Release Notes

ESI Compass 1.3 SR1 for amaZon

ESI Compass 1.3 SR1 for amaZon

Release Notes

Contents

1 Overview....................................................................................................................................2
1.1 Introduction.........................................................................................................................2
1.2 Using this document............................................................................................................2
1.3 Methods..............................................................................................................................2
1.4 Manuals..............................................................................................................................2
1.5 Operating Systems..............................................................................................................2
1.6 Software Configurations......................................................................................................2
2 Installation.................................................................................................................................3
2.1 General ..............................................................................................................................3
2.2 First time Installation...........................................................................................................3
2.3 Additional Installations.........................................................................................................6
3 Software Issues.........................................................................................................................6
3.1 Data Acquisition (HyStar 3.2 SR2)......................................................................................6
3.2 Data Processing (HyStarPP 3.2 SR2).................................................................................7
3.3 Data Acquisition (trapControl 7.0).......................................................................................8
3.4 Data Processing (DataAnalysis 4.0 SP2)............................................................................8
3.5 LibraryEditor 4.0..................................................................................................................8
3.6 QuantAnalysis 2.0...............................................................................................................9
3.7 Report Designer 4.5............................................................................................................9

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Release Notes
ESI Compass 1.3 SR1 for amaZon

1 Overview
1.1 Introduction
Description: This document provides information on how to install the product. In addition
information is given about certain limitations currently found in the ESI Compass 1.3 SR1 for
amaZon software comprising data acquisition, general data processing, QuantAnalysis and
HyStar software
ESI Compass 1.3 SR1 for amaZon supports the amaZon ETD, amaZon X and amaZon SL
instruments.

1.2 Using this document

This document should be reviewed with the key instrument operator during installation of the
ESI Compass 1.3 SR1 for amaZon software.

1.3 Methods
Application methods for some special use cases and ETD Tuning are included in the installation.
They can be opened from trapControl menu item ‘Method – New’.

1.4 Manuals
Several manuals are installed within ESI Compass 1.3 SR1 for amaZon software. These provide
an overview for performing several key tasks and analysis with the amaZon instruments and ESI
Compass 1.3 SR1 for amaZon software. These additional documents should answer most
questions. The manuals will be installed automatically during standard installation. You can open
them from the Windows start menu ‘Start -> Programs -> Bruker Daltonics ' folder and from the
'Start -> Programs -> Bruker Daltonics -> HyStar -> Hyphenation Guide’ menu item.

1.5 Operating Systems

The following operating systems are supported:
Windows XP Professional SP 3, US-English (Firewall disabled)
All other operating systems or languages are not supported.
Please Note: The Microsoft .NET Framework 1.1 and Microsoft .NET Framework 1.1 Hotfix
(KB886903) are required.

1.6 Software Configurations

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Release Notes
ESI Compass 1.3 SR1 for amaZon

ESI Compass 1.3 SR1 for amaZon software includes the following components:
HyStar 3.2 SR2 (Build 44)
trapControl 7.0 (Build 655)
DataAnalysis 4.0 (Build 234)
DataAnalysis 4.0.SP2 (Build 274)
LibraryServer 2.0.SP2 (Build 274)
ESI Tutorial Data 1.0 (Build 37)

2 Installation

2.1 General
• ESI Compass 1.3 SR1 for amaZon is tested and released for PCs delivered by
Bruker Daltonics with the amaZon instruments.
• It is not possible to install and run different versions of Compass software side-by-
side.
• You will need administrator permissions under Windows XP to install the software.
• ESI Compass 1.3 SR1 for amaZon software also supports Windows 'User'.
• Hard disk drive partitions – following partitions are required:
• Drive letter C: This partition contains the operating system and the Compass software.
• Drive letter D: It is recommended that this drive partition should be used for the storage
of all Method and Data files. It should be the largest partition.

2.2 First time Installation

2.2.1 Installing ESI Compass 1.3 SR1 for amaZon on an acquisition PC:
• The 'Compass ' DVD Browser will be launched automatically on loading the DVD into the
DVD-ROM drive. In the event that the browser does not open automatically you can start
it by clicking on ‘Launch.exe’ in the root directory of the DVD.
• First select 'Install', then click on 'trapControl 7.0’. (Make sure, the MS is switched on and
connected to the PC via LAN.)
• The 'trapControl 7.0’ setup dialog will pop up. Press the "Next" button and follow the
instructions.
• When you are asked to enter the setup type, it is recommended to select online and
complete and follow the instructions. When the "Set Data Path to" dialog opens, you will
have the option to change the path for your data. e.g. set your data path to D:\Data.
(recommended)

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• When the "Set Method Path to" dialog opens, you will have the option to change the path
for your methods. e.g. set your method path to D:\Methods. (recommended)
• When the 'Create Desktop Icons' dialog opens, you can check the check-box to get a
shortcut for trapControl on the desktop.
• When you are asked to load new firmware, choose yes.
• After completing the trapControl installation select 'Install' and 'HyStar 3.2' in the browser.
• When you are asked to enter the destination folder you have the option to change it. It is
recommended that installation is carried out on drive C.
• When the 'Create Desktop Icons' dialog opens, you can check the check-box to get a
shortcut for HyStar, HyStarPP and Hyphenation Guide on the desktop.
• When you are asked to enter the setup type, it is recommended that you select 'Typical'. If
you choose 'Custom' you can select the features to be installed from a list.
• Installation Qualification for HyStar will start automatically after completing the installation.
• HyStar 3.2 SR2 setup installs Bruker Compass 1.3 and Microsoft .NET Framework 2.0
automatically
• Select 'Install' and 'DataAnalysis 4.0' in the browser and follow the instructions. Temporary
licenses of 30 days duration are issued once upon initial installation.
• Select ‘Install’ and 'SP2 for DataAnalysis 4.0' in the browser and follow the instructions
• Additional installations for Videos and Demo Data are also available on the DVD.

2.2.2 Installing ESI Compass 1.3 SR1 for amaZon on an off-line PC for offline
processing
• It is not necessary to uninstall any other DataAnalysis or Compass software prior to
installing DataAnalysis 4.0 SP 2. Moreover, installation of DataAnalysis 4.0 or
DataAnalysis 4.0 SP 1 is a prerequisite before installation of DataAnalysis 4.0 SP 2.
• The 'Compass' browser will launch automatically when the DVD is loaded into the DVD-
ROM drive.
• First select 'install'. If DataAnalysis 4.0 or DataAnalysis 4.0 SP 1 is not yet installed on this
computer click on ‘DataAnalysis 4.0’.
• The DataAnalysis 4.0 setup dialog will pop up. Press the "Next" button and follow the
instructions.
• Next select ‘Install’ and 'SP2 for DataAnalysis 4.0' and follow the instructions.

2.2.3 Installing Library Server 2.0

• This installation is not necessary if DataAnalysis 4.0 SP 2 software is already installed. It
is only necessary on a computer which contains mass spectra libraries, yet, no
DataAnalysis processing software.

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2.2.4 Installing Tutorial Data

• This installation installs ESI Tutorial Data in the newly created folder ‘Tutorial Data’ in the
'Data' directory
• To remove ESI Tutorial Data go to the 'Add/Remove Programs' group in the 'Control
Panel' and select 'Remove'.

2.2.5 Licensing
• Registration Keys (License) are required in order to use particular parts of Compass 1.3
SR1 for amaZon. Keys are currently required for ESI Compass 1.3, ESI Compass 1.3
Charge Deconvolution Option, ESI Compass 1.3 Maximum Entropy Deconvolution Option
and HyStar 3.2 SR2.
• Temporary licenses of 30 days duration are issued on initial installation.
• License keys for the DataAnalysis 3.4 release or any of the DataAnalysis options are no
longer valid, except for the DataAnalysis 3.4, Charge Deconvolution and Maximum
Entropy Deconvolution Option, which are equivalent to the respecting ESI Compass 1.3
273 Option license above. These two license keys remain valid and applicable for
DataAnalysis 4.0, too.
• Registration Keys (Licenses) for HyStar options, like Fraction Collection, Peak Parking,
LC(n)/MS(n) etc. from previous HyStar releases are still valid.
• Registration Keys can be found in the software license certificate delivered to the
customer.
• License Manager will ask you to enter your Registration Keys the first time any of the
above mentioned processing programs are started after installation.
• If your software is already installed you may enter additional Registration Keys as well.
License Manager can be found in the Compass/License pull down menu in the programs
(except trapControl) and in the 'Bruker Daltonics > Administration' folder in the Windows
start menu.

2.2.6 Installation Qualification

• It is recommended that you run ‘Installation Qualification’ from the Start menu
Programs/Bruker Daltonics/Utilities after complete installation. The result is saved under
'C:\BDalSystemData\IQReports’ and indicates if your installation is correct. If a file is
corrupt (missing or modified) it is marked red. A fresh installation or repair will generally fix
any problems. There might be some warnings if a newer version of a program or program
part is installed. The warnings are marked in yellow and are not critical to the usability of
the program.

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2.3 Additional Installations

To make full use of the automation and scripting capabilities in DataAnalysis it is necessary to
install a specific component from Microsoft which cannot be included on this DVD.
The component is:
• ActiveX Control Pad 1.0
The installation of this component may not be necessary, e.g., if Microsoft Office is
installed.
ActiveX Control Pad 1.0 is used for designing dialogs for scripting in DataAnalysis or
AutomationEngine.
ActiveX Control Pad 1.0 can be downloaded from:
http://download.microsoft.com/download/activexcontrolpad/Install/4.0.0.950/WIN98MeXP/
EN-US/setuppad.exe
• If ActiveX Control Pad 1.0 is not installed, DataAnalysis will inform you and ask for
installation from the above location when the script editor is opened.

3 Software Issues
3.1 Data Acquisition (HyStar 3.2 SR2)

3.1.1 Common Issues

3.1.1.1 Multiple injections in one sample line: If acquisition is interrupted between
injections this line can be started again.
3.1.1.2 If psClient (ProteinsScape) is installed on the PC, HyStar has limited the number of
injections to 1.

3.1.2 Support of Agilent LC system

3.1.2.1 Convert HardwareSetup from version 3.1 to 3.2 SR2: Sometimes the G1313A
settings dialog is not displayed after clicking the 'Configuration...' button.
Workaround:
a. restart HyStar
b. define new name for the hardware setup
c. select all requested devices again (incl. required parameters)
d. save this file as active Hardware Setup
3.1.2.2 Convert Hardware Setup from versions older than 3.2 SR1 to 3.2.SR2: Please update
your existing Hardware Setup file (HSS) by connecting the LC-modules once more in
the ‘Settings’ dialog and saving it.

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3.1.2.3 Agilent 2position-10portvalve G1163A Connections (“1->2”, “1->10”) corresponding

to valve positions are displayed incorrectly in HyStar’s method editor as well as in the
acquisition window and should be ignored. Any value called “port 1 / 2” or “pos. 1 / 2”
is correct and should be used for setting valve positions directly or within the timetable.
The edit line for the timetable only allows the selection of “10->1” and “1->2”, those
options that lead to a correct (“port x”) value in the timetable must be used.
“Pos. 1” or “port 1” always corresponds to physical connection “10-1” and “port 2”or
“pos.2” corresponds to “1-2”.

3.1.3 Support of Hitachi LaChrom Elite system

3.1.3.1 The software module for control of Hitachi VWD does not send an error message to
HyStar if a leak is detected.
3.1.3.2 Older Hitachi methods containing a different column port (2 or 3) don’t work in
3.2.44. The column port is not switched if the method is loaded. Please save the
method once more and it will work.

3.1.4 Support of Dionex Ultimate 3000 system

3.1.4.1 If a prerun time is specified in the Sample Table of Hystar, this is not taken into
account by the timing of the Dionex DCMS link program.
This results in the retention (system) times being different. So, any time based events
in the DCMS Dionex program occur early by the amount of time specified by the
prerun. Workaround: Don't use the prerun time definition in the HyStar Sample Table.
3.1.4.2 3D data acquisition with a Dionex PDA detector
For acquisition of 3D data with a Dionex PDA detector, the file “PluginControl.ocx”
installed with the HyStar package has to be exchanged.
To install the new PluginControl.ocx follow the instructions below:
1. Close all open Compass/HyStar software.
2. Backup the original PluginControl.ocx file which is located in the HyStar-bin
directory (usually C:\Program Files\Bruker Daltonik\HyStar\bin).
3. Copy the updated PluginControl.ocx file from the DCMSLink installation CD (CD
Drive:\Additional Files\) to the above location.
4. Restart Compass/HyStar as appropriate.
The updated file is only compatible with DCMSLink 2.0.

3.2 Data Processing (HyStarPP 3.2 SR2)

3.2.1 In HyStarPP Report Setup, ‘Auto Peak Picking’ should be unchecked for automatic
reporting after an analysis.

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3.2.2 Ultimate3000 users: Do not open the *.u2 files created in an analysis with Ultimate
3000 and VWD.
These files are empty and create an error if they are opened in HyStarPP. Ultimate 3000
UV data are stored as *.unt-files, which can be opened in HyStarPP.

3.2.3 2D-UV (*.u2) files are not properly displayed in HyStarPP.

The UV spectrum in the upper data window is not updated. As a work-around open and
close any menu item; this will update the UV spectrum display. Alternatively, use
DataAnalysis 4.0 to display 2D-UV data.

3.3 Data Acquisition (trapControl 7.0)

3.3.1 Please make sure that the CI source is switched on if you have any ETD method
somewhere in your HyStar Sample Table. Otherwise HyStar will not start the method
and stays in ‘Waiting for system ready’. The only way out is to use the Process Cleaner.

3.3.2 It is not possible to load methods or analyses from esquire/HCT.

3.4 Data Processing (DataAnalysis 4.0 SP2)

3.4.1 While acquiring an analysis it is possible to open the partial analysis in
DataAnalysis. Do not open multiple instances of this analysis, especially after the
acquisition is completed. First close the partially opened analysis and then open the
analysis again after acquisition is completed.

3.4.2 The automation command 'Analysis.FindDissect' will not validate members of the
'Compounds' and 'Chromatograms' collection. Do not use a variable containing a
'Compound' or 'Chromatogram' object across an 'Analysis.FindDissect' call.
For example the following code fragment will cause an script error:
Chrom = Analysis.Chromatograms(1)
Analysis.FindDissect
MsgBox Chrom.Name '<--- this line will break since 'Chrom' is invalid

3.4.3 The automation command ‘Form.Close’ terminates the script. Only place this
command at the very end of the script (last line).

3.5 LibraryEditor 4.0

3.5.1 ETD and PTR spectra are handled as common MSn fragment spectra. The ETD or
PTR information is not contained in the mass-spectral libraries.

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3.6 QuantAnalysis 2.0

3.6.1 If Calibration Blocks are interrupted by a Sample, Blank or Quality Control, the
software will assume that the next calibration sample in the sequence will start a new
calibration block. The Calibration Type currently allows choosing between New and
Replace in the Worktable.

3.6.2 For importing the correct values for Inj.Vol. and Dil.Factor with a
HyStarSequenceFile (*.seq), the decimal symbol in your language settings must be a
point or period (.).

3.7 Report Designer 4.5

3.7.1 The F1 button is not working. Use the Help Menu to launch online help.

Descriptions and specifications supersede all previous information and are subject to change
without notice

Copyright © 2010
Bruker Daltonik GmbH
January 2010

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