Sample Details dialog box. The measurement
parameters are determined by the active method.
• Sample: Identifies each sample with a unique name. Type any
alphanumeric combination — for example, Sample01, Water 694
• Sample Details Dialog Box: Here you can enter specific information
about each sample. It contains the same entries as those on the Batch
tab. Note that this information does not change if you alter the Sample ID
on the Manual tab unless you manually edit it.
• Write to Dataset After Each Analysis: When selected, saves all data
acquired to the current dataset following each analysis.
• Save Current to Dataset: Saves all information from the last data
acquisition to the current dataset. Available only when Write to Dataset
After Each Analysis is not selected.
Sample Panel Batch Tab

Use the Batch tab to identify a group of samples for an automated determination,
to control the order in which samples are measured, and to initiate the
measurements. This tab is the primary measurement control interface on an
instrument configured with an autosampler.
Figure 9-3 Sample panel Batch tab

Items on the Sample Panel Batch Tab
• Analyze Batch: Analyzes all of the samples that are selected (highlighted)
in the Sample panel. When you click Analyze Batch, the Run List dialog
box appears and displays the running batch samples. To set plasma
AutoStop™ options, insert a priority sample into a running batch, or
append additional samples, see “Build Run List” in this section.
• Sample Template: Automatically enters values in the Sample ID and
Autosampler Location (A/S Loc.) fields for a batch of samples.
• Summary: Specifies the summary report type and the destination to which
it will be directed.
• Build Run List: Click to open the Run List dialog box, where you can
review the sequence of samples prior to running them, set plasma
AutoStop options, insert priority samples into a running batch, or append
additional samples.
• Use Manual Sampling (No Autosampler): Select this check box if you do
not use an autosampler. Note that, if using manual sampling, you must
aspirate each sample in turn.
Items in the Batch Table
• A/S (Autosampler) Location: Lists the autosampler position for the
sample — the location that the solution occupies in the autosampler tray.
Type the number corresponding to the position in the autosampler tray
where the sample solution will be placed.
• Batch ID: Identifies a group of samples with a batch label. Type a name
(any alphanumeric combination) to enter an individual Batch ID or click the
column heading and, on the Edit menu, click Fill Down to automatically
enter a Batch ID for a group of samples.
• Sample ID: Identifies each sample with a unique name. Type a name (any
alphanumeric combination) to enter an individual Sample ID.
• Measurement Action (*): Specifies when to run standard and blank
solutions, in addition to specifying the running of the sample solution. To
select a calibration action, right-click the appropriate cell of the Samples
data table, and click a Measurement Action. The following options are
available:
 Run Sample: Runs only the sample solution that is on the same line of
the Samples data table.
 Run Blank, Stds. and Sample: Runs the solvent blank, the standards
specified on the Method panel Calibration tab, and the sample solution
that is on the same line of the Samples data table.
 Run Blank and Sample: Runs the solvent blank solution and the
sample solution that is on the same line of the Samples data table.
 Run Standards and Sample: Runs the standards specified on the
Calibration tab of the Method panel, and the sample solution that is on
the same line of the Samples data table. Typically used with Additions
calibration.
 Run Diluted Sample: Runs the specified diluted sample. This is
applicable only if using an autodilution device.
 Run Blank and Diluted Sample: Runs the solvent blank solution and
the specified diluted sample. This is applicable only if using an
autodilution device.
 Run Standards and Diluted Sample: Runs the solvent standards and
the diluted sample as specified. This is applicable only if using an
autodilution device.
 Run Blank, Standards and Diluted Sample: Runs the solvent blank and
the specified standards and diluted sample. This is applicable only if
using an autodilution device.
• Method (*): Specifies the method to be used for measuring the related
sample solution and for all following samples, until a different method is
specified. Right-click to browse for a method file.
• Description: Type additional information or comments about an individual
sample solution.
• Sample Type (*): Identifies samples used for a quality control
determination or as part of the TotalQuant calibration sequence. This entry
is required when using either a Quantitative Analysis method with a QC
function or when performing TotalQuant measurements using standard
additions calibration. Right-click the Sample Type field. The Sample Type
dialog box appears. Select the appropriate option for your sample:
 Sample: Identifies the solution as a sample.
 QC Spike: Identifies the sample as a spike. When selected, a dialog
box appears where you can select the Spike Table you want to use for
the spike, and the parent (Spike Of) sample reference location. You
create a Spike Table using the Spike Tables window in the method.
The Sample Type field displays Spike  X of Y as the Sample Type,
where Y is the sample batch row number.
 QC Dilution: Identifies the sample as a dilution. When selected, a
dialog box appears where you can select the Dilution Factor and the
parent (Dilution Of) sample reference location. The Sample Type field
displays Dilution  DF:X of Y as the Sample Type, where Y is the
sample batch row number.
 QC Duplicate: Identifies the sample as a duplicate. When selected, a
dialog box appears where you can select the parent (Duplicate Of)
sample reference location. The Sample Type field displays Duplicate
of Y as the Sample Type, where Y is the sample batch row number.
 QC Reagent Blank: Identifies the sample as a reagent blank. If you
select this option, the system will subtract the concentration from all
subsequent samples until the next reagent blank. If you specify several
reagent blanks in succession, the system calculates the average
concentration of the set, then subtracts the average concentration from
all subsequent samples.
 TQ Addition: Specifies that the sample contains specific added
calibration elements in known quantities, as required during a Sample
Addition calibration in TotalQuant analyses. This lets the instrument
calculate intensity values using the TotalQuant algorithms.
 QC Duplicate Spike: Identifies the sample as a QC duplicate spike.
When selected, a dialog box appears for you to select the parent QC
spike sample (Duplicate Spike Of) reference location. The reference
location is the sample batch row number that the parent spike appears
on. The software performs an RPD (relative percentage difference)
calculation based on the results for the parent QC spike and the QC
duplicate spike. The Sample Type field displays Duplicate Spike of Y
as the Sample Type, where Y is the sample batch row number on
which the parent spike appears.
• Initial Sample Quantity (mg): Specifies the weight of the sample before
dilution.
• Sample Prep Volume (mL): Specifies the volume in which the initial
sample quantity has been diluted.
• Aliquot Volume (mL): Specifies the volume of an aliquot, when a small

amount of the sample (aliquot) is taken and diluted to a final volume.
• Diluted to Volume (mL): Specifies the total volume in which an aliquot is
diluted.
Note: If you are using an autodiluter, the Diluted to Volume field acts as a
multiplier of the Auto Diluter > Dilution Factor entered on the Method panel
Sampling tab. To maintain the dilution factor entered on the Sampling tab,
enter 1 in the Diluted to Volume field. The Dilution Factor Override field
overrides the Dilution Factor entered on the Method panel Sampling tab.
• Solids Ratio: Specifies the correction factor to use if you want the
software to convert dry sample weight to the wet sample weight. This
value should be entered as a decimal fraction, not as a percentage. For
example, for a ratio of 1:2, enter 0.5, not 50%.
• Wash Override (sec): Overrides the Wash time specified on the Method
panel Sampling tab. Specifies the time in seconds that the autosampler
provide a longer than usual wash cycle for samples where carry-over is a
concern.
• Dilution Factor Override: This column is enabled only when an
autodiluter (such as the ESI prepFast or the Cetac ADX-500) is selected
as the sampling device on the Method panel Sampling tab. Values entered
here override the dilution factors specified in the method; any value
between 2 and 200 is valid.
Items in the Run List Dialog Box
Use the Run List dialog box to display the sequence of samples prior to running
them within a batch. Here you can also set plasma AutoStop options, insert
priority samples into a running batch, or append additional samples.
The buttons on the right side of this dialog box are enabled or disabled depending
on whether the batch is running (in active analysis) or not. While the batch is
running, you can insert a priority sample or append samples to the end of the
batch.
Figure 9-4 Run List dialog box

• AutoStop: Turns off the plasma automatically following the batch analysis
or a QC failure, as specified in the Stop Criteria list. Here you can also
define an automatic wash, which will run after the batch prior to plasma
shutdown — click Wash parameters to configure.
Note that the AutoStop controls are not available when running a batch
using the Scheduler function, as the Scheduler has its own AutoStop
functionality.
• Pause After Every Sample: Pauses the analysis after each sample is
analyzed. Use this feature when analyzing multiple samples or QC flag
samples (QC dilutions, QC duplicate, QC spike, and QC duplicate spike)
without an autosampler. You can use the run list dialog box for manual
analysis without an autosampler when you want to add new samples to
the batch run as you proceed. When paused, click Append, add the new
samples to the end of the run list, and then click Continue.
• Status: Displays the status of the batch; priority and appended samples;
and wash and AutoStop functions.
• Run List table: Displays the following:
 A/S Loc.: Location of the sample in the autosampler (if any)
 Sample ID: An alphanumeric name used to identify each sample
 Batch Index: The row number of the sample from the Batch tab
 Sample Type: Identifies the type of sample being used, for example,
Blank, Standard, QC Standard
 Method: Method file used for running the sample
• Close: Click to close the Run List dialog box if the batch analysis is not
running.
• Analyze Batch: Starts analysis of the samples in the Run List table.
• Pause: Pauses the analysis after the current sample has been completed.
• Continue: Resumes the analysis when the analysis is paused.

• Priority: Opens a dialog box where you can insert a priority sample when
a batch analysis is running.
• Append: Opens a dialog box where you can append samples to the end
of the Run List table when a batch analysis is running.
• Printable View: Displays the contents of the run list in an Internet
browser, so that you can print the run list from there.
Measurement Status Dialog Box

Use the Measurement Status dialog box to terminate scanning on a single
sample, to terminate all measurements after the current sample, or to immediately
stop all measurements and cancel the determination.
Note: If you do not want the Measurement Status dialog box to appear during each scan,
on the Syngistix ball menu, click Help and then clear the check mark beside the
Show Measurement Status Dialog option.
Figure 9-5 Measurement Status dialog box

This dialog box includes a status indicator that is continually updated to indicate
the progress of the current determination. This is especially helpful if you are
performing measurements with large numbers of readings or multiple replicates.
Items in the Measurement Status Dialog Box
• Skip Delays (Skip the Sample Flush, Read Delay, and Wash times):
Proceeds directly to data acquisition without performing the defined delays
(Flush, Read, Rinse). Available only when performing manual analyses
where one or more delays are defined and the same solution is used
repeatedly.
• Skip Current (Skip Scanning of Current Sample): Stops the
measurement of the current sample and proceeds to the next sample
listed in the Samples data table. No calculations are performed for the
sample that is skipped.
• Stop after Current (Stop Scanning After Current Sample): Completes

the measurement of the current sample, then terminates the
determination. The data associated with all blank, standard or sample
solutions that were measured are listed in the dataset. Any calculations
performed, such as the calibration curve, are available for review.
• Stop (Stop Scanning): Terminates the determination by immediately
canceling all scanning for the current and all remaining samples. The data
associated with any blank, standard, or sample solutions that have already
been measured will be listed in the dataset. Any calculations performed,
such as the calibration curve, will still be available for review.
The software saves partial scans in the event that a scan is canceled
before all readings and replicates are completed. The partial data saved
depends on the Number of Replicates and Readings per Replicate method
parameters. The dataset file generated will be consistent with the method
parameters; that is, the raw data readings acquired will match the method
parameters. Data saved during a canceled scan appears in red on the
Dataset panel. The generation of partial dataset files is applicable to all
methods.
For methods with only one replicate, all readings received from the system
controller up to the point of cancellation are saved in the dataset file. The
method saved to the dataset file along with the raw data will have its
Reading per Replicate parameter truncated to match the actual number of
readings.
For methods with more than one replicate, only the readings for completed
replicates are saved in the dataset. Partial replicate readings are not
saved. The method saved to the dataset will have its Number of
Replicates parameter truncated to match the actual number of completed
replicates.
Chapter 10
Data Reprocessing
This section discusses the use of the data reprocessing tools and describes the
typical circumstances under which reprocessing is performed. Reprocessing
involves reanalyzing the raw acquired data using either the same or different
processing parameters as those used when the data was initially acquired.
• Previously Acquired Data on page 253
• Dataset File Organization on page 254
• Data Reprocessing Workflow on page 255
• Data and Parameter Considerations During Reprocessing on page 255
• Files Required for Reprocessing on page 256
• Dataset and Reprocessing Software on page 257
Previously Acquired Data

You can use the software to reprocess previously acquired analytical data, which
can be useful in a number of circumstances:
• If you find, after a determination, that a calibration standard was measured
incorrectly, or was made up to a different concentration than you entered in
the method, you can reprocess the data using a modified calibration which
excludes the standard or which contains the correct concentration entry in
the method.
• If analytical results are adversely affected by unexpected interferences,
you can modify the method parameters to include additional baseline
correction points or modify the elemental equations to correct for the
interferences, and then reprocess the determination to obtain the effect on
the resulting data.
• During method development, you can run one analysis, then alter the
method parameters slightly and go through varied scenarios without
rerunning the solution each time.
• When performing a determination on a sample for which you only have a
limited quantity, you can run the determination once, then fine-tune the
measurement without wasting the sample.
Click Reprocess on the Dataset panel to generate a duplicate report or a new
report using a different format. Select Use Original Conditions to generate a
duplicate report. If you do not select Use Original Conditions, you may select
whether to save the reprocessed results in a new data file (select the Save
Reprocessed Data check box).
Note: When reprocessing without original conditions, the software always uses the
conditions file and mass calibration attached to the current method.
253
Dataset File Organization

A dataset is composed of a series of individual data records. Each individual
record consists of the raw data from each solution measured during a series of
determinations, together with the following relevant information for specifying the
conditions under which the data was acquired:
• Method
• Conditions
• Calibration
• Mass calibration and resolution
• Report options
• Configuration
The software stores the data for each sample solution as an individual data file,
with the complete series of measurements in the dataset constituting a folder on
the hard disk of your computer. If a scan is canceled, the software saves partial
data to a dataset file depending on the Number of Replicates and Readings per
Replicate method parameters, and when the scan was canceled.
For methods with only one replicate, the system saves all readings received up
until the point of cancellation. The Readings per Replicate parameter of the
method saved to the dataset file with the raw data is truncated to match the actual
number of readings.
For methods with multiple replicates, only the readings for completed replicates
are saved in the dataset file. The Number of Replicates parameter of the method
saved to the dataset file is truncated to match the actual number of completed
replicates.
The software creates the individual file names using the Sample ID entered on the
Sample screen. If no specific entry exists at acquisition time, the software
describes each solution using a default name as follows:
Blank solutions: BLANK.000, BLANK.001, and so forth
STANDARD.001, STANDARD.002, and
Standards: so forth, or EXTERNAL STANDARD.002
for TotalQuant™ methods
SAMPLE.001, SAMPLE.002, and so
Samples: forth
Use the Dataset panel to view the contents of a dataset and reprocess the data
contained within.
Data Reprocessing
Data Reprocessing Workflow

The software stores the results from each measurement in a dataset file. The raw
data stored in this file can be reanalyzed using modified parameters in the same
method or by using an entirely different method.
When you reprocess data, the software can output your data as a report in the
same manner as your original report. The reprocessing function uses the
reporting instructions contained in the method used. Note that reprocessing does
not alter the acquired data; you can view the original results at any time using the
Dataset panel; to do so, select the Use Original Conditions check box, and then
click Reprocess.
If you do not select the Use Original Conditions check box, you can then decide
whether or not to save the reprocessed results in a new data file, using the Save
Reprocessed Data check box.
You can perform data reprocessing in any of several ways:
• Reprocess with original method, conditions, mass calibration, report
options, calibration, and configuration
• Reprocess the data using the same method, but using modified data
processing parameters
• Reprocess the data using the same method, but using a different (stored)
calibration
• Reprocess the data using a different method-include the standards during
the reprocessing
• Reprocess the data using a different method-use a stored calibration and
do not reprocess the standards
• Reprocess a TotalQuant determination using any of the above
combinations and using a different response file
• Reprocess the data using a different dual detector calibration (that is, a
different .dac file)
Data and Parameter Considerations During Reprocessing

Note: The software applies a proprietary and unique checksum value into the header
of each the binary data file generated during data acquisition. When the data file is
subsequently read back into the software or is reprocessed this checksum is verified. If the
data does not match this checksum (that is, if the file was altered in any way) the software
will not load or allow any reprocessing of the data.
Properly applied, reprocessing is used to investigate the effect of different data

processing parameters on your raw data set, to evaluate the effects of
modifications to your calibration, or to see the effects of applying a different
calibration.
The reprocessing function is not intended to serve as a substitute for data
acquisition under modified acquisition parameters. This means that during data
reprocessing, a number of logical considerations should be taken into account in
order for the reprocessed results to be of analytical significance.
The usefulness of reprocessed data depends primarily on the parameters under
which you collected the original data. You cannot reprocess where it would require
the software to fabricate data from conditions which are not measured. For
example, you cannot reprocess data with a method that contains a different
number of sweeps or dwell time than the method that was used to acquire the
data initially.
Note: If you previously used the NexION software, and you are reprocessing
data collected in the NexION software:
In the Reporter, the current standard's raw intensity is calculated and displayed; when
NexION data is reprocessed using original conditions and the next standard is
reprocessed, the software reads the calibration from the original dataset and, finding no
raw intensity value (as this measurement did not exist in the older software), reads the raw
intensity as zero. As a result, on the Reporter screen Calibration panel, the most recently
reprocessed standard displays a point with a non-zero intensity, and all earlier standards
are plotted with a zero calibration.
When reprocessing NexION data without original conditions, each point is simply
recalculated, and the Calibration panel is able to display points with correctly calculated
raw intensities.
Files Required for Reprocessing

Depending on the protocol you intend to follow for reprocessing, different files are
required. The following table summarizes the file requirements for a variety of
commonly performed reprocessing procedures:
To reprocess data using: The following files are needed:
the same method, but using modified original method file
data processing parameters
the same method, but using a different original method file; stored calibration
(stored) calibration file
a different method—include the new method file
standards during the reprocessing
a different method—use a stored new method file; stored calibration file
calibration and do not reprocess the
standards
any of the above combinations for a appropriate files from above, plus the
TotalQuant determination plus using a new response file
different response file
Data Reprocessing
Dataset and Reprocessing Software

The Dataset panel is displayed in its own screen, accessed via the Dataset icon
on the ribbon. This panel displays the results of a determination; use it to review
the samples run during a measurement, and to reprocess acquired data.
Figure 10-1 Dataset panel
Colors Used in the Dataset Panel

Colors used in the Dataset panel indicate the following:
• Black: Completed analysis
• Red: User-interrupted analysis
• Blue: An analysis where autodilution has taken place
• Green: Data reprocessed using different conditions than those used at the
time of data acquisition
Items in the Dataset Panel

The Dataset panel contains several controls and a dataset data table.
• Reprocess: Click to initiate a reprocessing sequence. Before clicking this
button, decide whether or not you want to use original conditions in the
reprocessing and either select or clear the Use Original Conditions check
box. Also, decide whether or not to save the reprocessed results in a new
data file, and either select or clear the Save Reprocessed Data check box.
• Use Original Conditions: Used to select whether or not you want to
reprocess data with the parameters specified during data acquisition. If
this check box is selected when you click Reprocess, all original
information is loaded into the workspace from the dataset. If this check box
is cleared when you click Reprocess, the conditions specified by the files
loaded in the workspace are used.
• Save Reprocessed Data: Used to specify whether or not you want to
save the reprocessed data in a new data file. If the Use Original Conditions
check box is selected, this check box is not available. If this check box is
selected when you click Reprocess, a new data file is created for each
reprocessed data file.
• Summary Report: Click to specify the summary report type and the
destination to which it will be directed.
• Load: This option loads one of the following file types from the open
dataset file into the current workspace. Select the file you want to open in
the dataset panel from the list, and then click Load.
 Method: Loads the method (.mth) file used when the data was
acquired. This overwrites any current method parameters, so save the
current method if applicable.
 Conditions: Loads the conditions (.dac) file that was used when the
data was acquired. If the dataset file is the result of a SmartTune™
optimization, it would contain the resultant values from the
optimization. Loading conditions from the dataset guarantees that the
dual detector calibration used at the time of data acquisition is also
used for reprocessing.
Note: If the method is also loaded, the .dac file associated with the
method will override this conditions file.
 MassCal: Loads the mass calibration (.tun) file used when the data
was acquired.
 Calibration: Loads the calibration (.cal) file used when the data was
acquired. If you want the calibration from a specific dataset file, you will
load the calibration that includes all calibration standards up to and
including that dataset file.
 RSP: Loads the response (.rsp) file that was used when the data was
acquired. When a TotalQuant method is loaded in the workspace, the
TotalQuant.rsp file from the current project folder is opened.
 Report Option: Loads the report options (.rop) file that was used when
the data was acquired.
 Configuration: Loads the configuration parameters that were used
when the data was acquired. If you select this option, the System
Configuration From Dataset dialog box appears. To apply the
displayed parameters in the current session, click Apply. Those
parameters are then available in the System Configuration dialog box.
Columns in the Dataset table
• Batch ID: Specifies the alphanumeric name used to identify the batch of
samples. If no Batch ID was used, this field is empty. For some sample
types, such as SmartTune optimizations, the sample type is displayed.
• Sample ID: Lists the unique alphanumeric name used to identify each
sample solution run. Because this is a required field, an entry will always
appear in this column.
Data Reprocessing
• Acquisition Date/Time: Specifies the exact month, day, year, and time at
which the original data was acquired. If the data was acquired on a
computer in the same time zone and daylight savings time bias as where
the time is being displayed, the local time is displayed. If the data was
acquired in a different time zone than the one where the time is being
displayed, the time zone name is also displayed. If the data was acquired
with a computer and operating system set to a language other than
English, the time zone is displayed in that language. The time and date are
displayed in the format specified in the regional parameters of Windows for
the current user.
• Method: Lists the name of the method file that was used to acquire the
data for the sample/standard/blank listed. The listing includes the
complete pathname for the method file; for example,
C:\Users\<Public>\Documents\PerkinElmer Syngistix\ICPMS\Method\pbtest.mth
• Description: Lists any notes or descriptive information entered in the
Sample panel at the time of determination.
• Read Type (*): Describes the original sample type designation for an
individual measurement and permits the operator to re-designate the
solution as a different type to permit analysis of the effect on a
determination. To view the list of available read types, right-click in the
appropriate cell of the data table. Select a sample type and click OK. The
following options are available:
 Blank
 Sample
 Quant External Standard
 Quant Standard Addition
 Unspiked
 TotalQuant External Standard
 TotalQuant Sample Addition
 Isotope Ratio Standard
 Isotope Dilution Standard
 QC Standard
 QC Spike
 QC Dilution
 QC Duplicate
 QC Reagent Blank
 QC Duplicate Spike
Selection of the Quant External Standard or Quant Standard Addition
option includes arrows that are used to designate which standard number
the solution should be used as, because more than one standard may
have been used to construct the calibration.
• Sample File Name: Lists the name assigned to the individual data record
(the individual sample, standard, or blank solution) within the dataset. The
file name is created by the software, using the Sample ID from the Sample
panel when the data was acquired. If no entry was made at acquisition
time, the system describes the solution using a default name:
Blank BLANK.000, BLANK.001, and so forth
solutions:
STANDARD.001, STANDARD.002, and so forth, or
Standards: EXTERNAL STANDARD.002 for TotalQuant methods
Samples: SAMPLE.001, SAMPLE.002, and so forth
• Acquisition Type: Specifies the instrument configuration used during the

data acquisition. The software automatically enters a description for Dual
Calibration Blank, Dual Calibration, and the QID function.
• Initial Sample Quantity (mg): Specifies the weight of the sample before
dissolution. You must also enter a value for the Sample Prep Volume.
• Sample Prep Volume (mL): Lists the volume in which the sample weight
has been dissolved. This field will be blank if no entry was made in the
Sample panel during the determination.
• Aliquot Volume (mL): Lists the volume of an aliquot, when a small
amount of the sample (aliquot) is taken and diluted to a final volume. This
field will be blank if no entry was made in the Sample panel during the
determination.
• Diluted to Volume (mL): Lists the total volume in which an aliquot is
diluted when a small amount of the sample (aliquot) is taken and diluted to
a final volume. This field will be blank if no entry was made in the Sample
panel during the determination.
• Solids Ratio: Specifies the correction factor to use if you want the
software to convert dry sample weight to the wet sample weight. This
value must be entered as a decimal fraction, not as a percentage; for
example, for a ratio of 1:2, enter 0.5, not 50%. This field will be blank if no
entry was made in the Sample panel during the determination.
• Cumulative Autodilution Factor: This column keeps track of the total
autodilution. For example, if a sample has been diluted twice at an
autodilution factor of 10 for each, the cumulative autodilution factor is
10 x 10 = 100.
• Technique: Specifies the analytical technique which was used for the
determination (Quantitative Analysis, Isotope Dilution, Isotope Ratio, Data
Only or TotalQuant method).
Chapter 11
Reports
This section describes the use of the Reporter™ functions. Included is information
on using the reporting templates to set up detailed sample reports; viewing live
sample batch data as you run your analyses; and producing hardcopy reports or
exporting data for analysis outside of the Syngistix™ software.
• Reporter™ Panels on page 261
• Report Views on page 262
• Enhanced Security Report View functions on page 275
• Report Options on page 282
• Report Options Templates on page 282
• Report Appearance on page 283
• Summary Reports on page 287
• Intensity versus Time Reports on page 287
• Reported Shutdown Values on page 263
• Exporting Current Sample Reports on page 288
Reporter™ Panels
The software provides three main panels on two Reporter screens to help you
track your analyses and create informative and attractive reports.
The Reporter icon accesses the Report View screen, where you view detailed
determination results for the current sample, and scrolling data for each sample in
your batch. The arrow submenu provides access to the Report Options screen,
where you define summary report contents and layout.
The arrow submenu also provides controls for managing QC (Quality Control)
functions. The following commands are available:
 Restart QC -- Click to restart a quality control analysis that has stopped
due to a QC action
 Clear QC Reagent Blank -- Click to clear reagent blank data that is
stored as part of a QC analysis
 Clear QC Logging Data -- Click to clear all QC logging data that is
stored with the dataset
The Reporter panels are as follows:
• Report View: Use this panel to view detailed information about your
current sample and to track data from multiple analyses as your sample
batches are processed. Scrolling results tables provide Raw and Net
Intensity views that display the measured signal data for each element
examined by the instrument, with or without related RSDs; a
Concentration view; an Unfactored Concentration view; a graphic
261
representation of Internal Standards plotted over time; and a QC (Quality

Control) view.
Click the small, square, gray button in the upper right corner to expand this
panel for better viewability.
• Calibration: Use this panel to view graphic calibration curve data for the
results listed in the Report View panel.
In multi-calibration view, click the small, square, gray button in the upper
right corner to expand this panel for better viewability.
• Report Options: Available on its own screen via the Reporter icon arrow
submenu, you use the Report Options panel to select the sections and
fields that will comprise the detailed content of your Current Sample
reports, and to adjust the relative positions of each item on the page and
the type style used to display the information.
Report Views
The Report View panel is made up of multiple tabs, each of which present the
running analytic data from your samples in a different way: these are the Current
Sample tab, Raw and Net Intensities tabs, Concentrations tab, Unfactored
Concentrations tab, Internal Standards tab, and QC tab.
Note: The Current Sample report is available for all analyses, while the Raw and Net
Intensities, Concentrations, Unfactored Concentrations, Internal Standards, and QC tabs
are populated only when running Quantitative Analyses.
When you initially start a new software session, or after you click Clear Data, the
Report View tabs are empty. They become populated as data is acquired,
regardless of whether or not the panel is open. As you run samples, the tabs are
updated in real time. The table-based tabs collect a scrolling list of sample results
collected during quantitative analyses to a maximum of 1000 samples, after which
the first samples scroll off the top of the list as new samples are added at the
bottom. Index numbering of the developing list goes up to a maximum count of
9,999 before rolling over to begin at 1 again.
To help you keep track of where you are in the data, your position in the scrolling
list on any table is retained when you move between the Raw and Net Intensities,
Concentrations, and Unfactored Concentrations tabs, so that you can compare
multiple types of data for a single sample without losing your place.
In the tables, sample data is displayed in alternating rows of white and gray to
improve readability. Additional color cues employed in the tables include the use
of a red font or cell background to indicate QC failures, and the Syngistix software
standard KED mode green and DRC mode yellow used in the column headers to
indicate analytes using profiles in these modes (UCT instruments only). On the
Concentrations tab, a purple font is used to denote internal standards, which are
also identified with an (IS) in the relevant analyte header. Note that all tables take
their base colors from your system colors; if you change from the default Windows
system colors, you may change the table background colors.
If you are using the Enhanced Security software, workflow change and traceability
management functionality can also be added, so that changes and analyses can
be reviewed and approved (or rejected), and e-signature and reason data
captured and displayed in the results tables.
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Raw and Net intensities

Analytical data produced in the Syngistix software is recorded initially at its Raw
(measured and unadjusted) intensity, which constitutes the actual response from
the detector. However, when analyzing higher concentrations of analytes for
calibration purposes, an intensity bias can occur in the form of suppression of the
analytical signal. To adjust for any suppression, internal standards are used. The
resulting intensity recorded after adjusting the raw values for internal
standardization and blank correction results in the Net Intensity. Cataloguing both
the raw and net intensities expands the scope of the analytical data, providing
information on any signal suppression or enhancement, as well as the linearity of
the calibration curve.
Reported Shutdown Values

Where a value exceeds the prescribed intensity or concentration limits, it is said to
be in shutdown. Shutdown values are indicated on Syngistix reports by the letter
S. If an intensity or concentration is reported in brackets in the Report View panel,
it means that the interference correction (or elemental equation) was in shutdown,
and a value of 2e6 for pulse mode or 2e9 for analog mode was substituted into the
equation. The resultant calculated intensity or concentration therefore reflects an
estimated value for the isotope. This estimated value is denoted by the presence
of brackets.
Because they cannot be precisely calculated, RSD, SD, % Recovery and %
Difference values based on intensity or concentration values that are in shutdown
will also themselves be classified as being in shutdown, and will also be marked
with an S. See Detector Shutdown on page 202 for more information about
shutdown conditions.
Current Sample tab

The Current Sample tab displays detailed information about the current or most
recent sample or optimization run through your system. Previous reports are
persisted in memory between runs and software sessions; they can be reviewed
by scrolling down the screen. Current Sample reports are available for all types of
analyses.The information displayed and format chosen is driven by either the
report template specified in the method associated with the sample, or the
currently open report template where none is specified. See Report Options
Templates on page 282 for more information about creating and modifying report
templates using the tools in the Report Options panel.
Figure 11-1 Report View Current Sample tab
Reports
Current Sample Report Example

In this example of a printed Current Sample report, the report contains a footer,
header, and four main sections: Sample Information, Replicates, Mean Values,
and Standard Deviations.
Raw Intensities tab

Applies to Quantitative Analyses only. The Raw Intensities tab displays the
unadjusted signal intensity for each element measured by the instrument. The
column headings consist of the analytes as named in the related method along
with the mass in amu. The relevant units are also displayed, again as defined in
the method, below the analyte name in parentheses; samples and standards may
be measured in different units, as required. Analytes that are acting as Internal
Standards are identified with an (IS) in the relevant analyte header.
Select the Show RSDs check box to display the related Relative Standard
Deviation values for each sample. You can also display additional columns to
show the sample acquisition date and time, reprocessed data flags, and QC
function status indicators — click Advanced to configure these options.
When the QC Status column is displayed, you can click on any Failed cell or the
corresponding Sample ID to go to the relevant detailed data section of the Report
View QC tab. (When the QC Status column is not displayed, any failed QC
measures can be identified by a red Sample ID cell; click on the Sample ID to
access the related item on the QC Tab.) Note that if a QC measure specifies that
there be a valid calibration in the current workspace, and none exists, the QC
Status column will appear blank, rather than showing Passed or Failed. The QC
status will also be blank if QC checking is not enabled in the given method; or
when it is enabled, but no QC limits have been specified.
If you are running the Enhanced Security™ software, depending on your software
configuration, workflow change and traceability management functionality may
also be added, so that sample runs can be reviewed and approved (or rejected),
and e-signature details captured and displayed in the acquired data results tables.
See Enhanced Security Report View functions on page 275 for more information.
Figure 11-2 Report View Raw Intensities tab
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Net Intensities tab

Applies to Quantitative Analyses only. The Net Intensities tab displays the
measured signal intensity for each element measured by the instrument, with any
related Internal Standards or Blank subtractions applied. The column headings
consist of the analytes as named in the related method along with the mass in
amu. The relevant units are also displayed, again as defined in the method, below
the analyte name in parentheses; samples and standards may be measured in
different units, as required. Analytes that are acting as Internal Standards are
identified with an (IS) in the relevant analyte header.
Figure 11-3 Report View Net Intensities tab
Concentrations tab
Applies to Quantitative Analyses only. The Concentrations tab displays the
adjusted sample concentration for each element measured by the instrument.
This tab also consists of a tabular display with the sample name in the first column
and masses in subsequent columns with the concentration units directly beneath.
The column headings consist of the analytes as named in the related method
along with the mass in amu. The relevant units are also displayed, again as
defined in the method, below the analyte name in parentheses; samples and
standards may be measured in different units, as required. Each row represents a
single sample.
Analytes that are acting as Internal Standards are identified with an (IS) in the
relevant analyte header, and a purple font is used to highlight the internal standard
values within the table (where a valid blank with internal standards has been
applied). For each internal standard, the IS percent recovery value is displayed,
together with the related intensity RSD (if RSDs are displayed).
Note: If you are reprocessing data with original conditions, the percent recovery value
does not appear.
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Figure 11-4 Report View Concentrations tab
Unfactored Concentrations tab

Quantitative Analyses only. This tab is similar to the Concentrations view, but
displays data measured without concentration or dilution factors. It consists of a
tabular display with the sample name in the first column and masses in
subsequent columns with the concentration units directly beneath. The column
headings consist of the analytes as named in the related method along with the
mass in amu. The relevant units are also displayed, again as defined in the
method, below the analyte name in parentheses; samples and standards may be
measured in different units, as required. Each row represents a single sample.
Analytes that are acting as Internal Standards are identified with an (IS) in the
relevant analyte header.
Figure 11-5 Report View Unfactored Concentrations tab
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Internal Standards tab

Applies to Quantitative Analyses only. This tab shows a graph illustrating the
percent recovery for each internal standard (IS) plotted over time. The data
displayed here is a subset of the data displayed on the Intensities tabs — only the
internal standards are displayed in graphic format. The internal standard recovery
is defined as the current IS intensity/IS intensity of active calibration blank. When
a new blank is run, all subsequent IS intensities are then applied against that
blank's IS intensities.
Note: The internal standards calculations performed on this tab are completely
independent of those performed through the QC functions; activation of QC checking in
the method is not required for the plotting of internal standards data on this tab.
Note: If you are reprocessing data with original conditions, the percent recovery value
does not appear.
Up to ten distinct colors are plotted at any one time; additional internal standards
are plotted using those same colors again, so that a color may appear more than
once in a single plot.
When you move your mouse over a point in the graph a screentip appears
displaying the following additional information for that point: row index and sample
ID numbers; analyte name and mass; % recovery; intensity; and units used for the
intensity.
Note: The legend of the Internal Standards graph can display only the number of internal
standards that can fit into the screen; where the number of standards exceeds this, the
legend simply indicates More…. This is a static indication, and not a clickable link leading
to additional information. To see more standards in the legend, expand the screen.
Figure 11-6 Report View Internal Standards tab
Blanks and normalization factors

On the Report panel Internal Standards tab, the internal standards plotted are
normalized against the most recent blank processed, for all samples, and across
multiple methods, until a new blank is introduced.
Each blank effects a new normalization factor specifically and only for those
internal standards listed in that blank, canceling all previous factors for all
subsequent internal standards.
If a blank is not present, or no internal standards are defined in the blank, then a
normalization factor cannot be defined, and no internal standards points are
plotted on the graph. Other situations in which normalization cannot be factored
include cases in which the intensity of an internal standard in the blank is zero, or
where the internal standard is in shutdown, or is in brackets (wherein one of its
equation analytes is in shutdown).
In addition, all existing normalization factors are cleared if you manually clear the
current Blank or Calibration & Blank. Also, if you open or create a new calibration
file, load a calibration on the Dataset panel, or run an operation that loads a new
calibration file (such as reprocessing a blank, standard, or sample using original
conditions), the normalization factors will again be cleared.
When the normalization factor is undefined or has been cleared, no points are
plotted on the graph until a new, valid blank is run and normalization is re-
established. In the case of reprocessing, no points are plotted as long as the Use
Original Conditions check box is selected, as sufficient data is not available.
Note: Where only a single blank has been run, no point is plotted on the graph; plotting
begin at the next sample. Also, when a new blank is run, no point is plotted on the graph
for the blank; plotting resumes immediately thereafter.
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QC tab
Applies to Quantitative Analyses only. This tab displays relevant Quality Control
data for samples run for which QC criteria has been defined in the selected
method. The data displayed includes the basic sample information, such as the
originating row index number and analyte sample information. Analytes that are
acting as Internal Standards are identified with an (IS) in the relevant analyte
header. When a sample falls outside of the specified QC criteria, the relevant data
is displayed in red text. QC data is displayed for only as long as the corresponding
sample entries appear on the Raw and Net Intensities, Concentrations, and
Unfactored Concentrations tabs.
The data on the QC tab is organized into the following categories: QC Standards;
QC Spikes; QC Duplicates; QC Dilutions; and Samples, Blanks, and Calibration
Standards:
• For QC Standards, which are grouped by standard number, the original
sample concentration is displayed, followed by the RSD and % recovery.
• QC Spikes display the % recovery of the spike. QC Duplicate Spikes are
also listed here, showing the % difference. For all QC Spikes and QC
Duplicate Spikes listed, this tab also displays the original row index of the
parent sample.
• QC Duplicates and QC Dilutions display the % difference of the duplicate
or dilution. For all QC Duplicates and QC Dilutions listed, this tab also
displays the original row index of the parent sample.
• The Samples, Blanks, and Calibration Standards section displays the
named information only where a sample fails the QC criteria specified —
Samples display sample concentration, IS % recovery, RSD, and SD
information; Blanks display measured intensity SD data; and Calibration
Standards display net intensity RSD data.
The categories are each displayed in their own collapsible tree format — click on
the + and - signs beside each header to expand and view or collapse and hide the
available data.
All QC types from the Method panel QC tab are considered in this section.
However, because the QC Calibration sub-tab deals with limits on the calibration
as a whole (such as slope, intercept, and correlation coefficient limits) rather than
on individual samples, no QC failure is flagged if an individual calibration standard
goes outside specified limits, and no data, sample names or analyte headers
appear in red if a calibration fails a QC check. When a calibration fails, the
calibration information is displayed on the Intensities, Concentrations, and
Unfactored Concentrations tabs, inserted with a Sample ID of Calibration Curve,
and expanded upon on the QC tab with the addition of Slope, Intercept, and
Correlation Coefficient values for each analyte. Also note that repeated samples
and diluted samples as a result of QC failure actions are not added to this tab as
QC Duplicates or QC Dilutions.
If a QC measure requires that there be a valid calibration in the current
workspace, and none exists, the QC Status column will appear blank, rather than
showing Passed or Failed, and the relevant cells on the QC tab will also appear
blank, as no data could be properly calculated.
You can also access the data on this tab from any of the other tabular report views
where a QC Status cell displays a Failed marker; simply click the Failed cell or
the corresponding Sample ID to go to the relevant row on the QC tab. Note that
QC failure messages are not displayed on this view — to view a failure message,
you must look at the relevant individual Current Sample report.
You can display additional columns to show the acquisition date and time, and
reprocessed data flags for relevant samples — click Advanced to configure this
option.
and e-signature and QC signoff details captured and displayed in the acquired
data results tables. See Enhanced Security Report View functions on page 275 for
more information.
Figure 11-7 Report View QC tab
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Enhanced Security Report View functions

If you are running the Enhanced Security software, e-signature data and review
cycle validation functions can also be made available in the Report View panel
tables.
If the Audit Trail and Challenge and Electronic Signatures check boxes are
enabled in the ES Setup window Select ES Features dialog box, Review,
Approve, and Reject buttons are added to the bottom of the Raw and Net
Intensities, Concentrations, Unfactored Concentrations, and QC tabs. Users with
the required permissions can click to select single acquired data rows (CTRL +
click to select multiple rows), and then indicate review, approval, or rejection of the
selected data. Samples, appended samples, batches, and reprocessed data can
all be validated in this way. Graphic calibration rows cannot be selected for these
review functions; however, the component Blank and Standard rows for any
calibration may be reviewed.
In the Advanced Report View Display Options dialog box, three additional check
boxes become available. You can use these to add columns displaying e-
signature details for the displayed data, as well as Reviewed By details and
Approval Status (see Advanced Report View Display Options dialog box on
page 278 for more information). If the Audit Trail > Quality Control Signoff
check box is also enabled on the Select ES Features dialog box, the Reviewed By
column on the Report View panel QC tab displays QC signatory credentials rather
than reviewer details.
Because the Reporter currently displays information for quantitative analyses
only, acquired data records for other types of analyses — such as Isotope Ratio or
TotalQuant analyses — cannot have the review functions applied to them.
The following screenshot illustrates a typical Report View panel with all ES
functions enabled. You can see the Review, Approve, and Reject buttons at the
bottom of the panel, and the Signed By, Reviewed By, and Approval Status
columns in the table:
Figure 11-8 Enhanced Security Report View Raw Intensities tab
Report View common controls

The following controls are common to multiple tabs in the Report View panel:
• Show RSDs: Enable this check box to display the related RSD (Relative
Standard Deviation) for each sample displayed in the report view tables. If
you have chosen to display RSDs onscreen and you click Export..., the
RSDs are exported to the worksheet corresponding to the tab where they
are displayed. And whether displayed or not, RSD information is always
exported to separate Intensity RSDs and Concentration RSDs sheets.
• Advanced… Click this button to open the Advanced Report View Display
Options dialog box, and configure display preferences for the report view
tabs. See Advanced Report View Display Options dialog box on page 278
for more information.
• Export... Click this button to export all current data from the Intensities,
Concentrations, Unfactored Concentrations, Internal Standards, and QC
tabs to Microsoft Excel. RSDs are always exported to a separate sheet in
the Excel workbook. Additional information, including the relevant dataset
name, method name, time and date of acquisition, reprocessing indicators,
and QC status is also made available in the exported file to provide more
clear and complete sample identification, even though it may not be
present in the onscreen report views in the Syngistix ICP-MS software.
See Exporting Current Sample Reports on page 288 for information about
exporting Current Sample reports.
Note: You do not need to have Microsoft Excel installed on the same computer
as your Syngistix ICP-MS software in order to perform a report view export. If
Excel is not installed, the export file will still be saved with all applicable data, and
with the Internal Standards graph drawn in .jpg form (rather than the usual
editable Excel graph object). You can then transfer the file to another computer, or
open the file with an Excel-compatible reader.
The default file format for the export function is .xlsx, but .xls is also generally
available. However, due to limitations in Microsoft Excel, if you are exporting more
than 256 columns of data, you can only export in .xlsx format.
Note: If you have a version of Microsoft Excel earlier than 2007 installed on your
computer, you will be allowed to save to .xlsx format, but you will not be able to
correctly open the resulting file in that version of Excel (the file will appear to
contain garbage information). In this case, you can choose to instead save to .xls
Reports
format, which will open in any version of Excel, or you can open the resulting .xlsx
file in an Excel-compatible viewer or on another computer running Excel 2007.
Tip! (UCT instruments only) If you will be printing your exported reports to a
black and white printer, append the profile or mode you are using to each
analyte name in your method so that this information is included in your print-
outs (otherwise, mode is indicated by color only)
Tip! In some cases, when exporting a large amount of data from the Reporter
utility to Microsoft Excel, a message will appear indicating that the software is
not responding, and asking whether you wish to terminate the process or wait.
This occurs simply due to the time elapsed and is NOT an indication that the
software has crashed or frozen. Indicate that you would like to Wait for the
program to respond; the process will continue. The export may simply take
longer than expected.
• Clear Data: Click this button to clear all current data from the report view
tabs, except the Current Sample report. Note that you may wish to export
your data before clearing in order to preserve it for future examination.
Tip! In the Reporter panel, if you have a particularly large amount of data (for
example, data collected under many columns heads as a result of multiple
sample acquisition methods or calibration tables), it may take several seconds
to switch tab views, and several minutes to export that data to Microsoft Excel.
To combat this issue, clear your Reporter data frequently, either by clicking the
Clear Data button, or by restarting the Syngistix software.
A right-click menu is also available in the Report View tables to allow you to
designate a sort order for your analyte headers (choose the same order
designated in your method, or sort by analyte, mass, or mode), or to access the
Advanced Report View Display Options dialog box. Screentips provide additional
information throughout the Report Viewer; move your mouse over select controls
and data points to access these tips.
Advanced Report View Display Options dialog box

On the Raw and Net Intensities, Concentrations, Unfactored Concentrations,
Internal Standards, and QC tabs, click Advanced... to define report view details.
You can specify how the analytes are sorted in the tables; whether or not to
display the acquisition date and time for each sample; whether or not to display
reprocessed data and QC pass/fail indicators where relevant; and set the number
of decimal places to display for Raw and Net Intensity, Concentration, RSD, SD,
and % Recovery values. If you are running the Enhanced Security software, you
can also specify what e-signature and validation data you wish to display.
Figure 11-9 Advanced Report View Display Options dialog box
Advanced dialog box controls

• Sort Analyte header by: Select the type of sort order to use for analytes
in the report view table headers.
• Display Reprocessed Data Indicators: Enable this check box to display
a Reprocessed Data column (R) on the tabular reporting tabs to indicate
when a sample was run using reprocessed data. Where reprocessed
sample data is present, an R will appear. Whether displayed onscreen or
not, reprocessed data information is always exported with the sample
data.
• Display Sample Acquisition Date and Time: Enable this check box to
display the Sample Acquisition Date and Time on the Raw and Net
Intensities, Concentrations, Unfactored Concentrations, and QC tabs.
Whether displayed onscreen or not, time and date information is always
exported with the sample data.
• Display Quality Control Status: Enable this check box to display the QC
status (Pass or Fail) on the Intensities, Concentrations, and Unfactored
Concentrations tabs. Whether displayed onscreen or not, QC status
information is always exported with the sample data.
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• If you are running the Enhanced Security software, three additional

information display options are available to provide additional information
for validation and traceability:
 Display Signed By check box: Enable this check box to add a
column to the Report View data tables that will display e-signature
details for acquired data records on the Raw and Net Intensities,
Concentrations, Unfactored Concentrations, and QC tabs.
 Display Reviewed By check box: Enable this check box to add a
column to the Report View data tables that will display reviewer details
for acquired data records on the Raw and Net Intensities,
If the ES Setup window Select Enhanced Security Features dialog box

Audit Trail > Quality Control Sign off check box is enabled, the
Reviewed By column on the Report View panel QC tab displays QC
Signoff credentials rather than reviewer details.
 Display Approval Status check box: Enable this check box to add a
column to the Report View data tables that will display approval status
information for acquired data records on the Raw and Net Intensities,
Note: These options are available only if the Audit Trail and Challenge and
Electronic Signatures check boxes are selected in the ES Setup window Select
ES Features dialog box.
• Raw Intensity field: Select the number of decimal places to display in the
reporting tables for Raw Intensity values. Valid values = 0-4
• Net Intensity field: Select the number of decimal places to display in the
reporting tables for Net Intensity values. Valid values = 0-4
• Concentration field: Select the number of decimal places to display in the
reporting tables for Concentration values. Valid values = 0-4
• RSDs field: Select the number of decimal places to display in the
reporting tables for RSD (Relative Standard Deviation) values. Valid
values = 0-4
• SDs field: Select the number of decimal places to display in the reporting
tables for SD (Standard Deviation) values. Valid values = 0-4
• % Recoveries field: Select the number of decimal places to display in the
reporting tables for Percent Recovery values. This field also governs the
number of decimal places that will appear for Percent Difference values on
the QC tab. Valid values = 0-4
Note: If you are reprocessing data with original conditions, the percent
recovery value does not appear.
Calibration Panel
Use this panel to view graphic calibration curve data for the results listed on the
Report View panel. A calibration row appears after the last calibration standard
defined in the method is run.
On any table tab on the Report View panel, click a single calibration cell to display
that calibration only; select an entire Calibration Curves row to display the
complete set of calibrations available (a vertical scroll bar allows you to view all
the displayed calibrations). The single calibration view displays information in
regular whole numbers, while the multi-calibration view uses scientific shortened
notation to save space. As on other report graphs, S indicates a value in
shutdown, and NaN means “not a number” (no data available). Horizontal and
vertical sliders allow you to adjust the area of focus along each axis; click the
square arrows button in the bottom right corner of any calibration graph to return
to the original view. In multi-calibration view, click the small, square, gray button in
the upper right corner to expand this panel for better viewability.
Figure 11-10 Reporter screen Calibration panel
Reports
Note: If you previously used the NexION software, and you are reprocessing
data collected in the NexION software:
In the Reporter, the current standard's raw intensity is calculated and displayed; when
NexION data is reprocessed using original conditions and the next standard is
reprocessed, the software reads the calibration from the original dataset and, finding no
raw intensity value (as this measurement did not exist in the older software), reads the raw
intensity as zero. As a result, on the Reporter screen Calibration panel, the most recently
reprocessed standard displays a point with a non-zero intensity, and all earlier standards
are plotted with a zero calibration.
.
When reprocessing NexION data without original conditions, each point is simply
recalculated, and the Calibration panel is able to display points with correctly calculated
raw intensities.
Calibration panel controls and indicators

• Print: Click the Print button to print the calibration graph or graphs
currently displayed in the Calibration panel.
• Statistics: This section displays statistical data on the quality of the
calibration fit.
 Eqn.: The slope and intercept line Equation of the calibration.
 Cor. Coeff.: The Correlation Coefficient is generated during the linear
regression of the data points and is a measure of the quality of the final
calibration curve.
 BEC: The Background Equivalent Concentration is the background
signal represented as an equivalent concentration and provides an
excellent means of gauging the true magnitude of noise. It is
calculated as the intensity of the blank, over the slope. The unit of the
detection limit is the same as that of the standard solution
concentration.
 DL: The Detection Limit, expressed as the concentration or quantity, is
derived from the smallest measure that can be detected with
reasonable certainty for a given analytical procedure. It is calculated as
three times the standard deviation of the blank, over the slope. The
unit of the detection limit is the same as that of the standard solution
concentration.
The BEC and DL are calculated using the most recent Blank run up to
that point in time; if a subsequent Blank is run, existing calibration rows
are not updated; rather, a new calibration row is created, and the BEC
and DL are recalculated.
• Calibration Table: This section displays intensity and concentration
information for the specified analyte.
 Net Intensity: Displays the net intensity value, blank corrected and
adjusted for internal standards.
 Apparent Conc.: Displays the apparent concentration.
Report Options
Use the reporting options functions to create custom reports for your
determinations. You can define a report with the exact content you need and in a
style that best conveys the information content on the page. The following are the
basic components of a report options template:
• A report option template consists of a series of sections that are placed
consecutively on the page or in the file
• Each report section consists of a series of fields that are structured within
each section
• All the available determination data can be included in a report. You select
the sections and fields that you want to include, then you adjust the pre-
defined formats, including position on the page, field names and font style
and size, according to your individual requirements
Report Options Templates

Using the Report Options panel, you can design or modify a report template to
create print or file output for individual sample analyses. You can specify both the
content and appearance of your reports, including location and type. New report
options files are linked to the type of method in memory when the file is created.
The software includes several pre-defined report templates. These templates
define how the data, reports, and file content will appear when printed. For
example, the masscal.rop file provides a printout of the contents of the mass
calibration .tun file.
Also provided are pre-defined templates for calibration, mass calibration,
optimization, conditions definition, and the different method types (Quantitative,
Isotope Method, Isotope Dilution, Data Only, and TotalQuant™ methods). The
masscal.rop and conditions.rop templates are method-independent; however,
when modified they become method-dependent.
Reports
Report Appearance
To make report design fast and easy, the software identifies default location and
type specifications for each item that you include in a report template. However,
you may want to change these parameters to make the report fit your
requirements. You can customize a variety of options including the title page,
headers and footers, row and column sizing and spacing, font types and styles,
number formats, and page breaks.
Report Options Template Example

The top half of the panel shows the report sections selected to appear in this
report. The bottom half of the panel shows the fields selected to appear in the
highlighted report section — in this case, the Sample Information section.
Report Options Controls

Use the Append, Insert, and Remove buttons in the Report Options template to
alter sections and fields in your reports. The Append buttons add a new section or
field to the bottom of your list, while the Insert buttons add a new field or section
immediately above the selected item in your list. You can also select multiple
sections and fields and Append or Insert them all at once.
Report Options for Sections

• Available Sections: Lists all the sections that are available for inclusion in
your report.
• Selected Sections: This is a read-only field. Shows the sections that are
selected. To select a section, click the section in the Available Sections
column and click Append or Insert.
• Section Title: Automatically fills the Section Title entry; however, you can
modify it.
• Column Offset: Indents from the left margin in hundredths of an inch. A

column offset of 100 is equal to one inch.
• Row Offset: Spaces lines for the report in hundredths of an inch. A row
offset of 100 is equal to one inch.
• Font: Specifies the style of typeface to be used for the section title. Right-
click to display the fonts options.
Report Options for Fields

• Available Fields: Lists the fields that can be included in your report.
• Selected Fields: This is a read-only parameter. Shows the fields that are
selected. To select a field, click the field in the Available Fields column and
click Append or Insert.
• Field Title: The software automatically fills the Field Title entry; however,
you can modify it.
• Column Offset: Indents from the left margin in hundredths of an inch. A
column offset of 100 is equal to one inch.
• Row Offset: Spaces lines for the report in hundredths of an inch. A row
offset of 100 is equal to one inch.
• Font: Specifies the style of typeface to be used for the field. Right-click to
display the font options.
Selected Fields for Isotope Ratio Methods
A select subset of fields are available in the Report Options panel when the
Replicates, Mean Values, and Standard Deviation sections are selected for an
Isotope Ratio method.
Replicates Section fields
• Repeat Title: Indicates replicate number, that is, Replicate 1, Replicate2,
and so forth.
• Reference Mass: The mass to which other masses of the same element
in the method are compared (ratioed).
• Analyte: The symbol representing each analyte in the method.
• Mass: The mass of each isotope in the method.
• Measured Intensity: The intensity measured and corrected for deadtime
and elemental equations.
• Blank Intensity: The measured intensity of the blank solution corrected
for deadtime and elemental equations.
• Net Intensity: The blank corrected measured intensities, calculated as
follows:
Net Intensity = Measured Intensity - Blank Intensity
• Correction Factor: The software automatically calculates an RCF (ratio
correction factor) from the results for the reference standard, as follows:
Reports
where:
The Standard Known Ratio is the user entry of the certified ratio for the
Standard.
• Ratio Normalized:
• Ratio Fraction:
• Mass Fraction: The Isotope Ratio mass fraction (wA) is the ratio of the
mass of isotope A to the total mass of all the isotopes:
mA
w A = -------------
-
 i m
The mass (mA) of any isotope is the ratio fraction multiplied by its isotopic
mass. Note that the isotopic mass value for the calculation must be the
isotopic mass from the elemental library up to six decimal places.
Mean Values Section fields
in the method are compared (ratioed).
• Analyte: The symbol for each analyte in the method.
• Measured Intensity Mean: The arithmetic mean of the replicate
measured intensity values.
• Blank Intensity: The arithmetic mean of the replicate measured intensity
values for the blank solution.
• Net Intensity Mean: The arithmetic mean of the replicate net intensity
values.
• Correction Factor Mean: The arithmetic mean of the replicate correction
factor values.
• Ratio Normalized Mean: The arithmetic mean of the replicate ratio
normalized values.
• Ratio Fraction Mean: The arithmetic mean of the replicate “ratio fraction”
values.
• Mode: (UCT instruments only) The operating mode.
• Gas: (UCT instruments only) The cell gas used.
• Profile: (UCT instruments only) The acquisition profile applied.
Note: If you are using the default acquisition profile names, be aware that they
already include both the mode and cell gas as part of the name, so that adding a
combination of Mode / Gas / Profile fields may result in redundant information in
your report. However, if you have created custom profiles using a unique naming
or identification system that does not include both of these pieces of information,
you may wish to include a combination of these fields to ensure that all necessary
data is captured.
Standard Deviation Section fields:

in the method are compared (ratio).
• Analyte: The symbol for each analyte in the method.
• Measured Intensity Std. Dev.: The standard deviation of the mean
intensity of all replicates.
• Blank Intensity Std. Dev.: The standard deviation of the mean measured
intensity of all replicates for the blank solution.
• Net Intensity Std. Dev.: The standard deviation of the mean net intensity
of all replicates.
• Correction Factor Std. Dev.: The standard deviation of the mean
correction factor of all replicates.
• Ratio Normalized Std. Dev.: The standard deviation of the ratio
normalized mean of all replicates.
• Ratio Fraction Std. Dev.: The standard deviation of the ratio fraction
mean of all replicates. The formula for Standard Deviation is as follows:
where:
 n = the number of replicates for the sample
 x = Ii or Ni or Ci or Ri
 Ii = the instantiate for analyte i
 Ci = the ratio correction factor for analyte i
 Ni = the net intensity for analyte i (Ii - IO), blank intensity subtracted
 IO = the intensity of the blank
 Ri = the (calculated) corrected (isotope) ratio
Reports
Summary Reports
Summary by Analyte and Summary by Sample reports capture the net value, SD,
and %RSD for the intensities and concentrations of analytes measured during
batch acquisition. The results can be sorted by analyte (Summary by Analyte) or
by sample (Summary by Sample).
There are two ways to generate a summary report: in real time after a batch
analysis or during the reprocessing of the data from a batch analysis.
Note: Summary reports are available for quantitative analysis methods only.
Summary Report after a Realtime Batch Analysis

Cross tab summary reports provide a convenient format for reporting summarized
sample ID and concentration data only. You can create a summary report with
sample IDs down the left side of the page and the analytes across the top of the
page or vice versa. This report format can be used when reprocessing data with
the same method only. A cross tab report displays a concise report of sample
runs.
Summary Report after Reprocessing a Batch Analysis

Cross tab summary reports provide a convenient format for reporting summarized
sample ID and concentration data. You can use this report format only when
reprocessing data with a single method. When you select Reprocess with Original
Conditions, the block of data highlighted for reprocessing on the Dataset panel
can contain multiple sample IDs, but they must all reference the same method.
Intensity versus Time Reports

You can also use the software to generate intensity versus time reports, allowing
you to examine spikes in signal intensity over multiple readings in time. The report
uses the intensity units specified in the method. These reports use a fixed,
comma-separated value format to export temporal values to a spreadsheet, and
are generally sent to file only; they are useful for the manipulation of transient
signal data by third party software packages.
The software automatically generates a report output file name for the intensity
versus time data by combining the Sample ID name with an .xl extension (rename
the extension to .xls to open in Microsoft Excel). The default output file location is
the Report Output folder of the \PerkinElmer Syngistix\ICPMS data directory.
Although intensity versus time data is not printed by the reporter software, the
output file name and the file path are included in other printed reports.
Note: When you create a method file that you wish to use with an Intensity vs Time
report, on the Method panel Timing tab, ensure that you specify both multiple
Readings/Replicate and multiple Replicates in order to capture sufficient data to establish
and analyze any intensity spikes or peaks in the data across the number of readings.
These fields must both read >0 to create the report.
Exporting Current Sample Reports

Reports created using a Report Option template are also the basis for the data
export facilities. Using the built-in export controls, you can easily create a text file
that can be imported into an outside software program for data analysis and
reporting. The software provides the ability to include all the information contained
in your printed report in either tab delimited or CSV (comma separated variable)
formats.
When creating a data file from a report, the following additional options are
available to you:
• File Report Format: Selects between tab delimited (Use Delimiter) or
comma separated variable (Use Separator) file formats and to specify
whether or not to include field titles in the report (Include Titles)
• File Write: Controls whether the measurement data from each series of
measurements will be added to the bottom of the destination file (Append),
whether the data will overwrite data that already exists in the destination
file (Overwrite), or whether the data will be new for each sample (New Per
Sample)
• Use International Character Set: Select to send international Unicode
characters to the file or serial port. When unchecked, ASCII characters are
sent. Select this option to send Unicode characters, such as Japanese
text.
Chapter 12
Graphic Data
This section describes the graphic viewing and manipulation tools.
• Graphic Displays on page 289
• Graphics Display Toolbar on page 289
• Realtime Panel on page 291
• Realtime Graphics Options Dialog Boxes on page 292
• Interactive Panel on page 295
• Interactive Graphics Options Dialog Boxes on page 298
• Composite Signal and Spectral Options on page 301
• Cell Parameter Optimize Options on page 302
• Calibration View Panel on page 303
Graphic Displays
The software provides extensive displays of signal and spectral data in realtime or
post-run. There are three main panels through which you work with graphic data:
• Realtime Panel
• Interactive Panel
• Calibration View Panel
While each of these panels is designed to support different requirements, the
functions available in each are similar, and all are supported by a set of common
controls.
Graphics Display Toolbar

The graphics panels share a common set of tools for managing the display and
appearance of graphic data. When a toolbar button is selected, it appears
depressed. Mouse-over screentips describe the function of each button.
Linear/Logarithmic Use to select a linear or logarithmic value
Plot Y‐axis plot
Grid Off/On Use to select no grid (with tick marks) or a full
grid plot background
Curve/Bar/Line Plot Use to select a curve (spectral), bar, or line
plot
289
Zoom Use to enlarge an area in a plot. Each time
you zoom, a number is assigned to the view,
with 0 the full display, 1 the first zoom, 2 the
second, and so on
To zoom in a plot, drag the cursor to draw a
box around the region you want to enlarge.
When you release the mouse button, the
graph is redrawn with the area inside the box
displayed at zoom scale
To switch between zoom levels, click the
Zoom button, and then click the number
associated with the zoom level you want to
use. To reset the zoom series, set the display
to zoom level 0, then redraw a different area
with the cursor. All remaining zoom levels in
the original series are deleted.
Print One/All Plots Use to control the output of plots to a printer
attached to the computer. To print a single
plot in a one‐plot display, click the Print One
button. To print a single plot in a multiple‐plot
display, click the plot you want to print, then
click the Print One button. To print all the
plots in a multiple‐plot display, click the Print
All button
Plot Options Use to define the colors used for plot axes,
labels, and tick marks, and to indicate
whether to display titles, labels, and sliders
Customize Fonts for Use to manage type parameters for plot
Titles and Labels labels and titles. Click and select Titles or
Labels from the list; the Font Options dialog
box appears. Select the preferred font
parameters and then click OK. The
parameters selected are applied to all plots
displayed
Zoom to Fit All Use to scale a plot. The software
automatically adjusts the y‐axis intensity to
maximize the display so that the largest peak
is on‐scale and shown at its maximum
intensity
Customize Line Use to select and apply a line width to the
Width displayed plot. Select from 1 pt, 2 pts, or 3
pts wide
Graphic Data
Realtime Panel
Use the Realtime panel for realtime viewing and interpretation of signal,
spectral, and numeric displays of data during an acquisition or
optimization. Here you can adjust the axis range and display parameters,
manage the printing of graphics data, specify the colors used, and control
the font and type size for title and label text.
The Realtime screen is accessed via the Realtime icon on the ribbon.
When accessed in this way, it consists of the Realtime panel only. The
Realtime panel, however, is also displayed in several other multi-panel
views (including the Sample screen, Conditions screen, Instrument
Diagnostics screen, and the SmartTune screen). This allows you to
monitor the results of various processes without having to switch between
screens.
Figure 12-1 Realtime panel

Items in the Realtime Panel
• Display Type: Controls the type of data displayed in the Realtime panel.
To select the data type to be displayed, click one of the following options
from the Display Type list.
 Signal: Displays the signal from a data acquisition. This option is
available for individual elements/analytes only. The graph displayed
has an x-axis listing time in seconds and a y-axis listing signal intensity
in cps (counts per second) or total ion counts. A maximum of six
elements/analytes can be displayed.
 Spectral: Displays the spectral results for a range of masses/analytes.
The graph displayed has an x-axis listing mass range in amu and a y-
axis listing signal intensity in cps or total ion counts. A natural
abundance spectral fingerprint of a single isotope can be overlayed.
 Numeric: Displays numerically the elapsed time (in seconds) for the
measurement and the raw (uncorrected) analyte intensity.
• Options: Displays the Realtime Graphics Options dialog box specific to

the Display Type selected. Here you can control the graphic display
parameters.
• Analytes: Displays the Analyte Display Options dialog box used to control
the analytes plotted in the graphics panel.
• Natural Abundance Spectral Fingerprint Overlay: Use this feature to
visually determine whether interference is present for an isotope of
interest. The natural abundance fingerprint is normalized for the isotope
selected as the reference isotope. The name of the reference isotope and
its mass value appear beside the histogram. You can also print the
histogram with the spectral overlay. This option is available only when
Spectral is selected as the display type.
Realtime Graphics Options Dialog Boxes

Use the Realtime Graphics Options dialog boxes to control the display of data in
the plot. Each display type has a unique set of graphics display options
associated with it.The dialog boxes are:
• Spectral Realtime Graphics Options
• Signal Realtime Graphics Options
• Numeric Realtime Graphics Options
Figure 12-2 Sample Realtime Graphics Options dialog box
Graphic Data
Items in the Realtime Options Dialog Boxes

Note that not all options appear in every dialog box.
• Display Options Group:
 Max cps or counts: Sets the maximum y-axis display value for the
spectral plot. Entries can be typed out without commas or other
character separator (for example, 5000000) or can be typed in
scientific notation (for example, 5e+6). The software automatically
converts any value not in scientific notation when the dialog box is
closed.
 Min cps or counts: Enter the minimum y-axis display value for the
character separator (for example, 5000000) or can be typed in
closed.
 Begin Mass: Enter the beginning mass, in amu (atomic mass units), for
the spectral plot. Valid entries are zero or any positive whole number.
Decimal entries are automatically converted to a whole number value.
 End Mass: Enter the end mass, in amu, for the spectral plot. Valid
entries are zero or any positive whole number. Decimal entries are
automatically converted to a whole number value.
 Use This Mass Range: Uses the parameter in the Display Options
group. If the check box is not selected, the changes made in the dialog
box will not take effect.
 Begin Time: Type a time point, in seconds, at which to begin graphing.
Valid entries are zero or any positive, whole number.
 End Time: Type a time point, in seconds, at which to end graphing.
 Use This Time Scale: Select to use the defined time scale.
 Plot Line Type: Click to set the line style for display of spectral lines in
the Interactive panel. Click to view the options available, then click to
select a line style.
 Line Color (Plot/Avg.): Click to set the display color for the spectral plot
lines, both the individual replicates and the averaged value. Clicking
either color block opens the Colors dialog box. To select a color, click a
color and click OK. You can exit the Colors dialog box without making a
change by clicking Cancel.
 Overlay/Refresh/Accumulate: Click to specify how individual replicate
measurements are plotted in the Realtime panel. Only those replicates
indicated by the Draw Replicates command will be plotted. Click
Overlay to plot all replicates on a single graph, overlaying the results of
the successive measurements. Click Refresh to clear the results from
one replicate before plotting the next replicate. Click Accumulate to
plot a line representing the total ion count data from a series of
replicates in a single plot. The Accumulate option is available only
when the Display Type is Spectral and the Processing Options
parameter is set to Counts.
• Detector Group:
 Pulse/Analog/Dual: Click to select the detector mode generating the

signal input to the plot. Click Pulse to select pulse mode. Click Analog
to select analog mode. Click Dual to acquire input from both sources.
Dual mode is active only after the detector has been calibrated.
• Processing Options Group: These options set the processing function to
display either total ion counts or counts per second.
 Spectral Peak: Use this control to specify how the data from the
individual spectral peaks is processed before it is displayed. There are
three options: Average, Sum, and Maximum. Click Average to average
the values of all the MCA Channels from each peak. Click Sum to add
the values of all the MCA Channels to create a total ion count for each
peak. Click Maximum to select the MCA channel with the maximum
value from each spectral peak. No processing can be performed on
the spectral profile when using Spectral Interactive graphics mode.
 Signal Profile: Use this control to specify how the signal profile is
displayed before further calculations are performed. There are three
options: average, sum, and maximum. Click Average to average the
readings from a profile. Click Sum to add the readings to create a total
count for each profile. Click Maximum to select the maximum reading
from each profile.
Analyte Display Options Dialog Box
Use the Analyte Display Options dialog box to select the analytes (to a maximum
of six, or five for Interactive Dual Detector plots) that will be plotted in the graphics
panels.
Figure 12-3 Analyte Display Options dialog box
Graphic Data
Interactive Panel
Use this panel for post-acquisition viewing and interpretation of signal and
spectral displays. Here you can adjust the axis range and display parameters,
manage the printing of graphics data, control the colors used on the display, and
to control the font and type size for titles and label text. The Interactive panel is an
integral part of calibrating and optimizing your instrument, and is also useful in
post-acquisition analysis of analytical data.
Figure 12-4 Interactive panel

Items in the Interactive Panel
• Display Type: Controls the type of data displayed in the Interactive panel.
Select from the following options:
 Signal: Displays the signal from a data acquisition. This option is
available for individual elements/analytes only. The graph displayed
has an x-axis listing time in seconds and a y-axis listing signal intensity
in cps or total ion counts.
 Spectral: Displays the spectral results for a range of masses/analytes.
The graph displayed has an x-axis listing mass range in amu and a y-
axis listing signal intensity in cps or total ion counts. A natural
abundance spectral fingerprint of a single isotope can be overlayed.
 TQ Spectrum: Displays a TotalQuant™ spectrum. The graph displayed
has an x-axis listing mass range in amu and a y-axis listing intensity in
counts per second. To facilitate viewing the full spectrum with the x-
axis expanded, a set of four arrow buttons permit you to scroll through
interferences (that is, analytes having the same mass) for the selected
analyte. The red section of each bar indicates the mass contribution of
the selected analyte.
 Composite Signal: Overlays, adds, subtracts or sets up a ratio for two
time-varying signals. It is also useful for blank-subtracted data. This
option is available for individual elements/analytes only. The graph
displayed has an x-axis listing time in seconds and a y-axis listing
signal intensity in cps or total ion counts.
 Composite Spectral: Overlays, adds, subtracts or sets up a ratio for
two mass spectra. It is also useful for blank-subtracted data. The graph
displayed has an x-axis listing mass range in amu and a y-axis listing
signal intensity in cps total ion counts.
 Optimization: Displays the graph resulting from an optimization scan
for one of the digital-to-analog converters controlling the instrument
hardware. This option is used in conjunction with the Conditions panel
during hardware optimization. The graph displayed has an x-axis
listing the range of DAC values to be scanned and a y-axis listing
intensity in cps.
 MassCal: Displays the graphs resulting from a mass calibration or
resolution adjustment performed during instrument optimization. This
option is used in conjunction with the Mass Calibration panel. Each
graph displayed has an x-axis listing the mass range in amu and a y-
axis listing intensity in cps. The individual graphs include a title bar
displaying the atomic symbol and the isotope mass for the analyte
results being plotted in that graph. When results are plotted, a line is
also automatically drawn to indicate the intensity at 10% of maximum
peak intensity (the point at which peak width is measured).
 Dual Detector: Use with the Interactive panel as part of the dual
detector calibration procedure. Dual detector calibration is used to
adjust the response behavior of the pulse and analog stages of the
dual detector to provide optimum data integrity when signal intensity
varies widely during a run employing both pulse and analog signal
detection. By selecting Analytes, the graph can be displayed for up to
five analytes used in the calibration procedure. Each graph has an x-
axis displaying pulse intensity and a y-axis displaying analog intensity.
Detector Response Function graph shows the relationship of the
analog to pulse signals across the mass range. Each point represents
a mass which has a valid dual detector calibration. The straight lines
between points indicate interpolated conversion factors. For an
accurate quantitation you must have a measured conversion factor for
each isotope of interest. Using the interpolated conversion factor may
result in analytical inaccuracies. The detector response functions
1-
----
2
should have the shape of a curve. A flattening of the detector
x
response function is an indication that the detector is near the end of
its useful life.
 QID function: Use with the Interactive panel as part of the QID™
calibration procedure. QID component scanning helps to adjust the
detection systems mass bias to provide optimum signal intensity
across the full mass range. You can configure this graph to display the
information for up to five analytes used during the scanning procedure.
The x-axis displays QID component voltage, and the y-axis displays
Graphic Data
signal intensity. On UCT instruments, there are corresponding QID

STD/DRC mode and QID KED mode options which provide similar
information about analytes entered in each of the system’s functional
modes.
 Cell Param Optimize: UCT instruments only. Displays a line graph of
the intensities of two solutions as a function of DRC parameters (cell
gas flow and rejection parameters) and estimated detection limits, one
analyte at a time. The element to be viewed is selected in the Analyte
list. If no analyte is selected, the first analyte from the list is displayed
in the Cell Parameter Optimize plot. The software indicates the gas
flow providing the lowest detection limit for each analyte with an X on
the graph. Click the X, and the optimum gas flow for the selected
analyte appears on the Conditions panel Cell Parameters tab.
Note: You can reprocess cell parameter information only if the start, end, and
step values for the parameter and profile used during acquisition are identical for
both the Blank and the Sample. You cannot reprocess datasets created in a
previous (prior to v2.0) version of the software.
• Options: Displays the Interactive Graphics Options dialog box specific to

the Display Type selected. Here you can control the graphic display
parameters.
• Analytes: Displays the Analyte Display Options dialog box, where you can
specify which analytes will be plotted on the graphics panel. This button
appears for all signal options except Composite Signal, Composite
Spectral, and Cell Param Optimize; in these cases, the Composite button
appears instead.
• Composite: Displays the Composite Signal Graphics Options, Composite
Spectral Graphics Options, or Cell Param Optimize Options dialog boxes.
Use these dialog boxes to specify which analytes will be plotted on the
graphics panel, and the manner in which the data will be combined for
composite display. This button appears only when you select the signal
option Composite Signal, Composite Spectral, or Cell Param Optimize.
• Draw Replicate: Use this function and the associated numeric entry fields
to specify which replicates in a given determination will be plotted in the
Interactive panel. To set the replicate number, click in the first field and
type the number of the first replicate you want to plot. Click in the second
field, after the word “to”, and type in the number of the last replicate you
want to plot. To draw the replicate, click Draw Replicate.
• Natural Abundance Spectral Fingerprint Overlay: Use this function to
visually determine whether interference is present for an isotope of
interest. The natural abundance fingerprint is normalized for the isotope
selected as the reference isotope. The name of the reference isotope and
its mass value appear beside the histogram. You can also print the
histogram with the spectral overlay. This functionality is available only
when you select the Spectral display type.
Interactive Graphics Options Dialog Boxes

Use the Interactive Graphics Options dialog boxes to control the display of data on
the plot. Each signal type has a unique set of graphics display options associated
with it. The dialog boxes are:
• Signal Interactive Graphics Options
• Spectral Interactive Graphics Options
• TQ Spectrum Interactive Graphics Options
• Composite Signal Interactive Graphics Options
• Composite Spectral Interactive Graphics Options
• Optimization Interactive Graphics Options
• MassCal Interactive Graphics Options
• QID Interactive Graphics Options (300/350Q instruments only)
• QID STD/DRC Mode Graphics Options (UCT instruments only)
• QID KED Mode Graphics Options (UCT instruments only)
• Cell Parameters Optimize Options (UCT instruments only)
Figure 12-5 Sample Interactive Graphics Options dialog box
Graphic Data
Items in the Interactive Graphics Options Dialog Boxes

Not all options appear on every dialog box.
• Display Options Group:
 Max cps or counts: Sets the maximum y-axis display value for the
character separators (for example, 5000000) or can be typed in
closed.
 Min cps or counts: Sets the minimum y-axis display value for the
character separators (for example, 5000000) or can be typed in
closed.
 Begin Mass: Sets the beginning mass, in amu, for the spectral plot.
Valid entries are zero or any positive whole number. Decimal entries
are automatically converted to whole numbers.
 End Mass: Sets the ending mass, in amu, for the spectral plot. Valid
entries are zero or any positive whole number. Decimal entries are
automatically converted to whole numbers.
 Use This Mass Range: Select this check box to use the parameter in
the Display Options group. If the check box is not selected, the
changes made in the dialog box will not take effect.
 Begin Time: Type a time point, in seconds, at which to begin graphing.
 End Time: Type a time point, in seconds, at which to end graphing.
 Use This Time Scale: Select to use the defined time scale.
 Plot Line Type: Sets the line style for display of spectral lines in the
Interactive panel. Click to display the options available, then click a line
style.
 Line Color: Avg: Sets the display color for the spectral plot lines, both
the individual replicates and the averaged value. Clicking either color
block opens the Color dialog box. To select a color, click a color and
click OK.
 Overlay/Refresh/Accumulate: Use these controls to specify how
individual replicate measurements are plotted. Only those replicates
indicated in the Draw Replicates command are plotted. Click Overlay
to plot all replicates on a single graph, overlaying the results of the
successive measurements. Click Refresh to clear the results from one
replicate before plotting the next replicate. Click Accumulate to plot a
line representing the total ion count data from a series of replicates in a
single plot. The Accumulate option is available only when the Display
Type is Spectral and the Processing Options parameter is Counts.
• Detector Group:
 Pulse/Analog/Dual: Click to select the detector mode generating the
signal input to the plot. Click Pulse to select pulse mode. Click Analog
to select analog mode. Click Dual to acquire input from both sources.
Dual mode is active only after the detector has been calibrated.
• Processing Options Group:
 cps/counts: Set the processing function to display either total ion
counts or counts per second.
 Spectral Peak: Use to specify how the data from the individual spectral
peaks is processed before it is displayed. There are three options:
average, sum, and maximum. Click Average to average the values of
the MCA Channels from each peak. Click Sum to add the values of all
the MCA Channels to create a total ion count for each peak. Click
Maximum to select the MCA channel with the maximum value from
each spectral peak. No processing can be performed on the spectral
profile when using Spectral Interactive Graphics mode.
 Apply Smoothing Factor: This check box is available only in the
Interactive panel. Use to start spectral smoothing in order to reduce the
effects of noise in high sensitivity measurements. You must have
multiple readings per replicate to use this option. The smoothing
function is a Savitzky-Golay moving average of the readings along the
spectral profile. When the check box is selected, the list beside it is
made available. Click to display the smoothing factor options (the
number of moving average points), based on the number of readings
per replicate used for data acquisition.
 Signal Profile: Use to specify how the signal profile is displayed before
further calculations are performed. There are three options: average,
sum, and maximum. Click Average to average the readings from a
profile. Click Sum to add the readings to create a total count for each
profile. Click Maximum to select the maximum reading from each
profile.
Graphic Data
Composite Signal and Spectral Options

Use these dialog boxes to overlay, add, subtract, or set up a ratio for two signals
or two mass spectra.
Note: You cannot overlay or reprocess datasets created in a previous version of the
Syngistix for ICP-MS software (prior to version 2.0) using these functions.
Figure 12-6 Composite Signal Graphics Options dialog box

Items in the Composite Signal and Spectral Graphics Options Dialog Boxes
Not all options appear on every dialog box.
• Concentration: Sets the concentration of the standard solution (in parts per
billion) that is used to optimize the reaction cell gas flow. This field is
available only when the Display Type is Cell Param Optimize.
• Show Composite Line Only: Select this check box to display the plot for
estimated detection limit in the cell parameter optimize display only. This
parameter is not available when the Display Type selected is Overlay.
• Calculate/Transform: Click Transform to perform the mathematical
equation you have selected. The Transform button is available only when
the Display Type is Composite Signal or Composite Spectral. Click
Calculate to process the data files selected for reaction cell parameter
optimization. The Calculate button is available only when the Display Type
is Cell Param. Optimize.
Cell Parameter Optimize Options

UCT instruments only. Use this dialog box to display reaction cell parameter
optimization plots.
Note: You cannot overlay or reprocess datasets created in a previous version of the
Syngistix for ICP-MS software (prior to version 2.0) using these functions.
Figure 12-7 Cell Parameter Optimize Options dialog box

To optimize reaction cell parameters on a UCT instrument, you must analyze two
different solutions—a matrix blank and a spiked matrix. In this dialog box, you
select the corresponding data files and click Calculate to view the optimization
results.
Note: You can reprocess cell parameter information only if the start, end, and step
values for the parameter and profile used during acquisition are identical for both the
Blank and the Sample.
For each analyte, the intensity of both solutions at each time interval is plotted as
a function of cell parameter value. The composite line graph represents either the
estimated detection limit calculated at each time interval, or the estimated
background equivalent concentration calculated at each time interval.
• Detection limit option: The estimated detection limit is calculated at each
time interval according to the equation:
Graphic Data
where:
I blk = the measured intensity for a blank solution, for example, deionized
water or matrix blank.
I std = the measured intensity for a standard solution, for example, 1 ppb
Iron.
Conc std = the concentration of the standard solution or spiked matrix.
Note: The unit of the detection limit is the same as that of the standard solution
concentration.
• Background equivalent concentration option: The background

equivalent concentration (BEC) is calculated at each time interval,
according to the equation:
BEC = I blk/(I stdI blk) . Conc std
where:
I blk = the measured intensity for a blank solution, for example, deionized
water or matrix blank.
I std = the measured intensity for a standard solution, for example, 1 ppb
Iron.
Conc std = the concentration of the standard solution or spiked matrix.
Calibration View Panel

Use the Calibration View panel for post-acquisition viewing and interpretation of
calibration curves generated from measurement of your standard solutions. Here
you can evaluate the quality of the calibration by viewing both the graphic plot of
the calibration points and reviewing statistical information on the curve fit. You can
also evaluate the effect of eliminating individual calibration points or of inserting
recalculated calibration data.
Figure 12-8 Calibration View panel

Items on the Calibration View panel
The following controls are available on this panel:
• Graphics Display Toolbar: This toolbar controls display and printing
parameters for the graphs shown on the panel
• Analyte: Select the isotope for which you want to view calibration data
• First/Prev/Next/Last: Use these buttons to view calibration data for the
first, previous, next, or last analyte
• Curve Type: Select the algorithm used to calculate the calibration line.
The options are Simple Linear, Linear Through Zero, and Weighted Linear
• Stats: Click this button to view statistical data on the quality of the
calibration fit, such as the correlation coefficient. When you toggle a point
out of the calibration calculations, the statistics are automatically updated
to reflect the change
• Options: Click this button to change the range of the X- and Y-axes.
Select Display Apparent Concentration in this dialog box to show the
analyte concentration of each point on the calibration curve
Appendix A
Diagnostics Message Reference

This section provides reference tables for the diagnostics parameters used in the system. The first
table provides descriptions of short fault codes and messages that may appear in the Instrument
panel. The second table provides a complete reference of all diagnostics and logging parameters.
• Diagnostics Fault and Status Code Reference on page 305
• Complete Diagnostics Parameter Reference on page 324
Diagnostics Fault and Status Code Reference

This section provides a reference for the fault and status codes that appear on the Diagnostics views
and in the logs. Here you can find meanings for the numeric codes that appear, as well as longer
explanations for some of the shorter messages. Note that not all of these parameters apply to all
instruments.
Note: Codes appearing that have a value of 1000 or more indicate a normal status operation.
component code/message condition

DRC Status RB Open Open: In standard mode
This readback to the ICM
indicates the state of the DRC™
hardware.
Closed Closed: Cell closed; in DRC/KED mode
Pressurizing Pressurizing
Open holdoff Open holdoff: Do not switch from
DRC/KED mode to standard mode; the
plasma is turned off
Vent holdoff Vent holdoff: Do not switch from
DRC/KED mode to standard mode when
the gas is turned off
Venting Venting: Cell is venting while switching
from DRC/KED mode to standard mode
Offline Offline: Cell vent valve is offline
Purge Purge: Cell collision cell gas change;
purge old gas
Fault Condition RB 1 Coolant flow when there should be none;
This readback to the ICM possible bad valve or valve leak
indicates a fault condition.
2 Argon pressure too low
3 Coolant (water) temperature too low
305

4 No or low coolant flow when coolant
valve is open
5 Vacuum pressure fault
6 Interface temperature too high
7 Torch box temperature too high
8 Coolant (water) temperature too high
9 Torch out of position
10 RFG HVPS filament voltage fault
11 Interface gate stuck
12 Global vacuum interlock fault
13 Global plasma interlock fault
14 Duplicate +24V power supply fault;
vacuum gauge supply
15 Duplicate ‐20V power supply fault;
vacuum gauge supply
16 Interface coolant temperature too low
17 QPS heatsink 1 or 2 temperature too high
18 DRC heatsink temperature too high
19 DC voltage power supply fault
20 Ion path voltage fault
21 Flow controller fault
22 Driver monitor fault
23 Turbo or roughing pump fault
24 Lens heatsink temperature too high
25 ICM temperature too high
26 ICP controller fault
27 RF exhaust cover open
28 RF generator thermostat tripped;
temperature too high
29 RF generator tube temperature too high
30 Torch mount out of position
31 Interface door open
32 Exhaust air flow fault; air flow too low
Gas Fault Condition RB 1 Nebulizer gas flow fault: Check gas
This readback to the ICM connection
indicates a mass/pressure flow
controller fault condition.
2 Plasma gas flow fault: Check gas
connection
3 Auxiliary gas flow fault: Check gas
connection
4 Makeup gas flow fault: Check gas
connection
5 Oxygen gas flow fault: Check gas
connection
6 Channel A gas flow fault: Check cell gas
connection
7 Channel B gas flow fault: Check cell gas
connection
8 Getter temperature outside prescribed
range: Check the air intake filter, fan
operation, ambient temperature, and the
exhaust and ventilation systems
9 DRC vent strap position fault: The vent
may not be fully closed. Check LEDs and
the DRC vent mechanism
10 Nebulizer gas flow back pressure fault:
Check gas connection
11 Channel C gas flow fault: Check cell gas
connection
12 Cell gas manifold temperature outside
prescribed range
13 Argon gas manifold temperature outside
prescribed range
ICP Fault Condition RB 1 ICP plate voltage outside prescribed
This readback to the ICM range
indicates a ICP controller fault
condition.
2 ICP plate current outside prescribed
range
3 ICP grid current outside prescribed range
4 ICP filament voltage outside prescribed
range

5 ICP filament current outside prescribed
range
(2000 series instruments) 6 SS‐RFG Q1 current outside prescribed
range
7 SS‐RFG Q2 current outside prescribed
range
8 SS‐RFG Q1 gate voltage outside
prescribed range
9 SS‐RFG Q2 gate voltage outside
prescribed range
10 SS‐RFG oscillation mode gate voltage
outside prescribed range
11 SS‐RFG driven mode gate voltage outside
prescribed range
12 SS‐RFG VDD supply voltage outside
prescribed range
13 SS‐RFG error. This indicates that an error
has been detected in the SS‐RFG system;
to determine the fault, see SS‐RFG
Error/Status RB on page 313, which lists
the related error codes
IPV Fault Condition RB 1 Repellor/QID fault
indicates a ion path voltage
fault condition.
2 AC rod offset (Std mode) fault
3 AC rod offset (DRC mode) fault
4 Deflector box fault
5 Deflector front fault
6 Deflector exit fault
7 Differential pumping aperture fault
9 Attractor lens fault
10 AFT voltage outside prescribed range
11 Detector analog CEM fault
12 Detector pulse CEM fault
13 Detector gate voltage outside prescribed
range
14 Detector analog CEM current fault
15 Detector pulse CEM current fault
16 DRC RF voltage outside prescribed range
17 DRC rod A voltage outside prescribed
range
18 DRC rod B voltage outside prescribed
range
19 DRC RF voltage (DAC) outside prescribed
range
20 DRC DC voltage (DAC) outside prescribed
range
21 DRC rod offset (DAC) fault
22 QPS current outside prescribed range
23 QPS RF detector compensator fault
24 QPS RF detector voltage outside
prescribed range
Monitor Fault Condition 1 Scanning relay failure
RB
indicates a monitor fault
condition.
2 “Ready to scan” relay failure
3 Chiller relay failure (in ACDP)
6 Interface solenoid valve relay failed
7 Interface water solenoid valve failed
9 Interface open solenoid valve failed
10 Oxygen solenoid valve failed
11 DRC cell close solenoid valve failed
12 Interface close solenoid valve failed
13 Argon gas solenoid failed
14 DRC cell open solenoid valve failed
15 Exhaust fan control solenoid failed
16 Roughing pump purge valve failed
24 Purge valve failed
27 Opto‐coupler OUT_D2 failed (turbo
enable)
Motor Task State RB 0 Stopped Stopped
indicates the state of the XYZ
motors.

1 Check torch box Wait for the torch box door to close
before initializing (check the torch box
access door; it may be open)
2 Disengage XYZ stage disengaging
3 Home Z At home Z position
4 Home Y At home Y position
5 Home X At home X position
6 Move to X zero Move to X position zero
7 Move to Y zero Move to Y position zero
8 Move to Z zero Move to Z position zero
9 Ready to move Ready to move
10 Moving X/Z Moving X and/or Z motors
11 Moving Y/Z Moving Y and/or Z motors
12 Waiting Waiting for motion to complete
13 To service Z Moving to service Z position
14 RFG opening Waiting for user to open the RFG access
door
15 At service At service position and door open
16 To interface Moving to interface
17 To service Y Move Y motor to service Y position
(2000 instruments)
18 Unlocked Motors unlocked
19 Locked Motors locked
20 Calibrating Z Calibrating Z
21 Calibrating Y Calibrating Y
22 Calibrating X Calibrating X
23 To interface Y Moving to interface position
(2000 instruments)
24 Service torch At torch service position
255 Failed Failed
Power Fault Condition RB 1 +24V DC power supply fault
indicates a power supply fault
condition.
2 +24V DC power supply motor fault
3 +24V DC power supply turbo drive fault
4 +20V DC power supply fault
5 ‐20V DC power supply fault
7 ‐15V DC power supply fault
9 ICM +3.3V regulator fault
13 QPS board +17V regulator fault
14 QPS board ‐17V regulator fault
21 QPS board +1.8V regulator fault
22 Lens board +550V DC/DC fault
23 Lens board ‐550V DC/DC fault
24 Lens board +275V DC/DC fault
25 Lens board ‐275V DC/DC fault
26 Lens board +5V regulator fault
27 Lens board ‐5V regulator fault
28 Lens board +15V regulator fault
29 Lens board ‐15V regulator fault
30 Vacuum gauge filament voltage outside
prescribed range
Pump Fault Condition RB 1 Turbo rotor speed outside prescribed
This readback to the ICM range
indicates a pump fault
condition.
2 Turbo motor temperature outside
prescribed range
3 Turbo controller temperature outside
prescribed range

4 Turbo bearing temperature outside
prescribed range
5 Turbo motor current outside prescribed
range
9 Roughing pump speed outside prescribed
range
10 Roughing pump current fault
11 Roughing pump voltage fault
12 Roughing pump power fault
14 Roughing pump controller temperature
fault
15 Roughing pump fault
RFG State RB 3 Igniting Igniting plasma
indicates the state of the RF
generator.
4 Plasma on Plasma is on
5 Interlock failure Interlock has failed; FGS PS is off
6 Testing Testing: Igniter or RF generator RF test
RFG Status RB 4 RF generator thermostat trip
indicates the status of the RF
generator.
5 Filament current
6 Filament voltage error
7 Ignition failure; plasma failed to light
within the seven second window
8 Global interlock failure
10 High voltage failure; the actual RF
generator HV PS high voltage output does
not equal the current setpoint
11 RF generator grid current too high:
Contact your local service representative
12 RF generator plate V/I ratio fault: Contact
your local service representative
13 Interface door open: Check the door
position and secure the latch
14 Torch mount open
15 RF exhaust cover open
16 Torch not in place
SS-RFG Error/Status RB 0 RFG and ICM not communicating
This readback to the ICM properly; check connections
indicates the status of the Solid
State RF generator.
(2000 series instruments)
1 RFG power transistor 1 is damaged
2 RFG power transistor 2 is damaged
3 RFG power transistor 1 is running over
the prescribed current
4 RFG power transistor 2 is running over
the prescribed current
5 The RFG power transistor is experiencing
an excessive current imbalance; the
current of transistor 1 is much greater
than the current of transistor 2
6 The RFG power transistor is experiencing
an excessive current imbalance; the
current of transistor 2 is much greater
than the current of transistor 1
7 RFG power transistor 1 cannot be biased
successfully
8 RFG power transistor 2 cannot be biased
successfully
9 The DC power being supplied to the
power transistor is incorrect; ensure that
the RFG breaker is on, and that the fuse
does not need replacing. Also check for
an issue with the DC Power Supply for the
power transistors
10 The value for the low voltage power
supply is incorrect
11 The RFG has overheated. Ensure that the
cooling system is operating properly. If
this error prevents the plasma from
igniting, manually run the coolant for 15
minutes before attempting to ignite the
plasma
12 The RFG has been overcooled

13 The current for RFG transistor 1 was too
low during ignition; internal feedback
components may have failed or
disconnected unexpectedly
14 The current for RFG transistor 2 was too
low during ignition; internal feedback
components may have failed or
disconnected unexpectedly
15 The light sensor is not functioning
properly
16 The light sensor may not be connected
properly
17 The onboard current monitor for RFG
power transistor 1 is not functioning
properly
18 The onboard current monitor for RFG
power transistor 2 is not functioning
properly
19 RFG transistor 1 is failing; the RFG has
shut down to prevent total transistor
failure
20 RFG transistor 2 is failing; the RFG has
shut down to prevent total transistor
failure
99 Unexpected plasma shutoff
100 The RF power output is lower than the
setpoint by more than 5 watts. This is
simply a warning; the RFG is still running
101 The RF power output is higher than the
setpoint by more than 5 watts. This is
simply a warning; the RFG is still running
1000 The RFG is idling and is ready to start the
ignition process
1001 The RFG has received the ignition
request, and is preparing to light the
plasma
1002 The RFG has received the ignition
request, and is in the process of lighting
the plasma
1003 The RFG has ignited the plasma
Roughing Pump Last Error DC bus overvoltage DC bus overvoltage
This readback from the
roughing pump controller to
the ICM indicates an error.
Overcurrent Overcurrent at drive output
IGBT overcurrent IGBT transistor overcurrent
Motor phase lost Loss of motor phase
Overspeed Overspeed
Static position Measured position does not vary; the
encoder is incorrectly connected or not
supplied with power or the shaft is not
turning
A, B, A\, B\ transposed A, B, A\, B\ signals wrong way round
u, v, w transposed u, v, and w commutation signals wrong
way round
U missing Some signals are present, but U signal is
missing
V missing Some signals are present, but V signal is
missing
W missing Some signals are present, but W signal is
missing
Pole pairs wrong The number of pairs of poles set is
incorrect; the revolutions measured
mechanically with A, B and electrically
with U, V, W are inconsistent, given the
number of pairs of poles entered
Autotune fault Autotune fault
Brake res. overload Braking resistor overload I x t
Motor overload Motor overload I x t
IGBT hot IGBT overheating detected by internal
sensor
Brake res. hot Internal braking resistor overheating
detected by thermal sensor
Thermal fault Motor thermal sensor has tripped
+24V PS overload Overload on the +24V power supply or
digital output
ADI1 current lost Loss of the current reference on analog
input ADI1
ADI2 current lost Loss of the current reference on analog
input ADI2

ADIO3 current lost Loss of the current reference on analog
input ADIO3
Serial link lost Loss of serial link communication
EEPROM/XPressKey EEPROM fault or transfer problem with
fault XPressKey
Phase lost Loss of a phase
Stator res. fault Trip during the measurement of the
stator resistance
Fieldbus lost Disconnection of the fieldbus during
operation
Safety fault Safety input fault
Channel U lost Channel U lost
Channel V lost Channel V lost
Channel W lost Channel W lost
Digital fault 1 User trip 1 via digital input
Serial fault 5 User trip 5 via serial link
Roughing Pump Status RB 0 Drive healthy
This readback from the
roughing pump controller to
the ICM indicates the pump
status.
1 Drive active
2 Zero speed
3 Running at or below minimum speed
4 Below set speed
5 At speed
6 Above set speed
7 Load reached
8 Drive output is currently limited
9 Regenerating
10 Braking IGBT active
11 Braking resistor alarm
12 Direction commanded
13 Direction running
14 Mains loss
Turbo Pump Error Code 0 Normal
This readback from the turbo
controller to the ICM indicates
an error code from the turbo
controller.
1 Turbo pump overspeed: Nominal speed
of the pump exceeded by over 10%. The
turbo pump may need to be serviced.
Contact your local service representative.
2 Turbo pump timeout: Maximum time for
passing through critical frequencies has
been exceeded; pump switched off. The
3 Turbo pump bearing over temperature:
Maximum bearing temperature
exceeded; pump switched off. The turbo
pump may need to be serviced. Contact
your local service representative.
4 Turbo pump short circuit: Short circuit in
the pump motor or the connecting cable;
pump switched off. The turbo pump may
need to be serviced. Contact your local
service representative.
5 Turbo pump over temperature:
Maximum temperature for the converter
has been exceeded; pump switched off.
Check the air intake filter, fan operation,
ambient temperature, and the exhaust
and ventilation systems. The turbo pump
may need to be serviced. Contact your
local service representative.

6 Turbo pump timeout: Maximum time
after which the pump must enter its
normal operation mode has been
exceeded; pump switched off. The turbo
7 Turbo pump motor over temperature:
Maximum motor temperature exceeded;
pump switched off. Check the air intake
filter, fan operation, ambient
temperature, and the exhaust and
ventilation systems. The turbo pump may
8 Turbo pump not connected: Pump could
not be identified or no pump is
connected; pump switched off. The turbo
60 Turbo pump short circuit: Short circuit in
the pump motor; pump switched off. The
Bearing temperature warning threshold
exceeded. The turbo pump may need to
be serviced. Contact your local service
representative.
Bearing temperature warning threshold
representative.
101 Turbo pump too slow: The frequency has
dropped below the normal operation
frequency by high load after normal
operation has been reached. The turbo
103 Turbo pump power failure: No power
supply during active operation of the
pump. The turbo pump may need to be
serviced. Contact your local service
representative.
106 Turbo pump too fast: Upper critical limit
frequency exceeded by overload; pump
switched off. The turbo pump may need
to be serviced. Contact your local service
representative.
116 Turbo pump too fast: Maximum overload
time exceeded; pump switched off. The
117 Turbo pump motor current low: No
motor current, or motor current too low;
118 Turbo pump motor connection error:
Error in the motor connection cable;
pump switched off.
125 Turbo pump current too high: Maximum
permissible permanent current
representative.
Error at the bearing temperature sensor.
Resistance out of range; pump switched
off. The turbo pump may need to be
representative.
Error at the bearing temperature sensor.
Resistance not in the plausible range;
128 Turbo pump motor temperature error:
Error at the motor temperature sensor.
Resistance not in the plausible range;

131 Turbo pump high load: Maximum high
load time exceeded; pump switched off.
The turbo pump may need to be
representative.
143 Turbo pump too fast: Pumping speed has
been exceeded by more than 15%; pump
representative.
144 Turbo pump bus error: Incorrect profibus
address; pump switched off. Contact your
145 Turbo pump bus error: Error during cyclic
exchange of data over the Profibus; the
watchdog timer has responded; pump
switched off. Contact your local service
representative.
201 Turbo pump CPU error: Error in the micro
computer; pump switched off. Contact
202 Turbo pump PLL synchronization
warning: Error in the pump speed
synchronization wiring. Contact your
203 Turbo pump invalid value: Internal
parameter value invalid—data error;
pump switched off. Contact your local
205 Turbo pump internal data error: Open
loop; pump switched off. Contact your
207 Turbo pump rotor blocked: Pump
representative.
208 Turbo pump PLL synchronization error:
Pump switched off. Contact your local
212 Turbo pump emergency off activated:
Pump switched off. Contact your local
213 Turbo pump power supply voltage too
high: Pump switched off. The turbo pump
214 Turbo pump power supply voltage too
low: Pump switched off. The turbo pump
216 Turbo pump memory error: Error in
external memory; pump switched off.
217 Turbo pump ID resistor error: Incorrect or
missing pump identification resistor;
pump switched off. Contact your local
222 Turbo pump hardware test error: Pump
representative.
223‐226 Turbo pump logical unit error: Error in
the programmed logical unit; pump
representative.
227 Turbo pump model error: No set of
parameters defined for the recognized
pump model; pump switched off. Contact
Turbo Pump Model RB 0 Turbo pump models TW 220/150, TW
This readback from the turbo 220/150/15
controller to the ICM indicates
the type of turbo pump.
1 Turbo pump models TW 400/300/25S
2 Turbo pump model TW 250S
3 Turbo pump model TW 70 H
4 Turbo pump models TW 300/TW 300 H
Turbo Pump Status RB 0 Normal
This readback to the ICM Pump status: In case of error, t0w has the
indicates the status of the value of 0 (not ready to be switched on)
turbo controller.
1 Ready to turn on
2 Speed increasing
3 Speed decreasing

4 Generator operation
5 Stand‐by
Motorized Vacuum Manifold 0 Position unknown
State RB VAC_VLV_MTR_RESET
This readback indicates the
position or state of the
motorized vacuum manifold
valve
(This will be blank if a
pneumatic vacuum manifold is
installed.)
1 Opening turbo
VAC_VLV_MTR_GOTO_
BACK
2 Turbo open only
VAC_VLV_MTR_BACK_
POS
3 De‐comp O‐ring
VAC_VLV_MTR_GOTO_
EDGE
4 At O‐ring edge
VAC_VLV_MTR_EDGE_
POS
5 Opening all slow
VAC_VLV_MTR_CREEP
6 Opening I/F (opening interface)
VAC_VLV_MTR_GOTO_
INTF
7 I/F open only (interface open only)
VAC_VLV_MTR_INTF_P
OS
8 Opening all fast
VAC_VLV_MTR_GOTO_
OPEN
9 All open
VAC_VLV_MTR_OPEN_
POS
XYZ Motor Control CYC_TST_ON Cycle test on
This software command to the
ICM controls the state of the
XYZ mechanism. When in
Service Mode, click the button
to access the XYZ torch control
dialog box
CYC_TST_OFF Cycle test off
Initialize Initialize
Stop Stop
Relax Relax
Lock X Lock X position
Lock Y Lock Y position
Lock Z Lock Z position
LOCK_XYZ Lock XYZ
Calibrate Calibrate
FACTORY_CAL Reset to factory calibration specifications
SET_IGN_POS Set plasma ignition position
CORR_CAL Correct calibration
SRV_POS 0x50 Send to service position (0x50)
IF_POS Send to interface position
Complete Diagnostics Parameter Reference

This section provides a reference for all diagnostics parameters, organized by system, subsystem,
and component, as they appear in the system diagnostics and logging functions.
sub
system system component description units
Analyzer Aux I/O Aux Device Enable RB This readback from the Aux I/O device NA
to the ICM indicates whether scanning
is enabled or disabled.
Analyzer Aux I/O Ready To Scan This ICM command instructs a relay to NA
enter the Ready to Scan state.
Analyzer Aux I/O Scan Polarity Enable This readback from the Aux I/O device NA
RB to the ICM indicates whether the
external contact closure is normally
open or closed.
Analyzer Aux I/O Scanning This ICM command initiates scanning in NA
an external device.
Analyzer Control +3.3V DC RB This readback from the ICM indicates Volts
the 3.3V local supply reading.
Analyzer Control Cone Access LED This ICM command turns the yellow NA
Yellow Cone Access LED on the front panel On
or Off.
Analyzer Control Cone Access LED This ICM command turns the green NA
Green Cone Access LED on the front panel On
or Off.
Analyzer Control ICM Board Temp. RB This is a readback to the ICM from the C
temperature sensor on the board.
Analyzer Control ICM Interlock LED This ICM command turns all the NA
Test interlock LEDs on the ICM faceplate On
or Off.
Analyzer Control System LED Fault This ICM command turns the red NA
System LED on the front panel On or
Off.
Analyzer Control System LED Ready This ICM command turns the green NA
System LED on the front panel On or
Off.
Analyzer Detector Analog Current RB This readback from the high voltage µAmps
board to the ICM indicates the detector
analog (negative) current.
Analyzer Detector Analog Voltage This is a command from the ICM to the Volts
high voltage board. Adjust the analog
(negative) voltage as required.
system sub component description units
system
Analyzer Detector Analog Voltage RB This readback from the high voltage Volts
analog (negative) voltage.
Analyzer Detector Discriminator This ICM command to the high voltage mVolts
Threshold board sets the discriminator threshold
value. Adjust the value as required.
Analyzer Detector Gate Voltage RB This readback from the high voltage Volts
gate voltage.
Analyzer Detector Pulse Current RB This readback from the high voltage µAmps
pulse (positive) current.
Analyzer Detector Pulse Voltage This ICM command to the high voltage Volts
board sets the pulse (positive) voltage.
Adjust the voltage as required.
Analyzer Detector Pulse Voltage RB This readback from the high voltage Volts
pulse (positive) voltage.
Analyzer DRC AFT This ICM command to the lens board Volts
sets the DRC AFT voltage. Adjust the
voltage as required.
Analyzer DRC AFT RB This readback from the lens board to Volts
the ICM indicates the DRC AFT voltage.
Analyzer DRC Cell Entrance Voltage This ICM command to the lens board Volts
sets the cell entrance voltage. Adjust
the voltage as required.
Analyzer DRC Cell Entrance Voltage This readback from the lens board to Volts
RB the ICM indicates the cell entrance
voltage.
Analyzer DRC Cell Exit Voltage This ICM command to the lens board Volts
sets the cell exit voltage. Adjust the
voltage as required.
Cell Exit Voltage RB This readback from the lens board to Volts
the ICM indicates the cell exit voltage.
Analyzer DRC Channel A Gas Flow This ICM command to the channel A mL/mi
mass flow controller sets the gas flow n
rate. Adjust the flow rate as required.
Analyzer DRC Channel A Gas Flow This readback from the channel A mass mL/mi
RB flow controller to the ICM indicates the n
gas flow rate.

system
Analyzer DRC Channel A Gas Valve This ICM command toggles the channel NA
A solenoid valve between the DRC flow
path and the Standard flow path.
Analyzer DRC Channel B Gas Flow This ICM command to the channel B mL/mi
Analyzer DRC Channel B Gas Flow This readback from the channel B mass mL/mi
gas flow rate.
Analyzer DRC Channel B Gas Valve This ICM command toggles the channel NA
B solenoid valve between the DRC flow
Analyzer DRC Channel C Gas Flow This ICM command to the channel C mL/mi
Analyzer DRC Channel C Gas Flow This readback from the channel C mass mL/mi
gas flow rate.
Analyzer DRC Channel C Gas Valve This ICM command toggles the channel NA
C solenoid valve between the DRC flow
Analyzer DRC Cell Manifold Temp. This readback indicates the C
temperature of the cell manifold in
degrees Celcius.
Analyzer DRC Cell Rod Offset This ICM command sends a cell rod Volts
offset voltage value to the DRC power
supply.
Analyzer DRC Cell Rod Offset RB This readback from the DRC power Volts
supply to the ICM indicates the cell rod
offset voltage setpoint.
Analyzer DRC DC Quad A RB This readback from the DRC power Volts
supply to the ICM indicates the quad A
DC voltage.
Analyzer DRC DC Quad B RB This readback from the DRC power Volts
supply to the ICM indicates the quad B
DC voltage.
Analyzer DRC DC Voltage This ICM command sends a DC voltage Volts
value to the DRC power supply.
Analyzer DRC DC Voltage RB This readback from the DRC power Volts
supply to the ICM indicates the DC
voltage.
system
Analyzer DRC DRC Power Supply This ICM command toggles the DRC NA
power supply between On and Off.
Analyzer DRC DRC Status RB This readback to the ICM indicates the NA
state of the DRC cell.
Analyzer DRC DRC Temp. Status RB This readback from the DRC power NA
supply to the ICM indicates whether
the temperature alarm is OK or has
been triggered. (300/350 series
instruments only).
Analyzer DRC DRC Venting Time This software command to the ICM s
indicates the delay time for switching
from DRC to STD mode. Adjust this
value as required.
Analyzer DRC Getter Heater This ICM command turns the heater on NA
the getter On or Off.
Analyzer DRC Getter Heater This readback to the ICM indicates the s
Running Time RB conditioning time for getter
regeneration.
Analyzer DRC Getter Regeneration This readback to the ICM indicates the NA
RB status of the getter regeneration.
Analyzer DRC Getter Temp. This ICM command sets the getter C
temperature.
Analyzer DRC Getter Temp. RB This readback from the getter C
temperature sensor to the ICM
indicates the getter temperature.
Analyzer DRC Heatsink Temp. RB This readback from the DRC power C
supply to the ICM indicates the
heatsink temperature.
Analyzer DRC Mode This parameter indicates the current NA
operating mode of the software
(Standard, KED, or DRC mode). Select a
new mode as required.
Analyzer DRC RF Detector RB This readback from the DRC power Volts
supply to the ICM indicates the RF
voltage.
Analyzer DRC RF Voltage This ICM command to the DRC power Volts
supply sets a value for the RF voltage.
Analyzer DRC RF Voltage RB This readback from the DRC power Volts
supply to the ICM indicates the RF
voltage setpoint.

system
Analyzer DRC Vent Open/Close This readback indicates the total NA
Cycles number of cell vent open/close cycles.
Analyzer DRC Vent Strap This ICM command instructs the cell NA
venting mechanism to Open or Close.
Analyzer DRC Vent Strap Closed RB This readback from the DRC vent NA
mechanism to the ICM indicates
whether the vent is closed.
Analyzer DRC Vent Strap Open RB This readback from the DRC vent NA
whether the vent is open.
Analyzer Fault Fault Condition RB This readback to the ICM indicates a NA
fault condition.
Analyzer Fault Gas Fault Condition This readback to the ICM indicates a NA
RB mass/pressure flow controller fault
condition.
Analyzer Fault ICP Fault Condition This readback to the ICM indicates a NA
RB ICP controller fault condition.
Analyzer Fault IPV Fault Condition This readback to the ICM indicates a NA
RB ion path voltage fault condition.
Analyzer Fault Monitor Fault This readback to the ICM indicates a NA
Condition RB monitor fault condition.
Analyzer Fault Power Fault This readback to the ICM indicates a NA
Condition RB power supply fault condition.
Analyzer Fault Pump Fault Condition This readback to the ICM indicates a NA
RB pump fault condition.
Analyzer Mass Filter AC Rod Offset This ICM command to the lens board Volts
sets the analyzer quadrupole AC rod
offset voltage. Adjust the voltage as
required (300/350Q instruments only).
Analyzer Mass Filter AC Rod Offset RB This readback from the lens board to Volts
the ICM indicates the analyzer
quadrupole AC rod offset voltage
(300/350Q instruments only).
Analyzer Mass Filter QPS +1.8V DC RB This readback from the QPS board to Volts
the ICM indicates the 1.8V local supply
reading.
Analyzer Mass Filter QPS +12V DC RB This readback from the QPS board to Volts
the ICM indicates the +12V local supply
reading.
system
reading.
reading.
reading.
Analyzer Mass Filter QPS ‐12V DC RB This readback from the QPS board to Volts
the ICM indicates the ‐12V local supply
reading.
reading.
reading.
reading.
Analyzer Mass Filter QPS Amplifier RB This readback from the QPS board to Amps
the ICM indicates the QPS amplifier
current.
Analyzer Mass Filter QPS DC Quad A RB This readback from the QPS board to Volts
the ICM indicates the DC mass voltage
on quad A of the analyzer quadrupole.
Analyzer Mass Filter QPS DC Quad B RB This readback from the QPS board to Volts
the ICM indicates the DC mass voltage
on quad B of the analyzer quadrupole.
Analyzer Mass Filter QPS Dithering This ICM command sets the dithering mAMU
Amplitude setpoint sent to the QPS board.
Analyzer Mass Filter QPS Dithering Switch This ICM command instructs the QPS NA
board to turn dithering On or Off.
Analyzer Mass Filter QPS Heatsink Temp. This readback from the QPS RF NA
Status heatsink temperature sensor to the
ICM indicates whether the
temperature is within normal range.
Analyzer Mass Filter QPS HVDC Quad A RB This readback from the QPS board to Volts
the ICM indicates the high voltage DC
on quad A of the analyzer quadrupole.

system
Analyzer Mass Filter QPS HVDC Quad B RB This readback from the QPS board to Volts
the ICM indicates the high voltage DC
on quad B of the analyzer quadrupole.
Analyzer Mass Filter QPS Modulation This readback from the QPS board to Volts
Amp. RB the ICM indicates the modulation
amplitude that controls dithering.
Analyzer Mass Filter QPS Power Supply This ICM command toggles the NA
quadrupole power supply between On
and Off.
Analyzer Mass Filter QPS RF Detector This readback from the QPS board to Volts
Comp. RB the ICM indicates the RF detector gain.
Analyzer Mass Filter QPS RF Detector RB This readback from the QPS board to Volts
the ICM indicates the RF detector
feedback value.
Analyzer Mass Filter QPS RF Heatsink 1 This readback from the QPS board to C
Temp. RB the ICM indicates heatsink 1
temperature.
Analyzer Mass Filter QPS RF Heatsink 2 This readback from the QPS board to C
Temp. RB the ICM indicates heatsink 2
temperature.
Analyzer Mass Filter QPS RF Output RB This readback from the QPS board to Volts
the ICM indicates the RF voltage.
Analyzer Mass Filter QPS RF Voltage Cal This ICM command sets the RFC ppm
setpoint value at the QPS board.
Analyzer Mass Filter Quad Rod Offset This ICM command sets the Volts
quadrupole rod offset value at the QPS
board.
Analyzer Optics Deflector Attractor This ICM command to the lens board Volts
sets the deflector attractor voltage.
Analyzer Optics Deflector Attractor RB This readback from the lens board to Volts
the ICM indicates the deflector
attractor voltage.
Analyzer Optics Deflector Box This ICM command to the lens board Volts
sets the deflector box voltage. Adjust
the voltage as required.
Analyzer Optics Deflector Box RB This readback from the lens board to Volts
the ICM indicates the deflector box
voltage.
system
Analyzer Optics Deflector Entrance This ICM command to the lens board Volts
Lens sets the deflector entry lens voltage.
Analyzer Optics Deflector Entrance This readback from the lens board to Volts
Lens RB the ICM indicates the deflector entry
lens voltage.
Analyzer Optics Deflector Exit Lens This ICM command to the lens board Volts
sets the deflector exit lens voltage.
Analyzer Optics Deflector Exit Lens RB This readback from the lens board to Volts
the ICM indicates the deflector exit
lens voltage.
Analyzer Optics Deflector Repellor This ICM command to the lens board Volts
sets the deflector repellor voltage.
Analyzer Optics Deflector Repellor RB This readback from the lens board to Volts
the ICM indicates the deflector repellor
voltage.
Analyzer Optics DPA Voltage RB This readback from the lens board to Volts
the ICM indicates the differential
pumping aperture voltage (300/350Q
instruments only).
Analyzer Optics Lens +15V DC RB This readback from the lens board to Volts
the ICM indicates the +15V local lens
board power supply reading.
Analyzer Optics Lens +5V DC RB This readback from the lens board to Volts
Analyzer Optics Lens ‐15V DC RB This readback from the lens board to Volts
the ICM indicates the ‐15V local lens
Analyzer Optics Lens ‐5V DC RB This readback from the lens board to Volts
Analyzer Optics Lens Board Temp. RB This readback from the lens board to C
the ICM indicates the lens board
temperature.
Analyzer Optics Lens PS +275V RB This readback from the lens board to Volts

system
Analyzer Optics Lens PS +550V RB This readback from the lens board to Volts
Analyzer Optics Lens PS ‐275V RB This readback from the lens board to Volts
Analyzer Optics Lens PS ‐550V RB This readback from the lens board to Volts
Analyzer Power +15V DC RB This readback from the low voltage DC Volts
Supply power supply to the ICM indicates the
+15V voltage.
+20V voltage.
+24V voltage.
+5V voltage.
Analyzer Power ‐15V DC RB This readback from the low voltage DC Volts
Supply power supply to the ICM indicates the ‐
15V voltage.
Analyzer Power ‐20V DC RB This readback from the low voltage DC Volts
Supply power supply to the ICM indicates the ‐
20V voltage.
Analyzer Vacuum Chamber High This ICM command turns all of the ion NA
Voltage path high voltage power supplies On or
Off.
Analyzer Vacuum Interface Isolation This ICM command turns the interface NA
Valve isolation valve On or Off.
Analyzer Vacuum Roughing Pump This ICM command turns the roughing NA
pump On or Off.
Analyzer Vacuum Roughing Pump This readback from the roughing pump NA
Alarm to the ICM indicates whether the pump
speed is within normal range.
Analyzer Vacuum Roughing Pump This readback from the roughing pump Ver.
Firmware Version controller to the ICM indicates the
version of roughing pump firmware in
use.
system
Analyzer Vacuum Roughing Pump Ctrl This readback from the roughing pump C
Temp. RB controller to the ICM indicates the
controller temperature.
Analyzer Vacuum Roughing Pump This readback from the roughing pump Amps
Current RB controller to the ICM indicates the
motor current.
Analyzer Vacuum Roughing Pump Duty This readback from the roughing pump %
Cycle RB controller to the ICM indicates the
pump duty cycle as a percentage,
where 100% indicates full power.
Analyzer Vacuum Roughing Pump This readback from the roughing pump hrs &
Hrs.Min RB controller to the ICM indicates how min
long the pump has been running, (hh.mm)
measured in hours and minutes.
Analyzer Vacuum Roughing Pump Last This readback from the roughing pump NA
Error controller to the ICM indicates the last
error registered.
Analyzer Vacuum Roughing Pump This readback from the roughing pump Watts
Power RB controller to the ICM indicates the
motor power.
Analyzer Vacuum Roughing Pump This ICM command instructs the NA
Purge Valve roughing pump purge valve to Open or
Close.
Analyzer Vacuum Roughing Pump This ICM command to the roughing Hz
Speed pump controller sets the pump speed.
Analyzer Vacuum Roughing Pump This readback from the roughing pump RPM
Speed RB controller to the ICM indicates the
pump speed.
Analyzer Vacuum Roughing Pump This readback from the roughing pump NA
Status RB controller to the ICM indicates the
pump status.
Analyzer Vacuum Roughing Pump This readback from the roughing pump Volts
Voltage RB controller to the ICM indicates the
motor voltage.
Analyzer Vacuum Roughing Pump This readback from the roughing pump Years &
Yrs.Days RB controller to the ICM indicates how days
long the pump has been running, (Y.ddd)
measured in years and days.
Analyzer Vacuum Turbo Backing This ICM command turns the turbo NA
Isolation Valve backing isolation valve On or Off.

system
Analyzer Vacuum Turbo Control FW Ver. This readback from the turbo controller NA
to the ICM indicates the converter
software on the turbo controller.
Analyzer Vacuum Turbo Control Hours This readback from the turbo controller hours
RB to the ICM indicates the operating
hours of the turbo controller.
Analyzer Vacuum Turbo Control Temp. This readback from the turbo controller C
RB to the ICM indicates the temperature
of the turbo controller.
Analyzer Vacuum Turbo Control Voltage This readback from the turbo controller Volts
RB to the ICM indicates the controller
supply voltage to the turbo controller.
Analyzer Vacuum Turbo Controller This readback from the turbo controller NA
Model to the ICM indicates the type of turbo
controller.
Analyzer Vacuum Turbo Normal Speed This readback from the turbo controller NA
RB to the ICM indicates whether the turbo
pump has reached normal speed.
Analyzer Vacuum Turbo Pump This ICM command turns the turbo NA
pump On or Off.
Analyzer Vacuum Turbo Pump Bearing This readback from the turbo controller C
Temp. RB to the ICM indicates the temperature
of the turbo pump bearings.
Analyzer Vacuum Turbo Pump Current This readback from the turbo controller Amps
RB to the ICM indicates the turbo pump
motor current.
Analyzer Vacuum Turbo Pump Error This readback from the turbo controller NA
Code to the ICM indicates an error code from
the turbo controller.
Analyzer Vacuum Turbo Pump Model This readback from the turbo controller NA
RB to the ICM indicates the type of turbo
pump.
Analyzer Vacuum Turbo Pump Motor This readback from the turbo controller C
Temp. RB to the ICM indicates the motor
temperature of the turbo pump.
Analyzer Vacuum Turbo Pump Speed This readback from the turbo controller Hz
RB to the ICM indicates the rotor speed
reading at the turbo controller.
Analyzer Vacuum Turbo Pump Speed SP This ICM command to the turbo Hz
controller sets the rotor speed.
system
Analyzer Vacuum Turbo Pump Speed SP This readback from the turbo controller Hz
RB to the ICM indicates the setpoint for
the turbo pump rotor speed.
Analyzer Vacuum Turbo Pump Start This readback from the turbo controller Starts
Counter to the ICM indicates the number of
starts of the turbo pump.
Analyzer Vacuum Turbo Pump Status This readback to the ICM indicates the NA
RB status of the turbo controller
Analyzer Vacuum Vacuum Chamber This ICM command instructs the NA
Vent Valve vacuum purge gas valve to Open or
Close.
Analyzer Vacuum Vacuum Gauge This ICM command turns the vacuum NA
gauge On or Off.
Analyzer Vacuum Vacuum Gauge This readback from the vacuum gauge Volts
Filament RB to the ICM indicates the filament
voltage.
Analyzer Vacuum Vacuum Gauge RB This readback from the vacuum gauge NA
to the ICM indicates whether the
vacuum gauge is OK or in a fault
condition.
Analyzer Vacuum Motorized Manifold This readback indicates the position or NA
State RB state of the motorized vacuum
manifold valve. (This will be blank if a
pneumatic vacuum manifold is
installed.)
Analyzer Vacuum Vacuum Pressure Full This readback from the vacuum gauge Torr
RB to the ICM indicates vacuum pressure
with a resolution of up to 1x10‐7 Torr.
Analyzer Vacuum Vacuum Pressure Low This readback from the vacuum gauge Torr
RB to the ICM indicates vacuum pressure
across a low range with high sensitivity,
with a resolution of up to 1x10‐8 Torr.
Analyzer Vacuum Vacuum Pressure This readback from the vacuum gauge NA
State RB to the ICM indicates whether the
vacuum pressure is OK or in a fault
state.
Analyzer Vacuum Vacuum Start Pressed This input from the system to the ICM NA
indicates whether the Vacuum Start
button is being pressed.
Analyzer Vacuum Vacuum State RB This readback to the ICM indicates the NA
state of the vacuum.

system
Analyzer Vacuum Vacuum Stop Pressed This input from the system to the ICM NA
indicates whether the Vacuum Stop
Analyzer XYZ +24V DC RB This readback from the XYZ control to Volts
the ICM indicates the localized 24V
power supply reading.
Analyzer XYZ +3.3V DC RB This readback from the XYZ control to Volts
the ICM indicates the localized 3.3V
power supply reading. (300/350 series
instruments only)
Analyzer XYZ Motor Control Reg. X This readback from the XYZ mechanism NA
RB to the ICM indicates the status of the
control register for the X horizontal
motor.
Analyzer XYZ Motor Control Reg. Y This readback from the XYZ mechanism NA
control register for the Y vertical motor.
Analyzer XYZ Motor Control Reg. Z This readback from the XYZ mechanism NA
control register for the Z depth motor.
Analyzer XYZ Motor Position X RB This readback to the ICM indicates the Steps
X horizontal motor position by step.
Analyzer XYZ Motor Position X SP This readback indicates the X horizontal Steps
RB motor setpoint position by step.
Analyzer XYZ Motor Position Y RB This readback to the ICM indicates the Steps
Y vertical motor position by step.
Analyzer XYZ Motor Position Y SP This readback indicates the Y vertical Steps
Analyzer XYZ Motor Position Z RB This readback to the ICM indicates the Steps
Z depth motor position by step.
Analyzer XYZ Motor Position Z SP This readback indicates the Z depth Steps
Analyzer XYZ Motor Task State RB This readback to the ICM indicates the NA
state of the XYZ motors.
Analyzer XYZ Torch Position X This ICM command sets the Y mm
horizontal torch position in millimeters.
Adjust the position as required.
Analyzer XYZ Torch Position X RB This readback to the ICM indicates the mm
X horizontal torch position in
millimeters.
system
Analyzer XYZ Torch Position Y This ICM command sets the Y mm
horizontal torch position in millimeters.
Adjust the position as required.
Analyzer XYZ Torch Position Y RB This readback to the ICM indicates the mm
Y vertical torch position in millimeters.
Analyzer XYZ Torch Position Z This ICM command sets the Z depth mm
torch position in millimeters.
Analyzer XYZ Torch Position Z RB This readback to the ICM indicates the mm
Z depth torch position in millimeters.
Analyzer XYZ Motor This readback indicates whether or not NA
Communication the XYZ motor system is
Status communicating correctly. (2000 series
instruments only)
Analyzer XYZ XYZ Motor Control This software command to the ICM NA
controls the state of the XYZ
mechanism. When in Service Mode,
click the button to access the XYZ torch
control dialog box.
Analyzer XYZ Motor Status X This readback indicates the status of NA
the X horizontal torch position motor.
(2000 series instruments only)
Analyzer XYZ Motor Status Y This readback indicates the status of NA
the Y vertical torch position motor.
Analyzer XYZ Motor Status Z This readback indicates the status of NA
the Z depth torch position motor.
Environment Cooling Coolant Flow State RB This readback to the ICM indicates the NA
state of the coolant flow.
Environment Cooling Exhaust Fan This ICM command turns the external NA
exhaust fan relay On or Off.
Environment Cooling Interface Water Flow This ICM command turns the interface NA
water flow On or Off.
Environment Cooling Recirculator This ICM command turns the NA
recirculator contact closure On or Off.
(300/350 series instruments only).
Environment Cooling Cooling Exhaust Flow This readback from the exhaust sensor F/M
RB interlock to the ICM indicates the
exhaust flow rate.

system
Environment Cooling Peltier Cooler Temp. This command sets the temperature C
SP for the PC3 Peltier cooler in degrees
Celcius.
Environment Cooling Peltier Cooler Temp. This readback to the ICM indicates the C
RB temperature of the PC3 Peltier cooler
in degrees Celcius.
Environment Cooling Peltier Cooler Switch This toggle control allows you to turn NA
On or Off the PC3 Peltier cooler on or off.
Environment Interlocks Argon Pressure RB This readback from the incoming gas NA
pressure interlock to the ICM indicates
whether the interlock is OK or in a fault
state.
Environment Interlocks Coolant Flow RB This readback from the water flow Gal/min
meter to the ICM indicates the flow
rate.
Environment Interlocks Coolant Temp. RB This readback from the coolant C
indicates the coolant temperature.
Environment Interlocks Coolant Temp. Status This readback from the main water NA
RB coolant temperature sensor to the ICM
indicates whether the temperature is
within normal range.
Environment Interlocks Exhaust Flow RB This readback from the exhaust sensor NA
interlock to the ICM indicates whether
the exhaust flow is OK or there is
insufficient flow.
Plasma Control Plasma LED This ICM command turns the blue NA
Plasma LED on the front panel On or
Off.
Plasma Control Plasma Start Pressed This input from the system to the ICM NA
indicates whether the Plasma Start
Plasma Control Plasma State RB This readback to the ICM indicates the NA
state of the plasma.
Plasma Control Plasma Stop Pressed This input from the system to the ICM NA
indicates whether the Plasma Stop
Plasma Gas Auxiliary Gas Flow This ICM command to the auxiliary gas L/min
controller sets the auxiliary gas flow
system
Plasma Gas Auxiliary Gas Flow RB This readback from the auxiliary gas L/min
controller to the ICM indicates the
auxiliary gas flow rate.
Plasma Gas Auxiliary Gas Status This readback to the ICM indicates NA
whether the auxiliary gas is On or Off.
Plasma Gas Makeup Gas Flow This ICM command to the makeup gas L/min
mass flow controller sets the makeup
gas flow rate. Adjust the flow rate as
required (300/350 instruments only).
Plasma Gas Makeup Gas Flow RB This readback from the makeup gas L/min
mass flow controller to the ICM
indicates the makeup gas flow rate
(300/350 instruments only).
Plasma Gas Nebulizer Gas Flow This ICM command to the nebulizer gas L/min
controller sets the nebulizer gas flow
Plasma Gas Nebulizer Gas Flow This readback from the nebulizer gas L/min
RB mass flow controller to the ICM
indicates the nebulizer gas flow rate.
Plasma Gas Nebulizer Gas Status This readback to the ICM indicates NA
whether the nebulizer gas is On or Off.
Plasma Gas AMS Gas Flow This ICM command sets the AMS gas L/min
flow rate. Adjust the flow rate as
desired (2000 series instruments only).
Plasma Gas AMS Gas Flow RB This readback indicates the AMS gas L/min
flow rate (2000 series instruments
only).
Plasma Gas AMS Gas Solenoid This ICM command instructs the NA
secondary (AMS) gas solenoid to Open
or Close (2000 series instruments only).
Plasma Gas Oxygen Gas Flow This ICM command to the oxygen gas L/min
mass flow controller sets the oxygen
required.
Plasma Gas Oxygen Gas Flow RB This readback from the oxygen gas L/min
mass flow controller to the ICM
indicates the oxygen gas flow rate.
Plasma Gas Oxygen Gas Solenoid This ICM command instructs the NA
secondary (oxygen) gas solenoid to
Open or Close.

system
Plasma Gas Plasma Gas Flow This ICM command to the plasma gas L/min
mass flow controller sets the plasma
required.
Plasma Gas Plasma Gas Flow RB This readback from the plasma gas L/min
controller to the ICM indicates the
plasma gas flow rate.
Plasma Gas Plasma Gas Status This readback to the ICM indicates NA
whether the plasma gas is On or Off.
Plasma Gas Atmospheric Pressure This readback to the ICM indicates the psia
atmospheric pressure of the gas supply.
Plasma Gas Argon Gas Supply This readback to the ICM indicates the psigf
Pressure pressure of the argon gas.
Plasma Gas Argon Gas Manifold This readback to the ICM indicates the C
Temp. temperature of the argon gas manifold.
Plasma Interface Gate Closed RB This readback from the interface gate NA
whether the gate is closed.
Plasma Interface Gate Open RB This readback from the interface gate NA
whether the gate is open.
Plasma Interface Gate Status RB This readback to the ICM indicates the NA
state of the interface gate.
Plasma Interface Interface Gate This ICM command instructs the NA
interface gate to Open or Close.
Plasma Interlocks Torch Over Temp. This readback from the torch over NA
Switch temperature sensor and the torch
interface switch indicate whether
either control has been tripped. (2000
series instruments only)
Plasma Interlocks Exhaust Cover Door This readback from the exhaust cover NA
Closed RB door interlock to the ICM indicates
whether the door is closed. (300/350
Plasma Interlocks Interface Temp. RB This readback from the interface C
indicates the interface temperature.
Plasma Interlocks Interface Temp. This readback from the interface to the NA
Status RB ICM indicates whether the
system
Plasma Interlocks RFG Temp. RB This readback from the RF generator C
power tube temperature sensor to the
ICM indicates the RF generator
temperature. (300/350 series
instruments only)
Plasma Interlocks RFG Thermostat RB This is a readback to the ICM from the NA
RF generator thermostat interlock.
Plasma Interlocks Torch Box Closed RB This readback from the torch box NA
interlocks to the ICM indicates whether
the torch box/RFG door is closed, or
has rotated to the open position.
Plasma Interlocks Torch Box in Place 1 This readback from the torch box NA
RB interlocks to the ICM indicates whether
torch box interlock 1 is in position or in
a fault state.
Plasma Interlocks Torch Box in Place 2 This readback from the torch box NA
RB interlocks to the ICM indicates whether
torch box interlock 2 is in position or in
a fault state.
Plasma Interlocks Torch Box Rotation This ICM command locks or unlocks the NA
Lock door that allows access to the torch
box, cones, and RF generator. When
unlocked, the door can then be
manually opened. (300/350 series
instruments only)
Plasma Interlocks Torch Box Temp. RB This readback from the torch box C
indicates the torch box temperature.
Plasma Interlocks Torch Box Temp. This readback from the torch box to the NA
Status RB ICM indicates whether the
Plasma Interlocks Torch Mount Position This readback from the torch mount NA
RB interlock to the ICM indicates whether
the torch mount is in operating
position or in a fault state.
Plasma Peristaltic Pump Control This readback from the peristaltic NA
Register RB pump indicates the status of the
control register.
Plasma Peristaltic Pump Speed This ICM command sets the peristaltic rpm
pump speed. Adjust the speed as
required.

system
Plasma RF Last RFG Command This readback to the ICM indicates the NA
Generator RB last command sent to the RF generator.
Plasma RF Power This ICM command sets the RF Watts
Generator generator power value. Adjust the
value as required.
Plasma RF Power RB This readback to the ICM indicates the Watts
Generator actual RF generator power value in
watts.
Plasma RF RFG Cooling Fan This ICM command turns the RFG NA
Generator cooling fan On or Off. (300/350 series
instruments only)
Plasma RF RFG Filament Current This readback from the RF generator to Amps
Generator RB the ICM indicates the filament current.
(300/350 series instruments only)
Plasma RF RFG Filament Voltage This ICM command sets the filament Volts
Generator voltage on the RF generator. (300/350
Plasma RF RFG Filament Voltage This readback from the RF generator to Volts
Generator RB the ICM indicates the filament voltage.
Plasma RF RFG Grid Current RB This readback from the RF generator to mAmps
Generator the ICM indicates the grid current.
Plasma RF RFG Plate Current RB This readback from the RF generator to mAmps
Generator the ICM indicates the plate current.
Plasma RF RFG Plate Voltage RB This readback from the RF generator to Volts
Generator the ICM indicates the plate voltage.
Plasma RF SS‐RFG DC Power This readback from the main external Volts
Generator Supply Voltage RFG DC power supply indicates the
voltage of the solid state RFG.
Plasma RF SS‐RFG Q1 Current This readback from the initial end of A
Generator the load coil indicates the Q1 value in
amps. This must be balanced with the
Q2 reading; they should generally be
within one amp of each other (around
22‐23 amps).
system
Plasma RF SS‐RFG Q2 Current This readback from the far end of the A
Generator load coil indicates the Q2 value in
amps. This must be balanced with the
Q1 reading; they should generally be
within one amp of each other (around
22‐23 amps).
Plasma RF SS‐RFG Temp. This readback from the solid state RFG C
Generator glycol cooling block indicates the
temperature in degrees Celcius. It
should be roughly equal to the
incoming temperature.
Plasma RF SS‐RFG Plasma This optical sensor senses plasma
Generator Brightness Level brightness to determine whether or
not the plasma is lit. The value should
generally be in the 900 range; if it is
unusually low, the plasma may not be
lit.
Plasma RF SS‐RFG Plasma IR This infrared sensor indicates whether NA
Generator Sensor or not the plasma is lit. (Not used)
Plasma RF SS‐RFG VDD Supply This readback indicate s the voltage of Volts
Generator the small driver transistors that power
the main transistors.
Plasma RF SS‐RFG Q1 Gate This readback indicates the Q1 gate Volts
Generator Voltage voltage on the field effect transistors.
Increase the voltage for greater plasma
power.
Plasma RF SS‐RFG Q2 Gate This readback indicates the Q2 gate Volts
Generator Voltage voltage on the field effect transistors.
Increase the voltage for greater plasma
power.
Plasma RF SS‐RFG Driven Mode This readback indicates the voltage of Volts
Generator Gate Voltage the driven mode portion of the hybrid
gate system, which is used to light the
plasma. (Not used)
Plasma RF SS‐RFG Oscillation This readback indicates the voltage of Volts
Generator Mode Gate Voltage the oscillation portion of the hybrid
gate system, which is used to run the
plasma at a set frequency.
Plasma RF SS‐RFG CPU Firmware This readback indicates the firmware NA
Generator Version version number of the RF generator
CPU.

system
Plasma RF RFG State RB This readback to the ICM indicates the NA
Generator state of the RF generator.
Plasma RF RFG Status RB This readback to the ICM indicates the NA
Generator status of the RF generator.
Plasma RF SS‐RFG Error/Status This readback to the ICM indicates a NA
Generator status or fault condition in the SS‐RFG
subsystem. This parameter works in
conjunction with the SS‐RFG
Error/Status Info parameter, which
displays the relevant data for the fault
or status code displayed. See SS‐RFG
Error/Status RB on page 313 for a list
of the related error codes.
Plasma RF SS‐RFG Error/Status This readback to the ICM works in NA
Generator Info conjunction with the SS‐RFG
Error/Status parameter to display the
relevant data for the fault or status
code indicated.
Appendix B
Nano Application
This section provides background information about using the Nano App for
Syngistix™ ICP-MS software.
Note: The Nano App software must be purchased separately and installed together with
the Syngistix for ICP-MS base software. See the Syngistix Installation Guide for details.
• Nano Application for Syngistix™ ICP-MS Software on page 345
• Understanding Nanoparticle Analyses on page 345
• Nano App Software Reference on page 346
• Analysis Screen on page 346
• Results Screen on page 361
Nano Application for Syngistix™ ICP-MS Software

The Nano App is the first commercially available ICP-MS software designed for
fast scanning and nanoparticle analysis. It allows for the characterization of
nanoparticle solutions using the Syngistix for ICP-MS software, and provides a
reliable method of determining the size distribution and composition of inorganic
engineered nanoparticles (ENPs) in complex samples. The Nano App leverages
the NexION instrument's fast data acquisition capabilities, high sensitivity, low
detection limits, and wide dynamic range to allow you to capture the short
transient signal of the nanoparticles. The obtained data is then processed to
distinguish between dissolved and nanoparticle signals, and analyze it for a single
analyte against a prepared nano standard. This methodology is designed to be of
particular use in detecting and characterizing nanoparticles and determining the
toxicity and exposure values of nanomaterials.
Understanding Nanoparticle Analyses

How you set up your nanoparticle analysis depends on the nanoparticle you are
looking for, and the standard solution you are measuring against. If you have a
standard sample containing the analyte in question, with a known particle size,
you can run the particle standard and measure for the characteristics of that
analyte in the standard, and then run your sample and compare your results to
that standard — no Transport Efficiency calculation is required in this case.
However, if your standard solution does not contain the analyte of interest, you
must proceed by using a dissolved calibration and applying the measured
transport efficiency to correct for the differences between the dissolved and
nanoparticle calibrations. However, if you have a standard sample containing the
analyte in question, with a known particle size, you can proceed by using either a
particle calibration, or a dissolved calibration corrected with a transport efficiency
value.
The Transport Efficiency value is a factor that shows the efficacy of the sample
delivery, taking into account loss due to sampling and nebulization; and the
differences between the ion transmission in the case of nanoparticle versus
dissolved solutions. The Transport Efficiency value is used in correcting a
345
dissolved calibration so that it can be used for converting the particle net area
intensity data into size information through a mass flux calibration curve. If this is
required and unknown, you must run at least one standard nanoparticle solution
with a known size or particle concentration. If you are calculating the TE based on
particle size, you can run multiple standards to gather more precise data for your
calibration (it is ideal if one of your standards contains particles close to the size of
the nanoparticles you are looking for).
To reduce the effect of analyte interferences on nanoparticle detection when
developing a method to run in DRC mode, you must adjust three key parameters -
the Gas Flow, RPq, and AFT settings - to suppress noise while allowing
nanoparticle signals to be distinguished from random background fluctuations.
This is especially true when looking at the particles close to the size detection
limits. A high gas flow can reduce background substantially, but if the gas flow is
too high, fluctuations in the dissolved standard can appear as peaks in your
results due to increased disturbance in the ion movement through the pressurized
cell. We recommend that you tune your method by running your nanoparticle
blank and nanoparticle standards as samples, reviewing the results, and
repeating - adjusting the key parameters between each run - until you have
achieved sufficiently low background interference without introducing unwanted
peaks in your particle blank. You can then finalize your cell parameters and begin
your analysis.
Note: Cell gas delays defined in the Syngistix Options dialog box Acquisition Profile tab
are applied to all DRC mode methods used in your nano analyses. All other default
settings configured in the Syngistix Options tabs do not apply to the Nano App methods
and analyses. You must enter all other settings you wish to have apply to your
nanoparticle measurements in the Nano App itself, or within the methods created for it.
Nano App Software Reference

The application has separate screens for nanoparticle analysis setup and data
review and processing.
Analysis Screen
The Nano App Analysis screen provides all the controls needed to set up and run
dissolved and nanoparticle calibrations, and sample characterizations, with
realtime results panels for parsing your data on the fly. It is comprised of three
tabbed sections for Sample analyses, Batch analyses, and Transport Efficiency
(TE) calculations, each of which is divided into several panels:
• Acquisition panel: This panel has different controls for each of the three
tabs, but is generally used to control the acquisition, and run the required
blanks and standards for building calibrations, and samples.
• Method panel: The Method panel is similar across all of the analysis tabs.
Use this panel to load, create, or modify the analytical methods you will
use in your nanoparticle calibrations and analyses. This panel has three
tabs — a Parameters tab, Calibration tab, and a Pump Settings tab
where you configure the various settings.
• Calibration panel: This panel is also similar across all of the analysis
tabs. The Calibration panel displays data, either for an existing loaded
Sample or Transport Efficiency calibration, or in real time, as a calibration
is performed by the software (updated and recalculated continuously over
the course of your analyses).
• Realtime Signal panel: The Realtime Signal panel displays the data and
progress of your measurements as they occur in real time.
• Realtime Histogram panel: This panel displays the calculated intensity
histogram appropriate for the solutions as they are processed.
Figure B-1 Nano App Analysis screen
Acquisition Panel
Use this panel to control the acquisition, and run the required blanks and
standards for building calibrations, and samples. This panel is slightly different for
each of the three analysis tabs; each is illustrated and explained following.
Sample Tab Acquisition Panel
Figure B-2 Nano App Analysis screen Sample Tab Acquisition Panel
Items on the Sample Tab Acquisition Panel
• Start/Stop Pump: Click this toggle control to start or stop the peristaltic
pump.
• Pump speed selector: Type (or click the arrows to select) the peristaltic
pump speed in rpm. Range = ±150 rpm.
• Sample Flow Rate: Type the measured sample flow rate in mL/min,
based on the installed pump tubing size and the selected pump settings.
Range = 0.001 to 3.
• Calibration Group:
 Calibration drop-down list: Select either a Dissolved or Particle
calibration type.
 Analyze Blank: Click to begin analysis of the blank solution.
 Analyze Standard: Click to begin analysis of the specified standard
solution. The number displayed corresponds to the standard solution
row in the Method panel.
• Analyze Sample: In the accompanying field, type the unique name of the
sample to be analyzed, and then click Analyze Sample to begin the
analysis.
• Transport Efficiency: Type the determined Transport Efficiency (TE) as a
percentage.
• Advanced: Click the Advanced button to access the Advanced Options
dialog box, where you can configure a counts override threshold, as well
as range and size settings for the related histogram display. See
Advanced Options Dialog Box on page 352 for more information.
TE Tab Acquisition Panel
Figure B-3 Nano App Analysis screen TE Tab Acquisition Panel

Items on the TE Tab Acquisition Panel
The Transport Efficiency function calculates the efficacy of the sample delivery,
taking into account loss due to sampling and nebulization, to provide the actual
delivery percentage.
pump.
Range = 0.001 to 3.
• Calculation type drop-down list: The TE can be calculated in one of two

ways depending on what is known about your standard solutions. Select
one of the following:
 Calculate based on particle size: To calculate the TE using particle
size, you must run both particle and dissolved standard calibrations;
the TE in this case is equal to:
 Calculate based on particle concentration: To calculate the TE

using particle concentration, you must know either the particle or the
mass concentration of your standard solution.
If you select this option, two additional fields appear at the bottom of
this panel:
— Mass Conc.: Type the mass concentration of the standard solution
in ng/L.
— Part. Conc.: Type the particle concentration of the standard
solution in parts/mL.
You can enter a value into only one of these fields; when you do so, the
other will become disabled.
calibration type.
solution.
 TE: Displays the determined Transport Efficiency as a percentage.
dialog box, where you can configure a counts override threshold.
(Redundant range and size settings for the histogram also appear here,
but have no bearing on the transport efficiency.) See Advanced Options
Dialog Box on page 352 for more information.
Batch Tab Acquisition Panel
Figure B-4 Nano App Analysis screen Batch Tab Acquisition Panel
Items on the Batch Tab Acquisition Panel
• Dataset Folder: This field indicates the name and location of the dataset
where the data from your batch analyses will be saved. Click Browse to
select a dataset folder location.
• Parameters in the Batch Table:
 A/S Loc.: Lists the autosampler position for the sample — the location
that the solution occupies in the autosampler tray. Type the number
corresponding to the position of the solution in the autosampler tray.
 Sample ID: Identifies each sample with a unique name. Type a name
(any alphanumeric combination) to enter an individual Sample ID.
 Measurement Action: Specifies an analysis or control action when
running the given row of the batch. To select an action, click Select
Action. The following options are available:
Run Blank: Runs the specified blank solution. Select either a Particle
or Dissolved solution.
Run Particle Standard: Runs the specified particle standard solution.
Run Dissolved Standard: Runs the specified dissolved standard
solution.
Run Sample: Runs the specified unknown sample solution.
AutoStop: Turns off the plasma automatically following the batch
analysis; this action must be placed last in the batch.
Pause: Pauses the batch analysis until you choose to resume it. Use
this feature when analyzing multiple samples without an
autosampler, or when adjustments are required to obtain the best

histogram curve fit for building a particle calibration.
 Method: Specifies the method to be used for measuring the related
solution. Click Browse to select a method file.
 Sample Flow Rate (mL/min): Type the measured sample flow rate in
mL/min, based on the installed pump tubing size and the selected
pump speed in the pump settings for the read delay. Range = 0.001 to
3.
 Transport Efficiency (%): Type the determined Transport Efficiency
as a percentage.
• Load: Click to load an existing nano batch file.
• Save: Click to save any changes you have made to the nano batch file.
• New: Click to create a new nano batch file.
• Analyze Batch: Performs all the measurement actions specified in the
batch.
Advanced Options Dialog Box
Use the settings in this dialog box to override the specified counts threshold and
customize the displayed histogram fitting range. This dialog box is common to all
of the analysis screen tab Acquisition panels.
Figure B-5 Nano App Analysis screen Advanced Options Dialog Box
Items on the Advanced Options Dialog Box
• Override Threshold: To override the existing counts threshold, select this
check box and type a preferred Counts value for the new threshold.
• Size Histogram Bin Size: Type a size in nm to indicate the size of bin in
which to group displayed histogram data points. Range = 1-100.
• Fixed Range for Size Histogram: To specify a particular fitting range for
the size histogram graphic display, select this check box. Then, in the Start
field, type the lower end of the range you wish to display in nm (range = 0-
29,999). In the End field, type the upper end of the range you wish to
display in nm (range = 1-30,000).The Start value must be lower than the
End value.
Method Panel
Use the Method panel to load, create, or modify the analytical methods you will
use in your nanoparticle calibrations and analyses. This panel is similar across all
of the Analysis screen main tabs.
The Method panel is composed of three tabs — a Parameters tab, Calibration
tab, and a Pump Settings tab.
Figure B-6 Nano App Analysis screen Method panel Parameters tab
Items on the Method Panel Parameters Tab
• Dwell Time and Scan Time: The Dwell Time is the length of time to
measure the analyte during a single reading in microseconds; the Scan
Time is the total acquisition time in seconds. These values are dependent
on one another, but a typical combination is a Dwell Time of 50 µs
(microseconds) with a Scan Time of 100 seconds.
The Dwell Time has an absolute range of 10-50 000 micro seconds, and
the Scan Time has an absolute range of 1-18 000 seconds. However, the
two times are validated against one another to prevent processing lag, so
that the actual values are valid only when the scan time is within the
allowable range for the selected dwell time (and vice versa), and the total
measurements are less than or equal to 6 000 000 data points.
• Conditions File: Unless you specify otherwise, the Nano App uses the
same default.dac Conditions file used by the base Syngistix software. To
define different conditions for your nano analyses, you can modify the
default.dac in Syngistix or create a custom conditions file and save it with
your nano method. If you do this, ensure that you save it with a unique
name to avoid future confusion.
• Analyte information: Select your analyte of interest from the drop-down
list; the table is automatically populated with the information for the most
abundant isotope. Review the remaining columns; generally you will use
the default values as presented; however you can make changes to suit
your needs if required.
 Analyte: Type or select the analyte of interest.
 Mass (amu): The mass of the selected isotope of the analyte of
interest. The most abundant isotope is selected by default, but you
may select an alternate isotope from the drop-down list if desired.
 Density: Type the density of the nanoparticle in g/cm3.
 Mass Fraction (%): Type the mass fraction of the nanoparticle that is
composed of the analyte, expressed as a percentage. A default value
of 100% is typically applied.
 Ionization Efficiency (%): Type the ratio of the ionization efficiency of
the nanoparticle to the ionization efficiency of the corresponding
dissolved analyte solution. A default value of 100% is typically applied.
 RPq: (Rejection Parameter q) Specifies the RF voltage applied to the
reaction cell quadrupole. Range = 0.2 to 0.8.
• Cell Parameters information: UCT instruments only.
 Profile: Select the acquisition profile to be used for the determination—
you can use the default Standard profile or any linked DRC mode
profile currently assigned to a physical gas channel. (You cannot use
unlinked profiles for this application.)
 Gas Flow (mL/min.): Type the desired flow rate for the cell gas
associated with the selected profile. Valid values = 0.1 to 7.288
mL/min. The default value is 0.3 mL/min.
 AFT (V): In DRC mode, the AFT system applies a linearly accelerating
axial field to the ion beam to decrease matrix effects, stabilize the
analyte signal, and increase the speed of the analysis during the
normal operation of the instrument. Type an axial field adjustment
value between ±500. The default value is 350.
The AFT function is especially effective in helping to control event

signal and duration. By increasing the AFT voltage, you can decrease
event duration to better resolve nanoparticle events when analyzing
samples with a high particle concentration. You can also optimize the
average detected event signal by varying the AFT voltage to achieve
the highest possible sensitivity, improving nanoparticle size detection
limits.
• Load: Click to Load an existing nano method.
• Save: Click to Save changes to the current nano method.
• New: Click to create a new nano method. Default values are automatically
populated; make any necessary changes and then save the method under
a unique name.
Figure B-7 Nano App Analysis screen Method panel Calibration tab
Items on the Method Panel Calibration Tab
• Dissolved Standard list: Type the known mass concentration of analyte
for each of your standard dissolved solutions in µg/L. You can define up to
seven standards, as applicable.
• Particle Standard list: Type the known most abundant size of
nanoparticles for each of your standard particle solutions in nm (in the
case of nanoparticles with a Gaussian size distribution, this is also the
mean size). You can define up to seven standards, as applicable.
a unique name.
Figure B-8 Nano App Analysis screen Method panel Pump Settings tab
Items on the Method Panel Pump Settings Tab
This tab displays peristaltic pump parameters for the method. Change the default
settings as necessary to override the pump settings for this nano method:
• Peristaltic Pump table settings:
and 999.
indicates clockwise rotation.
between 0 and 999.
indicates clockwise rotation. The Read Delay Speed is the speed that
will be used during the sample analysis.
acquisition. Type a value between 0 and 999.
cycle. Any value between ±150±150 (2000 series instruments) or ±48
tubing.
manually, using the pump speed control on the Acquisition panel.
a unique name.
Calibration Panel
The Calibration panel displays data, either for an existing loaded Sample or
Transport Efficiency calibration, or in real time, as a calibration is performed by the
software (updated and recalculated continuously over the course of your
analyses). This panel is similar across all of the Analysis screen main tabs.
Settings for the calibration display are configured on a floating Calibration Options
menu that overlays the panel.
Figure B-9 Nano App Analysis screen Calibration panel

Items on the Calibration Panel
• Calibration type drop-down list: Choose to display either Dissolved or
Particle calibration data.
• Sample table:
 Sample: The ID of the blank or standard solution.
 Conc.: (Displayed for Dissolved calibrations only) The mass

concentration of the analyte in the standard solution in µg/L.
 Diameter: (Displayed for Particle calibrations only) The diameter of
the most abundant particle in the standard solution in nm.
 Intensity: (For Dissolved calibrations) The average signal intensity for
the given blank or standard.
 Intensity: (For non-blank Particle calibrations) The most abundant
background subtracted peak area intensity observed for the particle
standard.
Note: To remove an entry from the Sample table, right-click the item and then
click Remove.
• Copy TE Calibration: Click this button to apply the existing Transport

Efficiency calibration to the selected sample calibration type.
• Items on the Calibration Options floating menu:
 Force Through Zero: Select this check box to ensure that the
calibration curve passes through zero. If cleared, the intercept will be
determined using the least squares method.
 Apply Blank Subtraction: Select this check box to subtract the blank
signal from all calibration points.
 Slope: This field displays the rate of change of intensity as a function
of concentration. Read-only.
 Intercept: This field displays the value at which the calibration curve
crosses the intensity axis. Read-only.
 R2: This field displays the coefficient of determination (range = 0-1),
which defines how closely your data aligns to the linear calibration plot
line. Read-only.
• Load: Click to Load an existing nano calibration file.
• Save: Click to Save the selected nano calibration.
Note: Ensure that you save your calibrations with a unique label. For future
reference, it may be useful to include a “particle” or “dissolved” marker to
differentiate the two types of calibration.
• Clear: Click to clear the calibration data currently being displayed.
Realtime Signal Panel
As you run each analysis, the Realtime Signal panel displays the data and
progress of your measurements as they occur.
Figure B-10 Nano App Analysis screen Realtime Signal panel
Realtime Histogram Panel

This panel displays the calculated intensity histogram appropriate for the solutions
being analyzed as they are processed. Settings for this display are configured on
a floating Histogram Options menu that overlays the panel.
Figure B-11 Nano App Analysis screen Realtime Histogram panel

Items on the Realtime Histogram Panel
• Histogram Options floating menu:
 Override: Select this check box to override the existing count
threshold with the value you type in the Override Threshold field.
 Apply: Click this button to apply the new threshold to the histogram
graphic display.
 Send to Results: Click this button to copy the data from this display
into the Results table.
• Zoom Out control: Click the zoom arrows button (arrows pointing out) to
the left of the horizontal slider to zoom out on the histogram display.
• Fitting window slider: Use the sliding window control to select the region of
interest and focus. A line plot of the histogram is plotted below the slider to
help guide you in selecting the region of interest.
For transport efficiency standards using particle concentration, you can

use the fitting window slider to help determine the number of peaks for
calculating the TE. When you select a subset of peaks to focus your area
of interest, the software recalculates and displays the number of actual
particles for the given selection.
•
Results Screen
The Nano App Results screen allows you to review in detail the calculated
histograms and related statistics calculated for each sample or analysis. Here you
can also reprocess your data by modifying the variables used for these
calculations. The following panels comprise the Results screen:
• File Options panel: The File Options panel displays the location of the
saved datasets, and provides some file handling options for each sample.
• Parameters panel: The Parameters panel displays key settings from the
method used for the selected sample or calibration.
• Calibrations panel: The Calibration panel displays the related dissolved
and particle calibration curves; if a transport efficiency value is specified,
the dissolved calibration is converted to a mass flux calibration curve.
• Results Table panel: This panel lists all the blank, standard, and sample
measurements for either the current sample set, or an existing dataset that
has been loaded in this space.
• Histogram panel: The Histogram panel displays the intensity or size
distribution for the selected sample.
Figure B-12 Nano App Results screen
File Options Panel

The File Options panel displays the location of the saved datasets for each
sample. Here you can also load existing datasets from previous measurements;
temporarily import samples from a different location into the Results table; load
dissolved or particle calibration files in order to recalculate the selected sample
profile; and export the calculated data for a single sample or the entire results
table in Microsoft Excel .xls or .xlsx format.
Figure B-13 Nano App Results screen File Options panel

Items on the File Options Panel
• Dataset Folder: Displays the location to which nano dataset files are
saved. Upon opening, it displays the default dataset location:
\\Users\<Public or My> Documents\PerkinElmer Syngistix\ICPMS
\Nano\Dataset. Click Browse to select a new location.
• View Dataset Files: Click to select a set of datasets to view in the current
results table.
• Dissolved Calibration File: Displays the name and location of the
currently loaded dissolved calibration file. Click Load to open an existing
dissolved calibration file for the selected sample.
• Particle Calibration File: Displays the name and location of the currently
loaded particle calibration file. Click Load to open an existing particle
calibration file for the selected sample.
• Export Current Sample: Click Export to export the data from the sample
file currently selected in the Results table, in Microsoft Excel .xls or .xlsx
format.
• Export Results Table: Click Export to export the data in the current
results table in Microsoft Excel .xls or .xlsx format.
Parameters Panel
The Parameters panel displays key settings from the method used for the
selected sample or calibration.
Figure B-14 Nano App Results screen Parameters panel

Items on the Parameters Panel
• Analyte table: Displays the analyte from the original analysis, as well as
its related settings. Depending on the sample type, you can adjust some of
these settings here for reprocessing purposes.
• Cell Parameters information: UCT instruments only. Displays the
acquisition profile used for the original analysis, as well as its related
settings.
• Sample Flow Rate: Displays the sample flow rate from the original
analysis.
• Dwell Time: Displays the dwell time setting from the original analysis.
• Scan Time: Displays the scan time setting from the original analysis.
• Transport Efficiency: Displays the transport efficiency used. You can
adjust the value directly, or, for TE standards, by modifying the calibration
or histogram options. Click Copy to Acquisition to copy the adjusted TE
value to the Transport Efficiency field on the Analysis screen Sample tab
Acquisition panel for later use.
• Threshold: Displays the counts threshold for peak detection for this
sample. If the threshold was overridden for this sample, the accompanying
Overridden check box is selected; if the check box is cleared, the
threshold was calculated for this sample.
Calibrations Panel
The Calibration panel displays the related dissolved and particle calibration
curves; if a transport efficiency value is specified, the dissolved calibration is
converted to a mass flux calibration curve.
Figure B-15 Nano App Results screen Calibrations panel

Items on the Calibrations Panel
• Calibrations Options: Use the controls on this floating menu to adjust the
calibration.
 Force Through Zero: Enable this check box to ensure that the
 Apply Blank Subtraction: Enable this check box to subtract the blank
For dissolved calibrations, this will subtract the blank from all points.
For particle calibrations, this will subtract the blank from the mean
dissolved intensity of the sample.
• Slope: Displays the rate of change of intensity as a function of
concentration or mass.
• Intercept: Displays the value at which the calibration curve crosses the
intensity axis.
• R2: The coefficient of determination (range =0-1). This defines how closely
your data aligns to the linear calibration plot line.
Results Table Panel
This panel lists all the blank, standard, and sample determinations for either the
current sample set, or an existing dataset that has been loaded in this space.
Figure B-16 Nano App Results screen Results Table panel

Items on the Results Table Panel
• Sample: Displays the sample type (sample, standard, or blank) or ID.
• Analyte: Identifies the analyte of interest for this sample.
• Most Frequent Size: The most abundant size of the detected particles in
the selected histogram region, measured in nm.
• Mean Size: The average size of the detected particles in the selected
histogram region, measured in nm.
• No. of Peaks: The number of nanoparticle event peaks detected in the
selected histogram region.
• Mean Inten. (counts): The average area intensity observed for
nanoparticle event peaks in the selected histogram region, measured as
counts per particle (with the background signal subtracted).
• Part. Conc. (parts/mL): Calculated particle concentration in the sample
solution based on the transport efficiency and the number of peaks
detected.
• Diss. Inten. (counts): Background dissolved intensity, calculated as the

average intensity per dwell time observed for detected dissolved
background.
• Diss. Conc. (ppb): Concentration of dissolved background signal in ppb,
calculated from the dissolved intensity, and based on the dissolved
calibration.
• Bin Size (nm): Displays the size of bin in which the data points are
grouped in nm.
• Start (nm): Indicates the lower end of the specified fitting range.
• End (nm): Indicates the upper end of the specified fitting range.
Histogram Panel
The Histogram panel displays the intensity or size histogram for the selected
sample, with data grouped by the selected bin size and plotted linearly along the
x-axis. Settings for this display are configured on a floating Histogram Options
Figure B-17 Nano App Results screen Histogram panel

Items on the Histogram Panel
 Bin Size (nm): Type a size in nm to indicate the size of bin in which to
group displayed histogram data points. Range = 1-100.
 Start (nm): Type the lower end of the fitting range you wish to display
in nm. Range = 0-29,999. The Start value must be lower than the End
value.
 End (nm): Type the top end of the fitting range you wish to display in
nm. Range = 1-30,000. The End value must be greater than the Start
value.
 Apply: Click to apply and save your settings.
 Switch to Dissolved / Switch to Particle toggle button: Click to show
either the dissolved or particle histogram data.
 Fitting options drop-down list: These options allow you manage how
well the calculated curve fits the histogram data. Select the curve type
that best fits the selected region of the histogram data. The available
options are:
 Gaussian: Fits a Gaussian Curve to the Histogram data in the
selected region and selects the maximum of the fitted curve as the
most abundant point observed.
 LogNormal: Fits a LogNormal Curve to the histogram data in the
selected region, and selects the maximum of the fitted curve as the
 Max. Intensity: Selects the point with the maximum frequency in
the selected region as the most abundant point observed.

• Zoom to Fit control: Click the zoom arrows button (arrows pointing in) to
the left of the horizontal slider to zoom to the specified fitting range on the
histogram display.
Appendix C
Single Cell Application

This section provides background information about using the Single Cell App for
Syngistix™ ICP-MS software.
Note: The Single Cell App software must be purchased separately and installed together
with the Syngistix for ICP-MS base software. See the Syngistix Installation Guide for
details.
• Single Cell Application for Syngistix™ ICP-MS Software on page 369
• Single Cell App Software Reference on page 371
• Analysis Screen on page 371
• Results Screen on page 385
Single Cell Application for Syngistix™ ICP-MS Software

The Single Cell App leverages the ability of the Syngistix for ICP-MS system to
perform ultra-rapid, continuous analysis of discrete pulses to foster the complete
ionization of individual cells in a plasma. Measurement of the resulting ions
determines metal levels in each cell; further extrapolation identifies the number
and percentage of cells containing metal within a given sample. This application is
ideal for the rapid detection and analysis of metals in a variety of matrices and
applications, such as determining the intrinsic metal content of cells prior to
sample exposure; measuring the rate of uptake and efficacy of metal-based
treatments; and studying the cellular uptake of nanoparticles in the environment.
Sample Preparation
Before running single cell analyses you must consider the composition of both the
media in which you have cultured your sample cells, and the standard you are
using for your analyses:
• Very complex media (such as RPMI), or those that are very high in salt can
suppress or interfere with the desired signals. In these cases, you may
need to transfer your cells to a less complex medium prior to analysis,
taking into account the amount of time your cells can survive in a less
complex media.
• If your cells must be separated from their exposure media, you will
generally need to wash and centrifuge them before resuspending them in
a fresh solution. We recommend a cycle in which you centrifuge and wash
the cells for at least three cycles, taking the delicacy of the given cells into
account: refer to the literature for your specific cells to determine the
appropriate procedures.
• It is the rapid, continuous measurement capabilities of the ICP-MS that
allows the Single Cell App to detect and analyze each cell individually.
Nevertheless, you may need to dilute samples having a particularly high
concentration of cells or particles, to avoid multiple cells being captured
369
simultaneously. Cell concentrations should ideally be in the 100,000

cell/mL range.
• To provide the most accurate data, cells used for analysis should be
unicellular and not aggregates; this will prevent the nebulizer from
becoming clogged.
• Because not all cells in a given sample will contain metals, you should
calculate the total cell number prior to analysis by flow cytrometry or
hemocytometer before running your analyses.
• For ionic and nanoparticle calibrations, you must match the matrix to the
target particles. In ionic uptake analyses, if the ionic component is very
high, or the uptake is very low, you will need to separate the cells from the
exposure medium to get an accurate measurement.
Optimizing the System for Cell Survival

To maximize the number of viable cells that reach the plasma, consider that the
nebulizer exerts a great deal of pressure on the cells, and several factors affect
the number of cells that survive nebulization and reach the plasma intact. You
need to take into account the delicacy of the cells in question, and then adjust the
nebulizer gas flow and the flow of your sample into the system (the pump speed)
until the optimal conditions for your samples are achieved. To do this, prepare test
cells in a suspension and count viable cells both before and after nebulization,
repeating the process with different settings until you have an acceptable result.
Understanding Transport Efficiency
The Transport Efficiency factor reflects the efficacy of the sample delivery, taking
into account cell loss due to sampling and nebulization, and differences in ion
transmission rates across varying types of solution. The Transport Efficiency
value is used in correcting a dissolved calibration so that it can be used for
converting the sample’s intensity data into mass information. If you require a
transport efficiency determination, you must run at least one standard
nanoparticle solution with a known analyte concentration.
Running Single Cell Analyses in DRC mode

To reduce the effect of elemental interferences on analyte detection when
developing a method to run in DRC mode, you must adjust three key parameters -
the Gas Flow, RPq, and AFT settings - to suppress noise while allowing true
signals to be distinguished from random background fluctuations. This is
especially true when looking at analytes close to the detection limits. A high gas
flow can reduce background substantially, but if the gas flow is too high,
fluctuations in the dissolved standard can appear as peaks in your results due to
increased disturbance in the ion movement through the pressurized cell. We
recommend that you tune your method by running your blank and standards as
samples, reviewing the results, and repeating - adjusting the key parameters
between each run - until you have achieved sufficiently low background
interference without introducing unwanted peaks in your blank. You can then
finalize your DRC parameters and begin your analysis.
Note: Cell gas delays defined in the Syngistix Options dialog box Acquisition Profile tab
are applied to all DRC mode methods used in your single cell analyses. All other default
settings configured in the Syngistix Options tabs do not apply to the Single Cell App
methods and analyses. You must enter all other settings you wish to have apply to your
particle measurements in the Single Cell App itself, or within the methods created for it.
Single Cell App Software Reference
The application has separate screens for cell analysis setup and data review and
processing.
Analysis Screen
The Single Cell App Analysis screen provides all the controls needed to set up
and run dissolved and particle calibrations, and sample characterizations, with
realtime results panels for viewing your data on the fly. It is comprised of three
tabbed sections for Sample analyses, Batch analyses, and Transport Efficiency
(TE) calculations, each of which is divided into several panels.
Figure C-1 Single Cell App Analysis screen

• Acquisition panel: This panel has different controls for each of the three
tabs, but is generally used to control the acquisition, and run the required
blanks and standards for building calibrations, and samples.
• Method panel: The Method panel is similar across all of the analysis tabs.
Use this panel to load, create, or modify the analytical methods you will
use in your particle calibrations and analyses. This panel has three tabs —
a Parameters tab, Calibration tab, and a Pump Settings tab where you
configure the various settings.
• Calibration panel: This panel is also similar across all of the analysis
tabs. The Calibration panel displays data, either for an existing loaded
Sample or Transport Efficiency calibration, or in real time, as a calibration
is performed by the software (updated and recalculated continuously over
the course of your analyses).
• Realtime Signal panel: The Realtime Signal panel displays the data and
progress of your measurements as they occur in real time.
• Realtime Histogram panel: This panel displays the calculated intensity
histogram appropriate for the solutions as they are processed.
Acquisition Panel
Use this panel to control the acquisition, and run the required blanks and
standards for building calibrations, and samples. This panel is slightly different for
each of the three analysis tabs; each is illustrated and explained following.
Sample Tab Acquisition Panel
Figure C-2 Single Cell App Analysis screen Sample Tab Acquisition Panel
Items on the Sample Tab Acquisition Panel
pump.
Range = 0.001 to 3.
calibration type.
solution. The number displayed corresponds to the standard solution
row in the Method panel.
• Analyze Sample: In the accompanying field, type the unique name of the
sample to be analyzed, and then click Analyze Sample to begin the
analysis.
• Transport Efficiency: Type the determined Transport Efficiency (TE) as a
percentage.
TE Tab Acquisition Panel
Figure C-3 Single Cell App Analysis screen TE Tab Acquisition Panel
Items on the TE Tab Acquisition Panel
The Transport Efficiency function calculates the efficacy of the sample delivery,
taking into account loss due to sampling and nebulization, to provide the actual
delivery percentage.
pump.
Range = 0.001 to 3.
• Calculation type drop-down list: The TE can be calculated in one of two

ways depending on what is known about your standard solutions. Select
one of the following:
 Calculate based on particle size: To calculate the TE using particle
size, you must run both particle and dissolved standard calibrations;
the TE in this case is equal to:
 Calculate based on particle concentration: To calculate the TE

using particle concentration, you must know either the particle or the
mass concentration of your standard solution.
If you select this option, two additional fields appear at the bottom of
this panel:
— Mass Conc.: Type the mass concentration of the standard solution
in ng/L.
— Part. Conc.: Type the particle concentration of the standard
solution in parts/mL.
You can enter a value into only one of these fields; when you do so, the
other will become disabled.
calibration type.
solution.
 TE: Displays the determined Transport Efficiency as a percentage.
dialog box, where you can configure a counts override threshold.
(Redundant range and size settings for the histogram also appear here,
but have no bearing on the transport efficiency.) See Advanced Options
Dialog Box on page 376 for more information.
Batch Tab Acquisition Panel
Figure C-4 Single Cell App Analysis screen Batch Tab Acquisition Panel
Items on the Batch Tab Acquisition Panel
• Dataset Folder: This field indicates the name and location of the dataset
where the data from your batch analyses will be saved. Click Browse to
select a dataset folder location.
• Parameters in the Batch Table:
 A/S Loc.: Lists the autosampler position for the sample — the location
that the solution occupies in the autosampler tray. Type the number
corresponding to the position of the solution in the autosampler tray.
 Sample ID: Identifies each sample with a unique name. Type a name
(any alphanumeric combination) to enter an individual Sample ID.
 Measurement Action: Specifies an analysis or control action when
running the given row of the batch. To select an action, click Select
Action. The following options are available:
Run Blank: Runs the specified blank solution. Select either a Particle
or Dissolved solution.
Run Particle Standard: Runs the specified particle standard solution.
Run Dissolved Standard: Runs the specified dissolved standard
solution.
Run Sample: Runs the specified unknown sample solution.
AutoStop: Turns off the plasma automatically following the batch
analysis; this action must be placed last in the batch.
Pause: Pauses the batch analysis until you choose to resume it. Use
this feature when analyzing multiple samples without an
autosampler, or when adjustments are required to obtain the best

histogram curve fit for building a particle calibration.
 Method: Specifies the method to be used for measuring the related
solution. Click Browse to select a method file.
 Sample Flow Rate (mL/min): Type the measured sample flow rate in
mL/min, based on the installed pump tubing size and the selected
pump speed in the pump settings for the read delay. Range = 0.001 to
3.
 Transport Efficiency (%): Type the determined Transport Efficiency
as a percentage.
• Load: Click to load an existing single cell batch file.
• Save: Click to save any changes you have made to the batch file.
• New: Click to create a new single cell batch file.
• Analyze Batch: Performs all the measurement actions specified in the
batch.
Advanced Options Dialog Box
Use the settings in this dialog box to override the specified counts threshold and
customize the displayed histogram fitting range. This dialog box is common to all
of the analysis screen tab Acquisition panels.
Figure C-5 Single Cell App Analysis screen Advanced Options Dialog Box
Items on the Advanced Options Dialog Box
• Override Threshold: To override the existing counts threshold, select this
check box and type a preferred Counts value for the new threshold.
• Mass Histogram Bin Size: Type a size in ag to indicate the size of bin in
which to group displayed histogram data points. Range = 1-5,000 ag.
• Fixed Range for Mass Histogram: To specify a particular fitting range for
the mass histogram graphic display, select this check box. Then, in the
Start field, type the lower end of the range you wish to display in ag (range
= 0-499,999,999). In the End field, type the upper end of the range you
wish to display in ag (range = 1-500,000,000). The Start value must be
lower than the End value.
Method Panel
Use the Method panel to load, create, or modify the analytical methods you will
use in your calibrations and analyses. This panel is similar across all of the
Analysis screen main tabs.
The Method panel is composed of three tabs — a Parameters tab, a Calibration
tab, and a Pump Settings tab.
Figure C-6 Single Cell App Analysis screen Method panel Parameters tab
Items on the Method Panel Parameters Tab
• Dwell Time and Scan Time: The Dwell Time is the length of time to
measure the analyte during a single reading in microseconds; the Scan
Time is the total acquisition time in seconds. These values are dependent
on one another, but a typical combination is a Dwell Time of 50 µs
(microseconds) with a Scan Time of 100 seconds.
The Dwell Time has an absolute range of 10-50,000 micro seconds, and
the Scan Time has an absolute range of 1-18,000 seconds. However, the
two times are validated against one another to prevent processing lag, so
that the actual values are valid only when the scan time is within the
allowable range for the selected dwell time (and vice versa), and the total
measurements are less than or equal to 6,000,000 data points.
• Conditions File: Unless you specify otherwise, the Single Cell App uses
the same default.dac Conditions file used by the base Syngistix software.
To define different conditions for your single cell analyses, you can modify
the default.dac in Syngistix or create a custom conditions file and save it
with your single cell method. If you do this, ensure that you save it with a
unique name to avoid future confusion.
• Analyte information: Select your analyte of interest from the drop-down
list; the table is automatically populated with the information for the most
abundant isotope. Review the remaining columns; generally you will use
the default values as presented; however you can make changes to suit
your needs if required.
 Analyte: Type or select the analyte of interest.
 Mass (amu): The mass of the selected isotope of the analyte of
interest. The most abundant isotope is selected by default, but you
may select an alternate isotope from the drop-down list if desired.
 Density: Type the density of the particle in g/cm3.
 Mass Fraction (%): Type the mass fraction of the particle that is
composed of the analyte, expressed as a percentage. A default value
of 100% is typically applied.
 Ionization Efficiency (%): Type the ratio of the ionization efficiency of
the particle to the ionization efficiency of the corresponding dissolved
analyte solution. A default value of 100% is typically applied.
 RPq: (Rejection Parameter q) Specifies the RF voltage applied to the
reaction cell quadrupole. Range = 0.2 to 0.8.
• Cell Parameters information: UCT instruments only.
 Profile: Select the acquisition profile to be used for the determination—
you can use the default Standard profile or any linked DRC mode
profile currently assigned to a physical gas channel. (You cannot use
unlinked profiles for this application.)
 Gas Flow (mL/min.): Type the desired flow rate for the cell gas
associated with the selected profile. Valid values = 0.1 to 7.288
mL/min. The default value is 0.3 mL/min.
 AFT (V): In DRC mode, the AFT system applies a linearly accelerating
axial field to the ion beam to decrease matrix effects, stabilize the
analyte signal, and increase the speed of the analysis during the
normal operation of the instrument. Type an axial field adjustment
value between ±500. The default value is 350.
The AFT function is especially effective in helping to control event

signal and duration. By increasing the AFT voltage, you can decrease
event duration to better resolve detected events when analyzing
samples with a high particle concentration. You can also optimize the
average detected event signal by varying the AFT voltage to achieve
the highest possible sensitivity, improving detection limits.
• Load: Click to Load an existing single cell method.
• Save: Click to Save changes to the current single cell method.
• New: Click to create a new single cell method. Default values are
automatically populated; make any necessary changes and then save the
method under a unique name.
Figure C-7 Single Cell App Analysis screen Method panel Calibration tab
Items on the Method Panel Calibration Tab
• Dissolved Standard list: Type the known mass concentration of analyte
for each of your standard dissolved solutions in µg/L. You can define up to
seven standards, as applicable.
• Particle Standard list: Type the known most abundant size of particles for
each of your standard particle solutions in nm (in the case of particles with
a Gaussian size distribution, this is also the mean size). You can define up
to seven standards, as applicable. The software converts each value
entered to the corresponding mass in ag, and displays both numbers.
Figure C-8 Single Cell App Analysis screen Method panel Pump Settings tab
Items on the Method Panel Pump Settings Tab
This tab displays peristaltic pump parameters for the method. Change the default
settings as necessary to override the pump settings for this single cell method:
• Peristaltic Pump table settings:
and 999.
indicates clockwise rotation.
between 0 and 999.
indicates clockwise rotation. The Read Delay Speed is the speed that
will be used during the sample analysis.
acquisition. Type a value between 0 and 999.
tubing.
manually, using the pump speed control on the Acquisition panel.
Calibration Panel
The Calibration panel displays data, either for an existing loaded Sample or
Transport Efficiency calibration, or in real time, as a calibration is performed by the
software (updated and recalculated continuously over the course of your
analyses). This panel is similar across all of the Analysis screen main tabs.
Settings for the calibration display are configured on a floating Calibration Options
Figure C-9 Single Cell App Analysis screen Calibration panel

Items on the Calibration Panel
• Calibration type drop-down list: Choose to display either Dissolved or
Particle calibration data.
• Sample table:
 Sample: The ID of the blank or standard solution.
 Conc.: (Displayed for Dissolved calibrations only) The mass
concentration of the analyte in the standard solution in µg/L.
 Mass: (Displayed for Particle calibrations only) The mass of the most
abundant particle in the standard solution in ag.
 Intensity: (For Dissolved calibrations) The average signal intensity for

the given blank or standard.
 Intensity: (For non-blank Particle calibrations) The most abundant
background subtracted peak area intensity observed for the particle
standard.
Note: To remove an entry from the Sample table, right-click the item and then
click Remove.
• Copy TE Calibration: Click this button to apply the existing Transport

Efficiency calibration to the selected sample calibration type.
• Items on the Calibration Options floating menu:
 Force Through Zero: Select this check box to ensure that the
 Apply Blank Subtraction: Select this check box to subtract the blank
 Slope: This field displays the rate of change of intensity as a function
of concentration. Read-only.
 Intercept: This field displays the value at which the calibration curve
crosses the intensity axis. Read-only.
 R2: This field displays the coefficient of determination (range = 0-1),
which defines how closely your data aligns to the linear calibration plot
line. Read-only.
• Load: Click to Load an existing single cell calibration file.
• Save: Click to Save the selected single cell calibration.
Note: Ensure that you save your calibrations with a unique label. For future
reference, it may be useful to include a “particle” or “dissolved” marker to
differentiate the two types of calibration.
• Clear: Click to clear the calibration data currently being displayed.
Realtime Signal Panel
As you run each analysis, the Realtime Signal panel displays the data and
progress of your measurements as they occur.
Figure C-10 Single Cell App Analysis screen Realtime Signal panel
Realtime Histogram Panel

This panel displays the calculated intensity histogram appropriate for the solutions
being analyzed as they are processed. Settings for this display are configured on
a floating Histogram Options menu that overlays the panel.
Figure C-11 Single Cell App Analysis screen Realtime Histogram panel
Items on the Realtime Histogram Panel
 Override: Select this check box to override the existing count
threshold with the value you type in the Override Threshold field.
 Apply: Click this button to apply the new threshold to the histogram
graphic display.
 Fitting options drop-down list: For particle standards only These
options allow you manage how well the calculated curve fits the
histogram data. Select the curve type that best fits the selected region
of the histogram data. The available options are:
 Send to Results: Click this button to copy the data from this display
into the Results table.
• Fitting window slider: For particle standards only Use the sliding window
control to select the region of interest and focus. A line plot of the
histogram is plotted below the slider to help guide you in selecting the
region of interest.

Results Screen
The Single Cell App Results screen allows you to review in detail the calculated
histograms and related statistics calculated for each sample or analysis. Here you
can also reprocess your data by modifying the variables used for these
calculations.
Figure C-12 Single Cell App Results screen

The following panels comprise the Results screen:
• File Options panel: The File Options panel displays the location of the
saved datasets, and provides some file handling options for each sample.
• Parameters panel: The Parameters panel displays key settings from the
method used for the selected sample or calibration.
• Calibrations panel: The Calibration panel displays the related dissolved
and particle calibration curves; if a transport efficiency value is specified,
the dissolved calibration is converted to a mass flux calibration curve.
• Results Table panel: This panel lists all the blank, standard, and sample
measurements for either the current sample set, or an existing dataset that
has been loaded in this space.
• Histogram panel: The Histogram panel displays the intensity or mass
distribution for the selected sample.
File Options Panel

The File Options panel displays the location of the saved datasets for each
sample. Here you can also load existing datasets from previous measurements;
temporarily import samples from a different location into the Results table; load
dissolved or particle calibration files in order to recalculate the selected sample
profile; and export the calculated data for a single sample or the entire results
table in Microsoft Excel .xls or .xlsx format.
Figure C-13 Single Cell App Results screen File Options panel
Items on the File Options Panel
• Dataset Folder: Displays the location to which single cell dataset files are
saved. Upon opening, it displays the default dataset location:
\\Users\<Public or My> Documents\PerkinElmer Syngistix\ICPMS \Single
Cell\Dataset. Click Browse to select a new location.
• View Dataset Files: Click to select a set of datasets to view in the current
results table.
• Dissolved Calibration File: Displays the name and location of the
currently loaded dissolved calibration file. Click Load to open an existing
dissolved calibration file for the selected sample.
• Particle Calibration File: Displays the name and location of the currently
loaded particle calibration file. Click Load to open an existing particle
calibration file for the selected sample.
• Export Current Sample: Click Export to export the data from the sample
file currently selected in the Results table, in Microsoft Excel .xls or .xlsx
format.
• Export Results Table: Click Export to export the data in the current
results table in Microsoft Excel .xls or .xlsx format.
Parameters Panel
The Parameters panel displays key settings from the method used for the
selected sample or calibration.
Figure C-14 Single Cell App Results screen Parameters panel

Items on the Parameters Panel
• Analyte table: Displays the analyte from the original analysis, as well as
its related settings. Depending on the sample type, you can adjust some of
these settings here for reprocessing purposes.
• Cell Parameters information: UCT instruments only. Displays the
acquisition profile used for the original analysis, as well as its related
settings.
• Sample Flow Rate: Displays the sample flow rate from the original
analysis.
• Dwell Time: Displays the dwell time setting from the original analysis.
• Scan Time: Displays the scan time setting from the original analysis.
• Transport Efficiency: Displays the transport efficiency used. You can
adjust the value directly, or, for TE standards, by modifying the calibration
or histogram options. Click Copy to Acquisition to copy the adjusted TE
value to the Transport Efficiency field on the Analysis screen Sample tab
Acquisition panel for later use.
• Threshold: Displays the counts threshold for peak detection for this
sample. If the threshold was overridden for this sample, the accompanying
Overridden check box is selected; if the check box is cleared, the
threshold was calculated for this sample.
Calibrations Panel
The Calibration panel displays the related dissolved and particle calibration
curves. If a transport efficiency value is specified, the dissolved calibration is
converted to a mass flux calibration curve.
Figure C-15 Single Cell App Results screen Calibrations panel

Items on the Calibrations Panel
• Calibrations Options: Use the controls on this floating menu to adjust the
calibration.
 Force Through Zero: Enable this check box to ensure that the
 Apply Blank Subtraction: Enable this check box to subtract the blank
For dissolved calibrations, this will subtract the blank from all points.
For particle calibrations, this will subtract the blank from the mean
dissolved intensity of the sample.
• Slope: Displays the rate of change of intensity as a function of
concentration or mass.
• Intercept: Displays the value at which the calibration curve crosses the
intensity axis.
• R2: The coefficient of determination (range =0-1). This defines how closely
your data aligns to the linear calibration plot line.
Results Table Panel
This panel lists all the blank, standard, and sample determinations for either the
current sample set, or an existing dataset that has been loaded in this space.
Figure C-16 Single Cell App Results screen Results Table panel
Items on the Results Table Panel
• Sample: Displays the sample type (sample, standard, or blank) or ID.
• Analyte: Identifies the analyte of interest for this sample.
• Most Frequent Mass: The most abundant mass of the detected particles
in the selected histogram region, measured in ag.
• Mean Mass: The average mass of the detected particles in the selected
histogram region, measured in ag.
• No. of Peaks: The number of event peaks detected in the selected
histogram region.
• Mean Inten. (counts): The average area intensity observed for event
peaks in the selected histogram region, measured as counts per cell (with
the background signal subtracted).
• Cell Conc. (parts/mL): Calculated cell concentration in the sample based
on the transport efficiency and the number of peaks detected.
• Diss. Inten. (counts): Background dissolved intensity, calculated as the
average intensity per dwell time observed for detected dissolved
background.
• Diss. Conc. (ppb): Concentration of dissolved background signal in ppb,
calculated from the dissolved intensity, and based on the dissolved
calibration.
• Bin Size (ag): Displays the size of bin in which the data points are
grouped in ag.
• Start (ag): Indicates the lower end of the specified fitting range.
• End (ag): Indicates the upper end of the specified fitting range.
Histogram Panel
The Histogram panel displays the intensity or mass histogram for the selected
sample, with data grouped by the selected bin size and plotted linearly along the
x-axis. Settings for this display are configured on a floating Histogram Options
Figure C-17 Single Cell App Results screen Histogram panel

Items on the Histogram Panel
 Bin Size (ag): Type a value in ag to indicate the size of bin in which to
group displayed histogram data points. Range = 1-5,000 ag.
 Start (ag): Type the lower end of the fitting range you wish to display.
Range = 0-499,999,999 ag. The Start value must be lower than the
End value.
 End (ag): Type the top end of the fitting range you wish to display.
Range = 1-500,000,000 ag. The End value must be greater than the
Start value.
 Apply: Click to apply and save your settings.
 Switch to Dissolved / Switch to Particle toggle button: Click to show
either the dissolved or particle histogram data.
 Fitting options drop-down list: These options allow you manage how
well the calculated curve fits the histogram data. Select the curve type
that best fits the selected region of the histogram data. The available
options are:

• Zoom to Fit control: Click the zoom arrows button (arrows pointing in) to
the left of the horizontal slider to zoom to the specified fitting range on the
histogram display.
Appendix D
Calculations & Algorithms

This section provides reference information about a variety of calculations and
algorithms used in the Syngistix for ICP-MS software.
• Slope, Intercept, Standard Deviation and Correlation Coefficient
algorithms for software calibration regressions on page 393
• Standard Addition Calculations on page 398
• Isotope Ratio Calculation on page 396
Note: Additional related sample information is appended at the end of the appendix.
Slope, Intercept, Standard Deviation and Correlation

Coefficient algorithms for software calibration regressions
Variables
A Slope
B Y‐axis intercept
C Number of calibration points (corrected for degrees of freedom)
R Linear correlation coefficient
SigmaA Standard deviation of A
SigmaB Standard deviation of B
Terms used in calculations
Delta Determinant used in calculating A and B
Variance Variance
SumX Sum of X (where X is concentration values of the calibration
standards)
SumY Sum of Y (where Y is intensity values of the calibration
standards)
SumX2 Sum of X*X for all calibration standards
SumY2 Sum of Y*Y for all calibration standards.
SumXY Sum of X*Y values
NumPts Total number of calibration points
Temp Temporary variable
SumW Sum of weights
393
Terms used in calculations
SumWX Sum of W*X for all calibration standards
SumWX2 Sum of W*X*X for all calibration standards
SumWY Sum of W*Y for all calibration standards
SumWY2 Sum of W*Y*Y for all calibration standards
SumWXY Sum of W*X*Y for all calibration standards
Simple Linear Calibration

The slope and intercept are calculated as follows
Delta = SumW * SumX2- SumX * SumX
A = (SumXY * SumW - SumX * SumY) / Delta

B = (SumX2 * SumY - SumX * SumXY) / Delta
Note: For Simple Linear fit, the weight is 1 for each standard and, therefore,
SumW = the number of calibration points.
The standard deviation of the slope and intercept are calculated as follows:
C = NumPts - 2
if (C > 0.0)
Variance =
(SumY2+ B * B * SumW + A * A * SumX2 -2.0*(B * SumY + A * SumXY - B
* A * SumX)) / C
(if (Variance / Delta) < 0.0) then it is an invalid fit.)
SigmaA = (Variance * SumW / Delta)

SigmaB = (Variance * SumX2/ Delta)
(else SigmaA = SigmaB = 0.0)

The correlation coefficient is calculated as follows:
Temp = Delta * (SumW * SumY2- SumY * SumY)
(if (Temp < 0.0) OR (if Temp = 0.0) then it is an invalid fit.)
R = (SumW * SumXY - SumX * SumY)/ Temp
Linear Through Zero Calibration
The slope is calculated as follows:
A = SumXY/ SumX2
The standard deviation of the slope is calculated as follows:
C = NumPts - 1
Variance = (SumY2- SumXY*A) / C

SigmaA = (Variance / SumX2)
R = SumXY / ( SumX2* SumY2)
Weighted Linear Calibration

The slope and intercept are calculated as follows:
Delta = SumW * SumWX2- SumWX * SumWX
A = (SumWXY * SumW - SumWX * SumWY) / Delta

B = (SumWX2 * SumWY - SumWX * SumWXY) / Delta
Note: For Weighted Linear fit, weight for each standard is calculated as 1 / X2 .
SumW = the sum of the weights of all standards.
The standard deviation of the slope and intercept are calculated as follows:
C = NumPts - 2
if (C > 0.0)
Variance =
(SumWY2+ B * B * SumW + A * A * SumWX2 -2.0*(B * SumWY + A *
SumWXY - B * A * SumWX)) / C
(if (Variance / Delta) < 0.0) then it is an invalid fit.)
SigmaA = (Variance * SumW / Delta)

SigmaB = (Variance * SumWX2/ Delta)
(else SigmaA = SigmaB = 0.0)

Temp = Delta * (SumW * SumWY2- SumWY * SumWY)
(if (Temp < 0.0) OR (if Temp = 0.0) then it is an invalid fit.)
R = (SumW * SumWXY - SumWX * SumWY)/ Temp
Isotope Ratio Calculation

The Syngistix software utilizes values derived from each replicate to calculate
statistics for the correction factor, ratio, and ratio fraction. The following are the
primary equations used to perform isotope ratio analyses.
Correction Factor Calculation

An internally calculated correction factor is calculated using a certified standard
as:
CorrFactor = Standard measured ratio
Standard known ratio
where:
Standard Measured Ratio = Net intensity of isotope in Standard
Net intensity of reference isotope in Standard
The Standard Known Ratio is the user entry of the certified ratio for the
Standard
Isotope Ratio Calculation

The correction factor is used to calculate the corrected ratio for samples as
follows:
Corrected ratio = (net intensity of isotope/net intensity of reference isotope)
ratio correction factor
For the fraction and percent formats:

Fraction ratio = Ratio / Sum of ratios in group
Percent ratio = Fraction ratio * 100
Precision
All values in the software are carried in double precision (as double type), as
follows:
Type name Bytes Range of value

double 8 1.7E +/‐ 308 (15 digits)
Standard Deviation
Standard deviation is calculated as the square root of the product between the
variance and the Bessel factor, as follows:
  n 1   n 1  2
   xk2    x k  
  
n 
SD( x )    k  0   
k 0

  n   n    n  1

    

where n = the number of replicates for the sample, and x = Ii or Ni or Ci or Ri
Ii = the intensity for analyte i

Ci = the ratio correction factor for analyte i
Ni = the net intensity for analyte i (Ii - I0); blank intensity subtracted
I0 = the intensity of the blank
Ri = the (calculated) corrected (isotope) ratio
and, n>1
Standard Addition Calculations

Signal Processing
Case 1: Blank subtracted before internal standard
INet = (Ianal – Iblk) / (Istd – Iblk, std)
Case 2: Blank subtracted after internal standard
INet = Ianal/ Istd – Iblk / Iblk, std
Case 3: No internal standard
INet = Ianal– Iblk
where:
INet: intensity used for concentration calculation
Ianal: obtained intensity for the analyte
Istd: obtained intensity for the internal standard
Iblk: obtained blank intensity for the analyte
Iblk, std: obtained blank intensity for the internal standard
Concentration and Standard deviation calculation in Standard
Addition
Intensities are corrected using Step 1.
The Calibration curve is obtained with unspiked sample #1 (unknown #1) and
spiked samples using a simple linear algorithm (see Slope, Intercept, Standard
Deviation and Correlation Coefficient algorithms for software calibration
regressions on page 393 for the calculation of the Simple Linear Calibration
parameters.)
For Standard Addition, the concentration of the spiked samples are listed in the
method and the concentration of the unspiked sample is considered as 0 in order
to generate the calibration curve.
Sheet 2 of the included file Calibration Validation_for Std Add.xls (see the end of
this section for appended Excel sheets) provides an example of analyzing
Unspiked Sample #1 and Unspiked Sample #2 for Pb 208 using standard
addition. The Corrected Intensities in Column 3 Sheet 2 are the Net Intensity
Means from the Syngistix software quantitation reports. Sheet 3 compares the
calculation of the Net Int. Mean (based on 3 replicates) between the Syngistix
software and Excel for Unspiked Sample #1.
For the first unspiked sample:
Cunspiked sample #1 = Iintercept / slope
where:
Cunspiked sample #1: analyte concentration of the unspiked sample #1
Iintercept: intercept of the calibration curve.
For a second unspiked sample immediately analyzed after sample #1, (that is, the
addition calibration), the concentration is calculated using the obtained intensity
directly:
Cunspiked sample #N = Iunspiked sample #N / slope
Cunspiked sample #N: analyte concentration of the unspiked sample #N

Iunspiked sample #N: intensity of the analyte in unspiked sample #N
N >1
The standard deviation of the concentration is calculated as:

SDconc, unspiked = Cunspiked * SDnet intensity / Inet
where:
SDconc, unspiked: standard deviation of the concentration
Cunspiked: mean analyte concentration
SDnet intensity: standard deviation of the net intensity
Inet: mean net intensity
Sheet 3 of the included file Calibration Validation_for Std Add.xls compares the
calculation of the Concentration Standard Deviation between the Syngistix
software and Excel for Unspiked Sample #1.
Calibration Validation for Standard Addition
Sheet 1: Cal. Regr._SL_WL_LZ
(DATA for Rh 103 SIMPLE LINEAR) (DATA for Rh 103 WEIGHTED LINEAR) (DATA for Rh 103 LINEAR Thru ZERO)
Std NumbeStd Conc. Corrrected InteW ELAN SW Std NumbeStd Conc. Corrected Intensity W WX WY ELAN SW Std NumbeStd Conc. Corrected Intensity ELAN SW
STD-1 1 42212.403 1 STD-1 1 42212.403 1.0000 1 42212.4 STD-1 1 42212.403
STD-2 10 399812.175 1 STD-2 10 399812.175 0.0100 0.100 3998.122 STD-2 10 399812.175
STD-3 20 827438.586 1 STD-3 20 827438.586 0.0025 0.0500 2068.596 STD-3 20 827438.586
C 1 C 1 C 2
SumW 3.0000000000000000 SumW 1.0125

SumX 31.000000000000 SumWX 1.15
SumY 1269463.16400000000 SumWY 48279.12122
SumX2 501.0000000000000000 SUMWX2 3.0000000000000000 SumX2 501
SumY2 8.46286E+11 SumWY2 5092021254 SumY2 8.46286E+11
SumXY 20589105.87 SumWXY 123565.5498 SumXY 20589105.87
Variance 137144941.2 Variance 1083564.988 Variance 77987574.57
Delta 542 Delta 1.715
Temp 5.02609E+14 Temp 4844528526
(B)Intercept -4172.023799 -4172.02 (B)Intercept 1595.907507 1595.91 (B)Intercept 0 0

(A)Slope 41354.16888 41354.2 (A)Slope 40576.75206 40576.8 (A)Slope 41096.01971 41096
R 0.999778135 0.999778 R 0.999805789 0.999806 R 0.999907843 0.999908
Sigma B(inter) 11259.24102 11259.2 Sigma B(inter) 1376.753049 1376.75 Sigma B(inter) 0 0
Sigma A(slope) 871.2662284 871.266 Sigma A(slope) 799.8212446 799.821 Sigma A(slope) 394.5425471 394.543
Sheet 2: Std Add_IS_noIS
Calibration Type : STANDARD ADDITION Calibration Type : STANDARD ADDITION (Blk Sub. after Internal Std) for unspiked Sample #1
(DATA for Pb 208 SIMPLE LINEAR) (DATA for Pb 208 SIMPLE LINEAR)
Std NumbeStd Conc. Corrected Intensity W ELAN SW Std Number Std Conc. Corrected Intensit W ELAN SW
((STD-1)) 0 17914.1220743356 1 ((STD-1)) 0 0.1840311119 1.0000000000
STD-2 5 39813.4189591270 1 STD-2 5 0.4471350994 1.0000000000
STD-3 10 80417.0926497383 1 STD-3 10 0.8667962958 1.0000000000
SumW 3.0000000000000000 SumW 3.0000000000

SumX 15.000000000000 SumX 15.0000000000
SumY 138144.63368320100 SumY 1.4979625071
SumX2 125.0000000000000000 SumX2 125.0000000000
SumY2 8372932889 SumY2 0.9851330657
SumXY 1003238.021 SumXY 10.9036384550
Variance 58308951.95 Variance 0.0040850266
Delta 150 Delta 150.0000000000
Temp 9.05229E+11 Temp 106.7261286522
(B)Intercept 14796.72594 14796.7 (B)Intercept 0.1579382438 0.1579380000

(A)Slope 6250.297058 6250.3 (A)Slope 0.0682765184 0.0682765000
R 0.985400389 0.9854 R 0.9913505413 0.9913510000
Sigma B(inter) 6970.709669 6970.71 Sigma B(inter) 0.0583454269 0.0583454000

Sigma A(slope) 1079.897698 1079.9 Sigma A(slope) 0.0090388347 0.0090388300
For Unspk #1 For Unspk #1

(analyzed 2 ppb) (analyzed 2 ppb)
Y= Ax +B Y= Ax +B
when Y=0 then when Y=0 then
conc= b /slope conc= b /slope
conc= 2.367363631 2.367363632 conc= 2.3132146670 2.3132146670
For Unspk #2 For Unspk #2

(analyzed 5 ppb) (analyzed 5 ppb)
conc= Intensity analyte/slope conc= Intensity analyte/slope
conc= 6.3698442798 6.36984428 conc= 6.5488854725 6.5488854725
Sheet 3: Raw Data_Intensity Calc.
Reported by Syngistix Software Reported by Excel
Rep Element Mass Measured Intensity Blank Intensity Net Intensity
BLANK
1
Rh 103 88195.40725456070
Pb 208 740.01916649640
2
Rh 103 86875.35569074810
Pb 208 680.01618438520
3
Rh 103 89877.84433694240
Pb 208 720.01814445720
Meas. Int. Mean Meas. Int. RSD Meas. Int. Mean Meas. Int. RSD
Rh 103 88316.20242741710 1.70397357750 88316.20242741710 1.70397357754
Pb 208 713.35116511290 4.28288639430 713.35116511293 4.28288639434
Rep Element Mass Measured Intensity Blank Intensity Net Intensity Net Intensity
UNSPIKED SAMPLE #1
1
Rh 103 99366.38102235590 88316.20242741710 11050.17859493880 11050.17859493880
Pb 208 18185.56765773140 713.35116511290 17472.21649261850 17472.21649261850
2
Rh 103 95079.35349491070 88316.20242741710 6763.15106749360 6763.15106749360
Pb 208 18826.39699415670 713.35116511290 18113.04582904370 18113.04582904380
3
Rh 103 96621.64974342930 88316.20242741710 8305.44731601220 8305.44731601220
Pb 208 18870.45506645750 713.35116511290 18157.10390134460 18157.10390134460
Intensities Meas. Int. Mean Meas. Int. RSD Blank Intensity Blank Int. RSD Meas. Int. Mean Meas. Int. RSD Blank Intensity Blank Int. RSD
Rh 103 97022.46142023200 2.23807662030 88316.20242741710 1.70397357750 97022.46142023200 2.23807662026 88316.20242741710 1.70397357754
Pb 208 18627.47323944850 2.05790097000 713.35116511290 4.28288639430 18627.47323944850 2.05790097003 713.35116511290 4.28288639434
Concentration
Net Int. Mean Conc. Mean Conc. SD Conc. RSD Net Int. Mean Conc. Mean Conc. SD Conc. RSD
Rh 103 8706.25899281490 -15.75163297460 -3.92863100910 24.94110302980 8706.25899281490 not calc. not calc not calc
Pb 208 17914.12207433560 2.36736363150 0.05065797930 2.13984783010 17914.12207433560 2.36736363131 0.05065797930 2.13984783013
STD-2
1 **(See Sheet 2 for Concentration Calculation)
Rh 103 89318.35171127300 88316.20242741710 1002.14928385590
Pb 208 39875.57458830370 713.35116511290 39162.22342319080
2
Rh 103 88817.24196834260 88316.20242741710 501.03954092560
Pb 208 39791.34020430250 713.35116511290 39077.98903918960
3
Rh 103 88954.08947612970 88316.20242741710 637.88704871270
Pb 208 41913.39558011370 713.35116511290 41200.04441500070
STD-3
1
Rh 103 93752.62828359060 88316.20242741710 5436.42585617350
Pb 208 82324.52494613220 713.35116511290 81611.17378101930
2
Rh 103 93587.55118824800 88316.20242741710 5271.34876083090
Pb 208 81662.74290040330 713.35116511290 80949.39173529040
3
Rh 103 90858.01536580880 88316.20242741710 2541.81293839180
Pb 208 79404.06359801810 713.35116511290 78690.71243290510
Calibration Validation with Internal Standard
Sheet 1: Calibration Regression Calculation
Calculation for Simple Linear Calibration
(Data for Fe 54 with Sc 45 Internal Standard)
Std Number Std Conc. Corrrected Intensity W

STD-5 25 0.03706245268379740 1
STD-6 50 0.11393236810672600 1
STD-7 100 0.18662093588529000 1
STD-8 250 0.45008543230315500 1
STD-9 500 0.88073794897814500 1
STD-10 1000 1.68358544142300000 1
STD-11 2500 4.04042930049130000 1
Calculated with Excel

SumW 7.0000000000000000
SumX 4425.0000000000000000
SumY 7.3924538798714100
SumX2 7575625.0000000000000000
SumY2 20.1869866855939000
SumXY 12362.8342985271000000
Variance 0.0051591053179436
Delta 33448750.0000000000000000
Temp 2898686484.2227000000000000
Calculation for Simple Linear Calibration
(B)Intercept 0.0387732472130817
(A)Slope 0.0016092748360180
SD Intercept 0.0341827095499463
R 0.9997916150559940
Calculation for Linear Through Zero Calibration

Calculated with Excel Calculated by Syngistix
(A)Slope 0.00163192269 0.001631922700
R 0.99970776585 0.999707765800
Sheet 2: Intensity Calc. for Cal Stds
Reported by
Reported by Syngistix Software Calculated by MS Excel Syngistix
Mean Fe Intensity Mean Fe Intensity

Mean Internal Ratioed to Internal Ratioed to Internal Ratioed to
Mean Non-Ratioed Ratioed to Internal Standardized Blank Standard, Blank Standard, Blank Internal Standard,
Rep Element Mass Measured Intensity Blank Intensity Blank Net Intensity Intensity Standard Intensity Subtracted Subtracted Blank Subtracted
Note: Ratioed intensity

calculated using mean values
for blank only. Calculations for
all other sample types done on
1 a per replicate basis.
Sc 45 371292.80931605100 0.18656225220 0.18041829720
Fe 54 69269.22273182700
2
Sc 45 375729.62068981800 0.17699454305
Fe 54 66502.09252256600
3
Sc 45 379635.92042376900 0.17769809635 375552.78347654600
Fe 54 67460.58036397130 67743.96520612140 0.180384670775186000 0.180384670775186000
STD-5
1
Sc 45 380433.73596480400 375552.78347654600 4880.95248825810
Fe 54 84638.83395553390 67743.96520612140 16894.86874941250 0.222479832764790000 0.042095161989604200
2
Sc 45 359129.60353395100 375552.78347654600 -16423.17994259500
Fe 54 76969.56150743020 67743.96520612140 9225.59630130880 0.214322519642004000 0.033937848866817800
3
Sc 45 379048.62485515500 375552.78347654600 3495.84137860920 372870.65478463700
Fe 54 81699.76836421820 67743.96520612140 13955.80315809680 81102.72127572740 0.215539017970156000 0.035154347194970100 0.037062452683797400 0.037062452700
STD-6
1
Sc 45 384622.73228687900 375552.78347654600 9069.94881033300
Fe 54 113306.69792297500 67743.96520612140 45562.73271685450 0.294591786734183000 0.114207115958997000
2
Sc 45 382987.65740952500 375552.78347654600 7434.87393297870
Fe 54 114867.10066415700 67743.96520612140 47123.13545803560 0.299923766319526000 0.119539095544340000
3
Sc 45 388226.30040246800 375552.78347654600 12673.51692592170 385278.89669962400
Fe 54 111978.27175783300 67743.96520612140 44234.30655171150 113384.02344832200 0.288435563592026000 0.108050892816840000 0.113932368106726000 0.113932368100
STD-7
1
Sc 45 380895.81140515100 375552.78347654600 5343.02792860460
Fe 54 145727.96037227100 67743.96520612140 77983.99516614960 0.382592709105071000 0.202208038329885000
2
Sc 45 375523.29882113900 375552.78347654600 -29.48465540740
Fe 54 139531.49325649000 67743.96520612140 71787.52805036890 0.371565475949200000 0.191180805174014000
3
Sc 45 388611.56955775600 375552.78347654600 13058.78608121000 381676.89326134900
Fe 54 134793.27853370300 67743.96520612140 67049.31332758200 140017.57738748800 0.346858634927157000 0.166473964151971000 0.186620935885290000 0.186620935900
STD-8
1
Sc 45 399079.40133567400 375552.78347654600 23526.61785912790
Fe 54 249027.22369507100 67743.96520612140 181283.25848895000 0.624004202826818000 0.443619532051632000
2
Sc 45 385286.26383463900 375552.78347654600 9733.48035809290
Fe 54 237881.57291028800 67743.96520612140 170137.60770416700 0.617415140998602000 0.437030470223416000
3
Sc 45 382551.18937648900 375552.78347654600 6998.40589994260 388972.28484893400
Fe 54 248654.81690141600 67743.96520612140 180910.85169529400 245187.87116892500 0.649990965409603000 0.469606294634417000 0.450085432303155000 0.450085432300
STD-9
1
Sc 45 383215.65300245200 375552.78347654600 7662.86952590550
Fe 54 418715.79994844600 67743.96520612140 350971.83474232500 1.092637517981990000 0.912252847206802000
2
Sc 45 387335.59736132600 375552.78347654600 11782.81388477990
Fe 54 403584.38721416900 67743.96520612140 335840.42200804800 1.041950158889440000 0.861565488114252000
3
Sc 45 389067.74149159600 375552.78347654600 13514.95801505010 386539.66395179100
Fe 54 408046.53688306400 67743.96520612140 340302.57167694300 410115.57468189300 1.048780182388570000 0.868395511613381000 0.880737948978145000 0.880737949000
STD-10
1
Sc 45 396836.17151828000 375552.78347654600 21283.38804173340
Fe 54 740318.21691332000 67743.96520612140 672574.25170719900 1.865551252752210000 1.685166581977030000
2
Sc 45 381109.39792646600 375552.78347654600 5556.61444991940
Fe 54 724845.10509712600 67743.96520612140 657101.13989100400 1.901934481387370000 1.721549810612180000
3
Sc 45 386998.64440554400 375552.78347654600 11445.86092899750 388314.73795009700
Fe 54 706049.84797019500 67743.96520612140 638305.88276407400 723737.72332688000 1.824424602454970000 1.644039931679780000 1.683585441423000000 1.683585441400
STD-11
1
Sc 45 373551.58495008500 375552.78347654600 -2001.19852646100
Fe 54 1525751.15241936000 67743.96520612140 1458007.18721324000 4.084445666649320000 3.904060995874130000
2
Sc 45 387324.29698268300 375552.78347654600 11771.51350613690
Fe 54 1665338.97960420000 67743.96520612140 1597595.01439808000 4.299598534296590000 4.119213863521400000
3
Sc 45 368630.14409541800 375552.78347654600 -6922.63938112810 376502.00867606200
Fe 54 1577146.36538671000 67743.96520612140 1509402.40018059000 1589412.16580342000 4.278397712853550000 4.098013042078360000 4.040429300491300000 4.040429300500
Index
Autodiluters 192
configuring 192
Symbols Autodilution
controls 157
.DAC parameters 137
Autodilution methods 157
AutoLens tab 148
Autosampler tab
quality control 238
A
Acquisition 159
fundamentals of data acquisition 159
peak hop 160 B
scanning 161
signal profile 162 Ball menu 23
Transient signal processing 163
Acquisition Profiles
unlinked 137
Addition calibration 171
Administrator
C
running as 76 Calibrating
Advanced Report View Display custom 143
Options 276 mass calibration 144
Advanced Report View Display Options Mass Calibration window 145
dialog box 278 resolution 144
Analyses 239 what happens 143
autodilution 157 Calibration
data only 159 addition 171
files required 240 Calibration tab 188
isotope dilution 156 Calibration View window 304
isotope ratio 158 external 171
order for UCT instruments 241 external standardization 169
quantitative analysis 155 fundamentals 168
reprocessing 253 quantitative analysis 168
scheduling 48 sample addition 173
techniques 155 standard addition 169
TotalQuant method 155 TotalQuant methods 171
Archiving understanding 303
in Enhanced Security 110 Calibration panel
Argon reports 280
checks 46 Calibration Standards tab
Audit Trails quality control 227
managing in ES 100 Calibration tab
NexION 100 quality control 222
security 103 Cell Parameters tab 141
Auditing Challenge dialog boxes 96
enabling auditing of file deleting in Checksum 255
ES 90 Comments 96
Auto Optimize tab 139 Concentrations
unfactored 273
401
Concentrations tab 268 Dissolved solids limitations 199

Conditions Documentation 15
Conditions panel 132 DRC mode 154
Conditions panel Dual Detector Calibration tab 135
Manual Adjust tab 137 Duplicate tab
Configuring quality control 234
Enhanced Security features 78
Cooling system
checks 46
Correction factor equation 284
Current Sample reports E
options 282
Electronic Signatures 94
Current Sample tab 263
example 265 Elemental library 31
Custom Elemental Library.xml file 31
calibrations 143 Enhanced Security
Custom reports 282 adding project folders 88
approve 105, 107
archiving 110
assigning project folders 89
assigning users to groups 87
challenge dialog boxes 96
D compacting the database 109
DAC 143 defining groups 85
Data defining reasons 94
exporting 288 deleting groups 88
reprocessing 253 deleting users 83
Data acquisition electronic signatures 94
fundamentals 159 enabling auditing of file deletion 90
peak hop 160 ES Tools 98
scanning 161 e-signatures 94, 96
features 74
Data management
file differences 109
checksum 255
file history 105
Data Only methods 159 file versioning 105, 107
Data processing 164 getting started 75
signal profile processing 165 introduction 73
spectral peak processing 164 logging in 76
Datasets logging into ES Setup 77
archiving in ES 110 managing audit trails 100
Dataset panel 257 managing password settings 92
file organization 254 reject 105, 107
Datestamp repairing the database 109
displaying in reports 278 restoring files 112
Deadtime corrections 144 review 105, 107
Defining Reasons for User Operations 94 running as administrator 76
Deleting security audit trail 103
enabling auditing of file deletion 90 selecting features 78
Detector shutdown 202 setting the current project folder 23
Devices setting up users 80
External Read Trigger 192 summary of settings 91
Diagnostics 55, 68, 305 unlocking user names 83
comprehensive 68 view files 105, 107
reference 305 Enhanced security
Service 68 comments 96
Digital to analog converter 143
Dilution tab
quality control 233
Index
Equations Groups
correction factor 284 adding 86
isotope dilution 156 assigning users 87
isotope ratio 158 defining in Enhanced Security 85
sample concentration 156 deleting in Enhanced Security 88
ES Setup
logging in 77
ES Tools
opening 98
overview 98 H
running as administrator 99
Help system
E-Signatures 94
using 16
E-signatures 96
Excel
exporting reports 276
Exporting
current sample reports 288
Exporting reports 276
I
External Read Trigger dialog box 192, Icons 24
193 Ignition
External standards 169 unsuccessful 46
Instrument
diagnostics 55, 68
Instrument window 53
Maintenance tab 56
F Torch Position tab 58
maintenance 56
Faults monitoring 53
reference 305 shutdown 47
FIAS sampling system 207 starting 44
File History 105 starting after extended shutdown 45
Files supported instruments 19
archiving in ES 110 torch position 58
comparing in ES 109 Instrument Diagnostics panel 68
Elemental Library.xml 31 Instrument Parameters panel 149
enabling auditing of deletion in ES 90 Intensity vs Time reports 287
history in ES 105 Interactive window 295
locations 30 Interferences
required for analysis 240 correcting 197, 200
restoring 112
correction examples 202
reviewing in ES 105, 107 dissolved solids limitations 199
sample file format 241 identifying 200
version control in ES 105, 107
isobaric overlaps 198
Folders matrix 197
setting current 23 matrix solvent-induced polyatomic
ions 199
matrix-induced polyatomic ions 199
plasma-induced polyatomic ions 198
spectral 198
G Internal standards 174
Graphs Internal Standards tab 271
Graphics Display toolbar 289 blanks and normalization factors 272
Interactive window 295 Isobaric overlaps 198
Realtime window 291 Isotope dilution 156
working with 289 Isotope ratio methods 158
equation 158
Modes
application 154
K DRC 154
example 154
KED mode 153 KED 153
Standard 153
Multiple software sessions 31
L
LogBook 147, 148
Instrument Parameters panel 149 N
Statistics panel 152 Net Intensities tab 267
Net intensity reports 263
NexION Audit Trail 100
Normalization Factors
in reports 272
M Notes
Maintenance 56 Notes tab 196
maintenance reminders 56
Manual Adjust tab 137
Mass calibration 144
Mass Calibration window 145
Mass discrimination 160 O
Matrix interferences 197 Online help 16
Matrix solvent-induced polyatomic Optimization Parameters
ions 199 unlinked 137
Matrix-induced polyatomic ions 199 Optimizations
Measurement Status dialog box 250 .DAC parameters 137
Menus scheduling 48
icons 24 SmartTune function 115
Syngistix ball menu 23 when to perform 123
Method panel Options
Periodic table 182 Options dialog box tabs 34
Methods 155 Options dialog box 34
analytical techniques 155
autodilution 157
data only 159
External Read Trigger dialog box 192
isotope dilution 156
isotope ratio 158
P
Method panel 175 Peak hop acquisition 160
Calibration tab 188 Peaks 164
Equation tab 185 spectral peak processing 164
External Read Trigger dialog Performance Checks
box 192 LogBook 147
Notes tab 196 Periodic table 182
Processing tab 183 Periodic Table panel 182
Report tab 194 Plasma-induced polyatomic ions 198
Sampling tab 191 Processing
Timing tab 176 data 164
Method panel tabs 175 signal profile processing 165
spectral peak processing 164
quantitative analysis 155
TotalQuant method 155 Profiles
signal profile processing 165
Index
Project Folders Report View window 261

adding in Enhanced Security 88 Reports 261
assigning to users 89 "S" shutdown values 263
Advanced Report View Display Options
dialog box 278
advanced settings 276
blanks 272
Q calibrations 280
concentrations 268
QC Action Controls tab current sample 263
quality control 236 custom 282
QC Measurement Frequency tab decimal places
quality control 225 Decimal Places
QC Standards tab displaying in reports 278
quality control 223
display settings 276
QC Std Internal Standards tab
displaying time and date 278
quality control 226
example 265
QID tab 133 Export button 276
Quality control 213 exporting current sample reports 288
Autosampler tab 238 intensity versus time 287
basic settings 216 internal standards 271
Calibration Standards tab 227 isotope ratio method parameters 284
Calibration tab 222 modifying appearance 283
common controls 218 net intensities 267
Dilution tab 233 normalization factors 272
Duplicate tab 234 raw and net intensities 263
instrument actions and QC raw intensities 266
functions 214 Report panels 261
QC Action Controls tab 236 Report tab 194
QC Measurement Frequency tab 225 Report View panel
QC Standards tab 223 common controls 276
QC Std Internal Standards tab 226 Concentrations tab 268
Quality control tabs 216
Current Sample tab 263
Sample Internal Standards tab 228
Internal Standards tab 271
Sample tab 229
software conventions 216 Net Intensities tab 267
software reference 216 Raw Intensities tab 266
Spike tab 231 Unfactored Concentrations
Spike Tables tab 235 tab 270, 273, 275
workflow 213 RSDs 276
Quantitative analysis 155 sorting 278
summary 287
templates 282
unfactored concentrations 270, 273,
275
R views 262
windows 261
Raw and net intensity reports 263 Reprocessing data 253
Raw Intensities tab 266 Resolution 144, 145
Read triggers 192 Restoring Files 112
Realtime window 291 Review Files dialog box 50
Reminders Review Files function 50
maintenance 56 Ribbon menu 24
Report Options panel 282 RSDs
Report Options window 261 showing in reports 276
Report View
Calibration panel 280
Report View panel 262
Software reference
Calibration View window 304
S Conditions panel 132
Dataset panel 257
Sample addition calibration 173 FIAS sampling system setup 208
Sample concentration 156 Graphics Display toolbar 289
sample concentration equation 156 Instrument window 53
Sample Internal Standards tab Interactive window 295
quality control 228 LogBook panel 148
Sample tab Mass Calibration window 145
quality control 229 Measurement Status dialog box 250
Sample units 190 Method panel 175
Samples Quality Control tabs 216
analyzing 239 Realtime window 291
creating a sample file with a text Report panels 261
editor 241 Review Files dialog box 50
Sample window 244 Sample window 244
Batch tab 245 Scheduler screen 49
Manual tab 244 SmartTune window 127
Sampling tab 191 Software sessions
multiple 31
Sampling Devices 192
external 192 Spectral interferences 198
FIAS 192 Spectral peak processing 164
Sampling systems 207 Spectral scanning 160
checks 47 Spike tab
FIAS 207 quality control 231
Scanning acquisition 161 Spike Tables tab
Scheduler function 48 quality control 235
Scheduler screen 49 Standard addition calibration 169
Security Standard mode 153
introduction to Enhanced Security 73 Standards
Security Audit Trail 103 external 169
Service internal 174
diagnostics 68 Starting
Sessions 31 after extended shutdown 45
instrument 44
Set Current Project Folder 23
software 44
Shutdown
Statistics panel 152
instrument 47
software 48 Status
reference 305
Shutdown values 263
Status bar 23
Signal
steady state 162 Steady state 162
Signal profile 162 Summary reports 287
Signal profile processing 165 Syngistix ball menu 23
Signature dialog box 94 Syngistix LogBook 148
Signature Points Syngistix Options dialog box 34
defining 94 System View panel 54
Signatures 96 Diagnostics tab 55
SmartTune function 115
default files 117
software reference 127
understanding 117
Software T
exiting 48 Templates
file locations 30 report templates 282
starting 44 Time vs Intensity reports 287
Timestamp
displaying in reports 278
Torch Position 58
Torches
checks 47
TotalQuant methods 155
calibration 171
Transient signal processing 163
Troubleshooting
ignition unsuccessful 46
Tuning
SmartTune function 115
U
UCT instruments
analysis order 241
Unfactored Concentrations tab 270, 273, 275
Units
concentrations 190
sample units 190
Unlinked profiles 137
Users
defining reasons for operations in ES 94
deleting in Enhanced Security 83
setting up in Enhanced Security 80
unlocking in Enhanced Security 83
Utilities
ES Setup 77
ES Tools 98
W
Workspaces
Review Files dialog box 50

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Syngistix™ Software for ICP-MS v.2.

Syngistix for ICP-MS software release April 2014

Syngistix for ICP-MS software Enhanced Security March 2015

Syngistix for ICP-MS software 2.0 October 2016

Syngistix for ICP-MS software 2.1 to support 2000 HW January 2017

Syngistix for ICP-MS software 2.2 to support April 2017

NEXION, PERKINELMER, PKI, PLASMALOK, and TOTALCHROM are registered trademarks

Chapter 1 Introduction to the Software . . . . . . . . . . . . . . . . . . . . .19

To start the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Chapter 2 Instrument and Device Control . . . . . . . . . . . . . . . . . . . 53

Getting Started — Administrator’s guide . . . . . . . . . . . . . . . . . . . . . .75

Repairing and compacting the databases. . . . . . . . . . . . . . . . . . . . . . 109

Chapter 4 Optimization Processes . . . . . . . . . . . . . . . . . . . . . . . . 115

Items on the Instrument Parameters panel Conditions tab . . . . . .150

Chapter 5 Method Development . . . . . . . . . . . . . . . . . . . . . . . . . .153

Report Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Chapter 6 Interference Correction . . . . . . . . . . . . . . . . . . . . . . . . 197

Chapter 7 Sampling Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

Chapter 8 Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

Sample Internal Standards Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

Chapter 9 Sample Preparation and Analysis . . . . . . . . . . . . . . . .239

Chapter 10 Data Reprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . .253

Chapter 11 Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .261

Net Intensities tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Appendix A Diagnostics Message Reference . . . . . . . . . . . . . . . 305

Understanding Nanoparticle Analyses . . . . . . . . . . . . . . . . . . . . . . . . . 345

Appendix C Single Cell Application . . . . . . . . . . . . . . . . . . . . . . .369

Items on the Method Panel Pump Settings Tab . . . . . . . . . . . . . . 380

Appendix D Calculations & Algorithms . . . . . . . . . . . . . . . . . . . . 393

Using this Software Reference Guide

Using the Help System

relationship between search terms. If no operator is specified, AND is used. For

To search for Use Example Results

Introduction to the Software

Supported Instrument Configurations

NexION® 2000 Series

nebulizer; ESI FastValve; ESI micropump; broad temperature spray

2000B 2000C 2000P 2000S

NexION® 2000B Base UCT Instrument

NexION® 2000P Productivity UCT Instrument

NexION® 300/350 Series

Software Layout and Organization

 Mass Calibration tuning file (.tun)

The arrow submenu provides access to the Report Options screen, where you

The CalibView icon accesses the Calibration View screen, where you analyze

The Review icon accesses the Review Files dialog box, where you load and

Navigating the Software

Syngistix ball menu Ribbon menu

Quick Access toolbar panels Help button

status bar click to expand Measurement Status

The Elemental Library

Multiple Software Sessions

During an Edit/Reprocess session, there is no access to the functions on the

Understanding Acquisition Profiles

Flexible profile and parameter configuration

• Unlinked DAC parameter option (blue)

Figure 1-2 Acquisition Profiles

Syngistix Options System Configuration

Syngistix Options Dialog Box Tabs

Figure 1-3 Syngistix Options dialog box Configuration tab

Items on the Configuration tab

Note: If you choose Oxygen here, the related parameters on the

pneumatic and (Version 2) motorized. Read only — the system