0302-2138C ChromNAV InstructionManual 2

ChromNAV
Data System
Instruction Manual
(Version 2.2B or later)
P/N:0302-2138C November 2016

Preface
This instruction manual is your guide for using ChromNAV, Chromatography Data System (for
this manual, it is referred to as “ChromNAV”). It instructs first-time users on how to use the
instrument, and serves as a reference for experienced users.
Before using ChromNAV, please read this instruction manual carefully, and make sure that the
contents are fully understood. This manual should be easily accessible to the operator at all
times during instrument operation. When not using ChromNAV, keep this manual in a safe
place. If this instruction manual becomes lost, order a replacement from your local JASCO
distributor.
Servicing
Contact your local JASCO distributor for instrument servicing. In addition, contact your JASCO
distributor before moving the instrument to another location. Consumable parts should be
ordered according to part number from your local JASCO distributor. If a part number is
unknown, give your JASCO distributor the model name and serial number of your instrument.
Do not return contaminated products or parts that may constitute a health hazard to
JASCO employees.
i
Notices
(1) JASCO shall not be held liable, either directly or indirectly, for any consequential damage
incurred as a result of product use.
(2) Prohibitions on the use of JASCO software
Copying software for purposes other than backup

Transfer or licensing of the right to use software to a third party
Disclosure of confidential information regarding software
Modification of software
Use of software on multiple workstations, network terminals, or by other methods
(not applicable under a network licensing agreement concluded with JASCO)
(3) The contents of this manual are subject to change without notice for product improvement.
(4) This manual is considered complete and accurate at publication.
(5) This manual does not guarantee the validity of any patent rights or other rights.
(6) If a JASCO software program has failed causing an error or improper operation, this may
be caused by a conflict from another program operating on the PC. In this case, take
corrective action by uninstalling the conflicting product(s).
(7) Windows is a registered trademark of Microsoft Corporation in the United States and other
countries. In general, company names and product names are trademarks or registered
trademarks of the respective companies. However, the TM and ® marks are not used in
all cases in this manual.
(8) JASCO and the JASCO logo are registered trademarks of JASCO Corporation in Japan
and other countries.
ii
Limited Warranty
Products sold by JASCO, unless otherwise specified, are warranted for a period of one year
from the date of shipment to be free of defects in materials and workmanship. If any defects in
the product are found during this warranty period, JASCO will repair or replace the defective
part(s) or product free of charge.
THIS WARRANTY DOES NOT APPLY TO DEFECTS RESULTING FROM THE

FOLLOWING:
(1) IMPROPER OR INADEQUATE INSTALLATION

(2) IMPROPER OR INADEQUATE OPERATION, MAINTENANCE, ADJUSTMENT OR
CALIBRATION
(3) UNAUTHORIZED MODIFICATION OR MISUSE
(4) USE OF CONSUMABLE PARTS NOT SUPPLIED BY AN AUTHORIZED JASCO
DISTRIBUTOR
(5) CORROSION DUE TO THE USE OF IMPROPER SOLVENTS, SAMPLES, OR DUE TO
SURROUNDING GASES
(6) ACCIDENTS BEYOND JASCO'S CONTROL, INCLUDING NATURAL DISASTERS
This warranty does not cover the consumable parts listed below:
(1) Tungsten lamp, and other light sources

(2) Mirrors in the light source section, and cell windows
(3) Fuses, batteries, glassware, chart paper and ink
THE WARRANTY FOR ALL PARTS SUPPLIED AND REPAIRS PROVIDED UNDER THIS
WARRANTY EXPIRES ON THE WARRANTY EXPIRATION DATE OF THE ORIGINAL
PRODUCT. FOR INQUIRIES CONCERNING REPAIR SERVICE, CONTACT YOUR JASCO
DISTRIBUTOR AFTER CONFIRMING THE MODEL NAME AND SERIAL NUMBER OF
YOUR INSTRUMENT.
JASCO Corporation
2967-5, Ishikawa-machi, Hachioji-shi
Tokyo 192-8537
JAPAN
iii
Notation Used
The following notational conventions are used throughout this manual:
Notation Meaning
[Measurement] menu Names of menus, commands, and text boxes are enclosed in
[Parameters...] command square brackets ‘[ ]’, followed by a description indicating
whether the function is a menu, command, text box, etc.
Shortcut keys used to select menus or commands are
underlined.
<OK>, <Cancel> Names of buttons are enclosed in angular brackets ‘< >‘.
Keyboard Operations
Notation Meaning
Shift Ctrl The key is enclosed in a square and shown in boldface.
Alt , F Keys that are to be pressed in succession are separated by
commas. In the example shown on the left, the Alt key is to
be pressed and released, followed by the F key.
Shift + Keys that are pressed simultaneously are separated by a
"plus" sign. In the example shown on the left, press the
key while holding down the Shift key.
Mouse Operations
Notation Meaning
Point Move the mouse pointer to the specified item.
Click Quickly press and release the mouse button.
Double-click Click the mouse button twice in rapid succession.
Drag Point to an item, click and hold down the mouse button.
Move the mouse with the button held down, and release
the button when the pointer is in the desired position.
iv
Contents
Preface......................................................................................................................... i
Servicing ..................................................................................................................... i
Notices........................................................................................................................ ii
Limited Warranty ...................................................................................................... iii
Notation Used ........................................................................................................... iv
Contents ..................................................................................................................... v
1. Introduction ......................................................................................................... 1
Overview ................................................................................................................. 1
About Project in ChromNAV .................................................................................. 2
Data Channel in Chromatogram ............................................................................ 3
Analog Channels ............................................................................................. 3
Digital Channels .............................................................................................. 3
Virtual Channels .............................................................................................. 3
3D Chromatogram ........................................................................................... 3
Method..................................................................................................................... 4
Filename and Caption ............................................................................................ 5
Specification ........................................................................................................... 5
Accessory ............................................................................................................... 6
2. Installation ........................................................................................................... 7
Computer Setting.................................................................................................... 7
Installation of the ChromNAV Package ................................................................. 7
3. Startup of ChromNAV ......................................................................................... 8
Launching Control Center ...................................................................................... 8
Initial Configuration ................................................................................................ 9
Creating User .................................................................................................. 9
3.2.1.1 Logon without Password ......................................................................... 10
Creating Project ............................................................................................. 11
Registering LC-Net II/ADC ............................................................................. 12
Registering of HPLC System ......................................................................... 12
ChromNAV Main Window ..................................................................................... 14
Navigation Window ............................................................................................... 16
Setup of Printer ..................................................................................................... 16
4. Data Acquisition ................................................................................................ 18
Type of Data Acquisition ...................................................................................... 18
Conditioning ......................................................................................................... 19
Setting Analytical Condition ........................................................................... 19
4.2.1.1 Setting in [CONFIG] Panel ...................................................................... 20
4.2.1.2 Setting in [AS] Panel ............................................................................... 21
4.2.1.3 Setting in [PUMP] Panel ......................................................................... 21
4.2.1.4 Setting in [OVEN] Panel.......................................................................... 22
4.2.1.5 Setting in [PDA] Panel ............................................................................ 22
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4.2.1.6 Entering Column Information .................................................................. 23
Saving Control Method .................................................................................. 23
Starting Conditioning ..................................................................................... 24
Data Acquisition by Acquisition Sequence ........................................................ 26
Creating Acquisition Sequence ...................................................................... 26
4.3.1.1 Fitting Block ............................................................................................ 27
4.3.1.2 Saving Acquisition Sequence.................................................................. 28
Loading Acquisition Sequence....................................................................... 29
4.3.2.1 Setting End Mode ................................................................................... 30
Running Acquisition Sequence ...................................................................... 31
4.3.3.1 Editing Acquisition Sequence during the Run ......................................... 32
4.3.3.2 Stopping Pump after Finishing ................................................................ 33
Data Acquisition by Manual Injector ................................................................... 33
Setting Single Run Configuration ................................................................... 34
Starting Single Run ........................................................................................ 35
4.4.2.1 Editing Configuration during the Run ...................................................... 36
4.4.2.2 Exiting Single Run .................................................................................. 36
5. Data Analysis ..................................................................................................... 37
Opening Chromatogram....................................................................................... 37
About Active Chromatogram .......................................................................... 38
Chromatogram Information ............................................................................ 39
Displaying Chromatogram ............................................................................. 40
Peak Integration .................................................................................................... 41
Automatic Peak Processing ........................................................................... 41
5.2.1.1 Setting Peak Method .............................................................................. 41
5.2.1.2 Verifying Peak Method ............................................................................ 43
5.2.1.3 Saving Peak Method ............................................................................... 44
5.2.1.4 Applying Peak Method ............................................................................ 45
Manual Peak Processing ............................................................................... 46
5.2.2.1 Adding Peak ........................................................................................... 46
5.2.2.2 Deleting Peak ......................................................................................... 47
5.2.2.3 Applying Manual Peak Processing .......................................................... 48
Peak Identification ................................................................................................ 49
Changing Peak Annotation ............................................................................ 49
Setting Peak ID Table .................................................................................... 50
Verifying Peak ID Table ................................................................................. 53
Saving Peak ID Table .................................................................................... 53
Applying Peak ID Table ................................................................................. 54
Quantitative Analysis ........................................................................................... 55
Calibration Method ........................................................................................ 55
Report Style ................................................................................................... 57
Data Processing Method ............................................................................... 59
Recalculation Sequence ................................................................................ 61
5.4.4.1 Creating Recalculation Sequence ........................................................... 61
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5.4.4.2 Running Recalculation Sequence ........................................................... 64
Browsing Result of Data Analysis .................................................................. 64
5.4.5.1 Browsing Calibration Curve .................................................................... 64
5.4.5.2 Browsing Quantity................................................................................... 65
6. Three-dimensional Chromatogram .................................................................. 67
Extracting Chromatogram and Spectrum ........................................................... 67
Assigning to Virtual Channel .......................................................................... 68
Detecting Spectral Peak ................................................................................ 69
Browsing Bird’s-eye View .................................................................................... 69
Comparing Contour Map ...................................................................................... 70
Ratio Chromatogram ............................................................................................ 71
On-Peak Spectrum and Spectral Library............................................................. 74
Extracting On-Peak Spectra .......................................................................... 75
Creating Spectral Library ............................................................................... 76
6.5.2.1 Registering On-Peak Spectrum in Library ............................................... 77
6.5.2.2 Creating Spectral Search Method ........................................................... 79
Searching in the Library 1 .............................................................................. 79
Searching in the Library 2 .............................................................................. 81
Peak Purity Calculation ........................................................................................ 83
Creating Peak Purity Method ......................................................................... 84
Calculating Peak Purity.................................................................................. 85
7. Various Features ............................................................................................... 86
Changing Analytical Conditions during the Run ................................................ 86
Temporary Change of Analytical Conditions .................................................. 86
Changing and Overwriting Gradient Profile .................................................... 86
Email Notification ................................................................................................. 87
Method Template .................................................................................................. 89
Application Template ........................................................................................... 91
Creating Application Template from Project ................................................... 93
Creating Project from Application Template ................................................... 93
8. Maintenance ...................................................................................................... 95
Module Diagnosis Information............................................................................. 95
Application Log .................................................................................................... 96
Replacing Project and Copying Methods............................................................ 97
Backup and Restoration of Project ................................................................... 100
Backing up Project ....................................................................................... 100
Restoring Project ......................................................................................... 102
Backup and Restoration of ChromNAV Environments .................................... 102
Backing up ChromNAV Environments ......................................................... 103
Restoring ChromNAV Environments............................................................ 103
Checking Software Version of ChromNAV ................................................... 104
Upgrading Projects ...................................................................................... 104
vii
viii
1. Introduction
Overview
(1) About ChromNAV Data System
ChromNAV is the standalone Data System to control the JASCO HPLC systems, UHPLC
systems, SFC systems, or SFE systems (for this manual, they are referred to as the “HPLC”
systems.), acquire chromatograms, and analyze chromatograms.
(2) Registering and controlling multiple HPLC systems configured JASCO modules
Up to four HPLC systems configured by JASCO LC-4000 series, X-LC (LC-3000) series,
LC-2000 series, LC-1500/900 series, micro21LC series modules (except a part of modules)
can be controlled in one ChromNAV (one PC).
(3) Various kinds of information from various data acquisition views

The Data Acquisition window in ChromNAV has a view to monitor chromatograms by specified
wavelengths, a view to monitor a 3D chromatogram from the PDA Detector, and a view to
show a progress of the running data acquisition. It also has a function to monitor each
analytical conditions of each module, and a function to monitor the status of the HPLC system.
(4) Acquisition sequence mode and single run mode

ChromNAV has two different ways to acquire chromatograms. One of them is well used in the
HPLC system configured an autosampler, and another is well used in the HPLC system
configured a manual injector.
(5) Providing the low running cost

In a long time automatic data acquisition such as an unmanned and overnight running,
ChromNAV can stop solvent flows, temperature controls, and detector lamps to reduce
running cost when the data acquisition has been finished. In the HPLC system configured
LC-4000 series modules, ChromNAV can also turn off their modules for the power saving.
(6) Various kinds of data analysis from various data analysis views
The Data Analysis window in ChromNAV has a view to show and analyze chromatograms, a
view to show and analyze a 3D chromatogram using spectra extracted from it, a view to
recalculate multiple chromatograms automatically and continuously. To determine parameters
for the peak detection, the peak identification, and the quantitative calculation, ChromNAV can
show the chromatogram of “Test Injection” acquired in advance as reference. Their
parameters can be tested and showed as the virtual results in the reference chromatogram,
and they can be changed directly and tested again if any values of them are not good.
1
(7) Feature enhancements by optional add-in programs
Not only Quantitative Analysis but Molecular Mass Distribution Calculation can be performed
when an optional Molecular Mass Distribution Calibration Program has been installed. The
(Semi-) Preparative HPLC system can be configured when an optional Fraction Collector
Controller has been installed, and the fractionation can be performed using various and
advanced parameters compared with standalone fraction collectors.
(8) Customizing for your application

Jasco may provide any Application Templates for dedicated HPLC systems to measure
specified analyte or HPLC systems of dedicated configuration (ex. High Pressure Gradient
System, GPC/SEC System, etc.). The Application Template will provide appropriate settings,
Method parameters, and preferences for each purpose to support operators. It can be also
created newly from any existing Project in ChromNAV.
About Project in ChromNAV

ChromNAV will store and manage all acquired data, parameters for the data acquisition, and
parameters for the data analysis into some “container”. In ChromNAV, it is called as [Project]
for the “container”.
Multiple (different) Projects can be created in one ChromNAV system, and each Project is
comprised an independent “database”. There is not any restriction in ChromNAV to use
multiple Projects separately. For example, they can be used separately by “types of analyte”,
or they can be used separately by operators (Users).
If the same Project has been used for long time and number of data and Methods has
increased, the response from ChromNAV may become slow. To prevent such a phenomenon,
it is good idea to replace Project with the new one per a month or per a quarter.
Only one Project can be used for one HPLC system simultaneously in ChromNAV. Any data
and Methods in all different Projects cannot be used, however, data and Methods in different
Project can be copied to the current Project in some dedicated Window to manage Projects if
necessary.
Figure 1.1 Image of Project
2
Data Channel in Chromatogram
A chromatogram file acquired in ChromNAV may include multiple chromatograms. They are
separated and categorized by the ways of data input (or extraction).
All data channels to measure the same sample will be stored in the same chromatogram file.
Note: Chromatograms (and Methods) are not files in Windows because they are
not saved in the storage, but stored in the database as the Project. For this
manual, “file(s)” will be used for convenience of explanation.
In ChromNAV, all data channels in the chromatogram will be opened or closed when the
corresponding chromatogram file is opened or closed. Only any data channel in the
chromatogram having multiple data channels cannot be opened or closed.
Analog Channels
The signal from the [INT OUT] terminal in the detector to [CHn] terminal in the LC-Net II/ADC is
called as the “Analog Channel”. CH1 – CH4 will be assigned for analog channel
chromatograms.
Digital Channels
The signal from the PDA detector to the PC via the USB interface (2.0 or later) or the SCSI
interface is called as the “Digital Channel”. It is independent 2D (X/Y) chromatogram separated
from 3D (X/Y/Z) chromatogram acquired in the PDA detector. CH5 – CH8 will be assigned for
digital channel chromatograms.
Virtual Channels
The different signal transferred by the same way as the “Digital Channel”, and extracted from
3D chromatogram acquired in the PDA detector, is called as “Virtual Channel”. CH9 – CH16
will be assigned for virtual channel chromatograms.
In the data acquisition with the PDA detector in ChromNAV, a parameter if it saves the 3D
chromatogram in the Project can be available (because the data size of the 3D chromatogram
is huge), however, the 3D chromatogram must be saved to record to show and analyze virtual
channel chromatograms.
3D Chromatogram
The three dimensional signal structured by the retention time (X), the wavelength (Y), and the
absorbance unit (Z) from the PDA detector to the PC via the USB or the SCSI interface is
called as the “3D Chromatogram”. It can be shown as the contour map view or bird’s-eye view.
Chromatograms at any wavelengths and spectra at any retention times can be extracted from
it. The 3D chromatogram is convenient because various data analysis can be done with it, but
a data size is much huge compared with 2D chromatograms.
3
Method
The file to include parameters for the data acquisition or the data analysis is called as the
“Method”. In ChromNAV, there are several kinds of Methods for different purposes.
The list of all Methods in ChromNAV shows as below. For this manual, all of them are called as
Method(s), even if some of them don’t have names of “method”.
Acquisition Sequence
Sample Information Table
Control Method
Peak Method
Peak ID Table
Calibration Method
Data Processing Method
Post Run Method
Peak Purity Method
Spectral Search Method
MW Calculation Method (Optional)
Collection Method (Optional)
Tray Layout (Optional)
Report Style
Sequence Report Style
Of course, all Methods are not always required in every cases. Number of required Methods
and types of required Methods depend on your application.
Take care of the combination of Methods because some Method may need to be nested in the
different type of Method to be used. Examples of typical combination of Methods to be nested
as follows;
[ Peak Method], [ Report Style], or [ MW Calculation Method] may be nested in

[ Data Processing Method].
[ Sequence Report Style] may be nested in [ Post Run Method].
4
In [ Acquisition Sequence], many types of Mehods such as [ Sample Information
Table], [ Control Method], [ Peak ID Table], [ Calibration Method], or [ Data
Processing Method] may be nested.
They are categorized between for the data acquisition and for the data analysis, however, all
Methods can be created both of in [Data Acquisition] Window and in [Data Analysis] Window.
Filename and Caption

In ChromNAV, all data (chromatograms) and Methods are stored in the Project with filenames.
All alphanumerical characters and a part of symbolic characters are available for filenames.
Unavailable characters for filenames are as follws;

“ (Space)” or “. (Period)” for the first character
“ (Space)” or “. (Period)” for the last character
“\ (Backslash)”, “/ (Slash)”, “: (Colon)”, “; (Semicolon)”, “, (Comma)”
“’ (Singlequote)”, “” (Doublequote)”, “<”, “>”, “?”, “*”, “|”
ASCII control characters like CR or LF
In tables shown in ChromNAV, captions for several rows or columns can be also edited.
Unavailable characters for captions are as follows;

“ (Tab)”, “; (Semicolon)”, “, (Comma)”
ASCII control characters like CR or LF
Specification
Software Language English or Japanese
Number of Controllable HPLCs Maximum 4 systems
Number of Data Channels 4 Analog channels, 4 Digital channels, and 8 Virtual
channels
Sampling Interval (LC-Net II/ADC) 10 – 4000 msec (100 – 0.25 Hz)
Sampling Interval (PDA Detector) 10 – 4000 msec (100 – 0.25 Hz), 1 – 64 nm
Number of Injections Maximum 999 in one data acquisition
Data Acquisition Time Maximum 999.9 min
On-Flow Spectrum UV spectrum in UV detector
UV spectrum in 4WL-UV detector
Ex and Em spectra in FP detector
CD and UV spectra in CD detector (Stopped-Flow
method is strongly recommended)
5
Accessory
Serial Number (written in the CD-ROM package)
Installation CD-ROM
Spectra Manager Ver.2
Installation Manual
Instruction Manual (this document)
6
2. Installation
Computer Setting
Note: To connect the PC with the office LAN, install a different Ethernet interface to
separate the HPLC LAN from the office LAN.
CAUTION : Do not connect any USB modules (PDA detectors or Fraction

Collector Controllers) with the PC before installation because their
drivers will be also installed during installation of ChromNAV.
Adjust settings and parameters in Windows as ChromNAV works appropriately.

Refer to the Installation Manual for the details.
Installation of the ChromNAV Package

In the installation CD, an installation program of Spectra Manager 2, an installation program of
Adobe Reader, sample data (Projects, Application templates, and Spectral libraries), and
related documents such as an instruction manual, will be included except an installation
program of ChromNAV.
Refer to the Installation Manual for the details.
7
3. Startup of ChromNAV
Launching Control Center

Turn on the PC and all modules in the HPLC systems.
CAUTION : The PDA detectors of the USB types do not equip any LCD panels.
Each LED lamp will vary as follwos when the detector has been
started up completely;
[Power] LED : Lighted by blue.
[PC Link] LED : Not lighted.
[D2] LED : Lighted by blue (not blinked).
[WI] LED : Lighted by blue.
CAUTION : Not only JASCO PDA detectors of the SCSI types but all of SCSI
devices must be started up completely before the corresponding PC
is turned on.
In the LCD screens in the PDA detectors, “NORM (Normal)” will be
displayed when they have been turned on completely.
After all modules has launched correctly, double click the icon on the desktop. Then,
[Logon] dialog box will be displayed.
Figure 3.1 [Logon] Dialog Box
Enter “Administrator” in the [User Name] input box, remain a blank in the [Password] input box.
Click <Logon> button, then [Control Center] window will be displayed.
Note: Only the first character “A” must be capital in the initial User Name.
8
Figure 3.2 [Control Center] Window
The Control Center is the initial screen shown after logging on in ChromNAV. In this window,
initial configuration can be done, ChromNAV main window can be launched, and the window to
manage Projects can be launched.
Initial Configuration
Initial configuration of ChromNAV can be done in [Control Center] window. For the details,
refer to online help. Here, important configuration is described.
Creating User
Click [Management Tools] tab in the left pane in [Control Center] window, and click [User] icon
in the left pane. Then, [User] screen will be displayed in the right pane and the list of registered
Users will be displayed in it.
Select [Operation] > [New] in the menu or click (New) button in the toolbar in [Control Center]
window, then [New User] dialog box will be displayed.
9
Figure 3.3 [New User] Dialog Box
For User Name, all alphanumeric characters and a part of symbolic characters can be used
except some forbidden characters. Forbidden characters are as follows.
Space or “. (Period)” as the first character

Space or “. (Period)” as the last character
“ \ (Backslash) ”, “ / (Slash) ”, “ : (Colon) ”, “ ; (Semicolon) ”, “ , (Comma) ”
“ ‘ (Singlequote) ”, “ “ (Doublequote) ”, “ < ”, “ > ”, “ ? ”, “ * (Asterisk) ”, “ | (Vertical Bar) ”
ASCII control characters
Non ASCII characters
For Password, only alphanumeric characters can be used. Up to six characters are required in
the initial settings.
Enter in [User Name], [Full Name], [Password], [Retype Password] input boxes and click
<Create> button, then an icon of the new User will be displayed in the right pane in the [Control
Center] window.
3.2.1.1 Logon without Password

Change a parameter in the System Policy in [Control Center] window if the logon password is
not necessary.
Click [System Policy] icon in the left pane in [Control Center] window, then [System Policy]
screen will be displayed in the right pane and the current settings will be displayed in it.
Select [Operation] > [Edit] in the menu or click (Edit) button in the toolbar in [Control Center]
window, then [System Policy] dialog box will be displayed.
10
Figure 3.4 [System Policy] Dialog Box
Enter “0” in [Min. Length] input box and click <OK> button. Then, in [New User] dalog box,
blanks can be accepted in [Password] and [Retype Password] input boxes to create the new
User without a password.
Creating Project
Click [Project] icon in the left pane in [Control Center] window, then [Project] screen will be
displayed in the right pane and the current settings will be displayed in it.
Select [Operation] > [New] in the menu or click (New) button in the toolbar in the [Control
Center] window, then [New Project] dialog box will be displayed.
Figure 3.5 [New Project] Dialog Box
[GPC] or [FC] check boxes will be displayed when optional Molecular Mass Distribution
Calculation Program or Fraction Collector Controller has been installed. Check appropriate
check boxes for your optional add-in program.
[Application Template] list will be displayed when any Application Template has been installed.
Specify an appropriate Application Template name or “Not use” in the list.
11
Enter any name in [Project Name] input box, enter any information in [Description] input box if
necessary.
Click <New> button in the dialog box, then an icon of the new Project will be displayed in the
right pane in [Control Center] window.
Registering LC-Net II/ADC

Click [LC-Net II/ADC] icon in the left pane in [Control Center] window, then [LC-Net II/ADC]
window, then [Register LC-Net II/ADC] dialog box will be displayed.
Figure 3.6 [Register LC-Net II/ADC] Dialog Box
Enter the MAC address in [MAC Address] input boxes. MAC address is shown at the
upper-right corner in the front panel in the LC-Net II/ADC. Do not need to edit from the first
value to the fourth value [00:C0:28:00] because there are original values for JASCO products.
Enter remaining two values by alphanumeric characters.
Click <Register> button in the dialog box, then an icon of the new LC-Net II/ADC will be
displayed in the right pane in [Control Center] window.
CAUTION : If a red-cross mark shows on the icon of the LC-Net II/ADC, it

means the LC-Net II/ADC does not connect with the PC. Click
(Refresh) button in the toolbar in the dialog box to refresh [LC-Net
II/ADC] screen, and check if the red-cross mark is removed.
Check IP addresses of the LC-Net II/ADC and the PC if the mark
cannot be removed.
Registering of HPLC System

Click [HPLC System] icon in the left pane in [Control Center] window, then [HPLC System]
12
window, then [HPLC System Registration] dialog box will be displayed.
Figure 3.7 [HPLC System Registration] Dialog Box
Enter any name in [HPLC System Name] input box.
Specify appropriate LC-Net II/ADC by its MAC address in [Selected LC-Net II/ADC] list. Then,
the IP address of the LC-Net II/ADC will be displayed in [IP Address] column.
Specify appropriate value of sampling intervals for Analog Channels (CH1 – CH4) by msec.
100 – 500 msec for HPLC and 10 – 100 msec for UHPLC are well-used.
Set parameters for Analog Channels in [Data Channel Settings] table. Check all [Use] check
boxes to be used for the data acquisition. Enter any names in [Name] columns if necessary. Do
not always need to modify any other values (Scale Factors and Units) in the table.
Specify the start mode in the HPLC system. Normally, “LC-Net II/ADC (Start on Injection)”
should be specified. Specify “PDA Only (Start on Injection)” in case that only one PDA detector
is configured as detector modules in the HPLC system and controlling any modules except the
PDA detector is not required.
Specify and register all modules in the HPLC system in [HPLC Modules] table. Specify model
names in [Model Name] columns, note that specify “LC-Net II/ADC” in [Valve/Event] row.
If an USB type PDA detector or a FC-2088-30 Fraction Collector Controller is configured, enter
corresponding serial number in [Serial No. / Port] column.
If an ELS detector is configured, specify the COM port number in [Serial No. / Port] column.
13
Note: When multiple modules of the same type are installed in the HPLC system
(ex. Pumps, Ovens, UV Detectors, and BPRs), set each model name in the
same row as each module number.
Click <OK> button in the dialog box, then an icon of the new HPLC System will be displayed in
the right pane in [Control Center] window.
ChromNAV Main Window

ChromNAV main windows can be launched in [Control Center] window.
Click [ChromNAV] tab in the left pane in [Control Center] window, then [Start ChromNAV]
screen will be displayed in the right pane and the list of registered HPLC Systems will be
displayed in it.
In the right pane, double click the corresponding icon of the HPLC system. Then, [Open
Project] dialog box will be displayed.
Note: Double click the [Start in Analysis Mode] icon for the data analysis only.
Figure 3.8 [Open Project] Dialog Box
Look for the Project name to be used and click it to highlight, and click <Open> button. Then,
[ChromNAV] window (the main window of ChromNAV) will be displayed.
14
Figure 3.9 [ChromNAV] Window
Two buttons, [Acquisition] and [Analysis], will be displayed at the lower-left corner in the
window. Click each button, then the window configuration will be changed. For this manual,
they are called as the “Data Acquisition Window” for [Acquisition] button and the “Data Analysis
Window” for [Analysis] button.
At the upper-left field in their windows, several icons will be displayed vertically. Click each
button, then the configuration of the right pane in the window, the menu bar, and the tool bars
will vary. For this manual, they are called as the “view(s)”.
Furthermore, several tabs will be displayed at the bottom of in [PDA] view. Click each tab, then
the configuration of the right pane in the window and the tool bars. For this manual, they are
called as the “panel(s)”.
Figure 3.10 (Example) [General] panel in [PDA] view in the data analysis window
15
Navigation Window
For this manual, it is called as the “Navigation Window” for the left pane in [ChromNAV] window.
As described above, buttons to switch between the data acquisition window and the data
analysis window, and icons to replace the actual view will be displayed in the Navigation
Window. The following information will be also displayed in the window;
In the Data Acquisition window, a monitor to show conditions of all modules configured in the
actual HPLC system. The monitor will be always displayed in all Views in the window, even if
the same information of them can be referred in [System Monitor] view in the window.
In the Data Analysis window, a list of opened Chromatogram files with their Executed
Sequence will be displayed, and a list of all Method files related to an “Active (described later)”
Chromatogram file to be acquired and analyzed.
Figure 3.11 Navigation Window
Setup of Printer
Select [File] > [Print Setup] in the menu in [ChromNAV] window, then [Print Setting] dialog box
will be displayed.
Figure 3.12 [Print Setup] Dialog Box
16
Specify any printer name in [Printer] list and click <OK> button.
17
4. Data Acquisition
The data acquisition is performed in the Data Acquisition window. ChromNAV provides various
and useful functions for the data acquisition. For example, it can record detailed information for
the samples to be injected, analyze data immediately just after each data acquisition has been
finished, and output results to the printer or the file in Windows, etc.
Here, well-used and simple operation is described to explain the basis of the data acquisition in
ChromNAV.
Figure 4.1 Data Acquisition Window
Type of Data Acquisition

In ChromNAV, two modes are available for the data acquisition.
[Acquisition Sequence] Mode

One way is to set required number of samples in the “Acquisition Sequence” table beforehand,
and load it in [Acquisition Sequence Monitor] view to run. It is suitable for the data acquisition
with an autosampler.
[Single Run] Mode

Another way is to repeat the same measurement with the same Methods and the same
parameters in [Single Run Monitor] view. It is suitable for the data acquisition with a manual
injector.
In any data acquisition, only one way is available. The way to change the data acquisition
mode is as follows;
In the Data Acquisition window, select [View] > [Change Acquisition Mode] in the menu and
select [Acquisition Sequence Mode] and [Single Run Mode].
18
Figure 4.2 Data Acquisition Modes
Configuration in the Data Acquisition window will be changed when the data acquisition mode
has been changed. In the Navigation Window, the [Acquisition Sequence Monitor] icon and the
[Single Run Monitor] icon will be replaced each other. Configuration of the control buttons is
also changed in the middle of the Data Acquisition window.
Figure 4.3 Control Buttons in Data Acquisition Window
Conditioning
The ways to condition the separation column and the HPLC system are the same between in
[Acquisition Sequence] mode and in [Single Run] mode.
Setting Analytical Condition

Create “Control Method” to set modules parameters in the HPLC system before conditioning.
Select [File] > [Method Editor] > [Control Method] in the menu or click (Edit Control Method) button
in the toolbar in the Data Acquisition window, then [Control Method Editor] dialog box will be
displayed.
[HPLC Modules Configuration] table will be displayed in the right side in the dialog box. Click
(Import Configuration) button in the toolbar in the dialog box, then all module names configured in
ChromNAV ([Control Center] window) will be imported in [HPLC Modules Configuration] table
automatically.
On the other hand, they will not be imported automatically and they must be set manually if
[Control Method Editor] dialog box is opened in Data Analysis window. Therefore, it is more
useful to open the dialog box in the Data Acquisition window.
19
Figure 4.4 Modules Configuration
4.2.1.1 Setting in [CONFIG] Panel

Enter the time in [Method Time] input box by min. “Method Time” means the time from the
sample injection to the next sample injection. Especially, when the gradient elution is
performed, longer time must be set because the time to initialize the gradient composition is
required after the gradient elution has been finished.
CAUTION : “Method Time” is not data acquisition time.

Take care of the difference from “Acquisition Time” entered in
[Acuiqsition Sequence] dialog box or [Single Run] view.
To shorten Method Time, take care of the following relationship;
When any PDA detector has configured in the HPLC system:

[Method Time] ≥ ( [Acquisition Time] + [Injection Delay] + 0.2(minI )
When any PDA detector has not configured in the HPLC system:
[Method Time] ≥ ( [Acquisition Time] + [Injection Delay] + 0.1(minI )
Refer to the description of “Acquisition Time” in [Acquisition Sequence] dialog box or [Single
Run] view.
Configure module names manually in [HPLC Modules Configuration] table when [Control
Method] dialog box has been opened in the Data Analysis window.
After configuration, all buttons of all modules will be displayed on the right of [CONFIG] button.
20
4.2.1.2 Setting in [AS] Panel
Click (AS) button to set parameters for the autosampler. They will be displayed in the right
side of [Control Method Editor] dialog box. Number and types of parameters will vary according
to the model name.
Specify “Partially Fill” or “Full Loop” in [Injection Method] list.

The “Partially Fill” method is to fill a part of the sample loop with the sample solvent. So, the
injection volume must be smaller than the volume of the sample loop.
CAUTION : In “Partially Fill” method, the Injection Volume must be within

approximately an half of the sample loop volume or less to conserve
its actual volume.
On the other hand, the “Full Loop” method is to fill the whole of the sample loop with the sample
solvent. So, the injection volume is equal to the sample loop volume.
CAUTION : Normally, “Direct” method cannot be used. It is necessary to

customize internal tubings and an injection port by an optional kit in
order to use the method.
Enter the correct value in [Loop Volume] by µL.
The total time of the data acquisition can be shortened to reduce the running cost if “On” is
chosen in [Sample Auto Preload] list because the autosampler will start to prepare the next
sample injection before the current sample has been finished.
4.2.1.3 Setting in [PUMP] Panel
Click (PUMPn) button to set parameters for the pump. They will be displayed in the right side
of [Control Method Editor] dialog box. Number and types of parameters will vary according to
the model name.
In [PUMPn] panel, two tabs, [Initial Condition] and [Time Program], will be displayed. But,
parameters in [Time Program] tab are not always required. They are required in case that the
gradient elution is performed.
In [Initial Condition] tab, specify appropriate mode in [Pump Mode] list. Specify “ISO” for the
isocratic elution mode. Specify appropriate one according to the module configuration for the
gradient elution mode.
Enter an appropriate value in [Flow] input box by mL/min. Enter the total flow rate in case of the
gradient elution mode.
21
Enter an appropriate value in [Max. Press] input box by MPa. ChromNAV shows an error and
aborts the conditioning or the data acquisition when the back pressure in the pump has
increased to the value.
Enter initial values in [Composition A] to [Composition D] by percent in case of the gradient

elution mode.
Click [Time Program] tab.
To set the time program, enter elapsed time since the sample has been injected in [Time]
column at the first row in the table and specify “Composition” in [Function] column. Then,
[Value #n] columns will be available depended on the gradient elution mode.
Here, an example to set the gradient elution programs.

“Compositions (A/B) changes from [100/0] at 0.00(min) to [0/100] at 20.00(min), keeps for
5.00(min), and backs to the initial compositions.” should be set as follows;
Figure 4.5 Example of Time Program Settings
4.2.1.4 Setting in [OVEN] Panel
Click (OVENn) button to set parameters for the column oven. They will be displayed in the
right side of [Control Method Editor] dialog box. Number and types of parameters will vary
according to the model name.
Enter an appropriate value by °C in [Temperature] input box.
4.2.1.5 Setting in [PDA] Panel

JASCO has been providing various types of HPLC detectors.
Here, settings of the PDA detector are described as an example.
Click (PDA) button to set parameters for the PDA Detector. They will be displayed in the right
side of [Control Method Editor] dialog box. Number and types of parameters will vary according
to the model name.
22
In [PDA] panel, three tabs, [Initial Condition], [Channel], and [Time Program], will be displayed.
Set parameters in [Channel] tab to acquire Digital Channels (CH5 – CH8) or Virtual Channels
(CH9 – CH16). Parameters in [Time Program] tab are not always required.
In [Initial Condition] tab, the data size of 3D chromatogram can be reduced if values in [Start
WL], [End WL], [WL Interval], and [Sampling Interval] input boxes are adjusted, however,
number of data points of chromatograms or spectra extracted from the 3D chromatogram may
become poor to be analyzed by reducing the data size. So, do not take care of the data size of
3D chromatogram so much if there is much free disk space in the PC.
It is strongly recommended to enter the same value in [Sampling Interval] input box as the
value in [Sampling Interval] in LC-Net II/ADC entered in [Control Center] window to compare
Digital/Virtual Channel chromatograms with Analog Channel chromatograms.
Click [Channel] tab.
Set any Digital Channels or Virtual Channels to be acquired if necessary. Specify

“Chromatogram” in [Type] column at the row for appropriate channel number, and enter a
wavelength in [WL #1] column.
Note: Virtual Channels (CH9 – CH16) are not available when “On” is set in [Do not
save PDA data] list in [Initial Condition] tab.
4.2.1.6 Entering Column Information

Click (Column Information) button in the toolbar in [Control Method Editor] dialog box, then
[Column Information] dialog box will be displayed. Enter any information and click <OK> button
if necessary.
Saving Control Method

Click (Save) button in the toolbar in [Control Method Editor] dialog box, then [Save As Control
Method] dialog box will be displayed. Enter an appropriate name in [Filename] input box and
click <Save> button.
23
Figure 4.6 [Save As Control Method] Dialog Box
Click <×> button in [Control Method Editor] dialog box, then the dialog box will be closed.
Starting Conditioning
Click (MONIT) button in the middle of the Data Acquisition window, then [Monitor Baseline]
dialog box will be displayed.
Figure 4.7 [Monitor Baseline] Dialog Box
Click <…> button for [Control Method], then [Open Control Method] will be displayed. Click the
filename of the Control Method (analytical conditions) created beforehand to highlight and click
<Open> button, then the filename will be displayed in [Control Method] input box in [Monitor
Baseline] dialog box.
Enter appropriate value by min in [X-Axis Scale] input box in the dialog box.
Click <OK> button in the dialog box, then all modules will start to work and ChromNAV will start
to monitor baselines.
In [System Monitor] view, operating states of all modules in the HPLC system will be shown.
In [Chromatogram Monitor] view, actual baselines of Analog Channels and Digital Channels
will be shown.
24
Figure 4.8 Baseline Monitor ([Chromatogram Monitor] View)
Specify any data channel in [Channel] list in the toolbar in [Chromatogram Monitor] view. The
data channel to be shown in the monitor will be changed.
Click (Stacked) or (Overlaid) button in the toolbar in the view. Multiple data channels will be
shown simultaneously by the stacked graphs image or overlaid graphs image.
In [PDA Monitor] view, actual baselines of 3D chromatogram by the contour map image and
Virtual Channels, and the latest spectrum will be shown.
Figure 4.9 Baseline Monitor ([PDA Monitor] View)
Click (A-ZERO) button in the middle of the Data Acquisition window when the baseline has
been stable. The intensities of the baselines will be shifted at zero (except a part of detectors).
CAUTION : For emergency stops of the pumps, click (STOP) button in the
middle of the Data Acquisition window.
25
Take care that heaters in the ovens and lamps in the detectors will
not be turned off automatically at that time.
Data Acquisition by Acquisition Sequence

A data acquisition mode to set required number of samples in the “Acquisition Sequence” table
beforehand, and load it in [Acquisition Sequence Monitor] view to run. It is suitable for the
HPLC system with an autosampler.
To activate the “Acquisition Sequence” mode, select [View] > [Change Acquisition Mode] >
[Acquisition Sequence Mode] in the menu in the Data Acquisition window.
Creating Acquisition Sequence

Click (Edit Acquisition Sequence) button in the toolbar in [ChromNAV] window, then [Acquisition
Sequence Editor] dialog box will be shown.
Figure 4.10 [Acquisition Sequence Editor] Dialog Box
Set required columns as follows;
Specify “UNK” in the list in [Type] column. “STDn” means the standard sample, and “UNK”
means the unknown sample. Here, specify “UNK” for all samples.
Note: [Type] settings can be changed later.
Enter the position of the vial in the autosampler in [Sample #] column. In case of the manual
injector, enter appropriate number (1 to 9999 by a positive integer) to be identified.
Enter an appropriate value by µL in [Injection Volume] column.
26
Enter an appropriate filename in [Chromatogram Name] column. Take care a part of symbolic
characters cannot be used.
Enter an appropriate value by min in [Acquisition Time] column.

To lengthen the Acquisition Time, take care of the following relationship;

[Acquisition Time] ≤ ( [Method Time] - [Injection Delay] - 0.2(minI )
Refer to the description of “Method Time” in [Control Method Editor] dialog box.
Click <…> button shown in [Control Method] column, then the popup menu will be displayed.
Select [Open] in the menu, then [Open Control Method] dialog box will be displayed.
Click the filename of the Control Method (analytical conditions) created beforehand to highlight
and click <Open> button. Then, the filename will be displayed in [Control Method] column.
4.3.1.1 Fitting Block

In the Acquisition Sequence table, one row means one sample (one injection). For example,
five rows from the beginning (the row #1 to the row #5) must be set if five sample vials exist to
be measured.
To set multiple rows in the Acquisition Sequence table, the “Fit Block” function can be used.
Parameters in [Fit Block] dialog box vary depend on each column.
Here, two examples are described as follows;
Drag multiple rows in [Sample #] column to highlight and click the right button, then [Fit Block –
Sample #] dialog box will be displayed.
Figure 4.11 [Fit Block – Sample #] Dialog Box
Enter “1” in [Start Number] input box and enter also “1” in [Increment by] input box, and click
<OK> button. Then, continuous values for positions of vials incremented by one will be entered
automatically in [Sample #] columns.
27
Figure 4.12 Results of Fitting Block (Sample #)
Drag multiple rows in [Chromatogram Name] column to highlight and click the right button, then
[Fit Block – Chromatogram Name] dialog box will be displayed.
Figure 4.13 [Fit Block – Chromatogram Name] Dialog Box
Click <OK> button without any modifications, then the same name with numeric characters
incremented by one as suffixes will be entered automatically in [Chromatogram Name]
columns.
Figure 4.14 Results of Fitting Block (Chromatogram Name)
It can be used for remaining columns to complete the table.
Figure 4.15 Results of Fitting Block (All Columns of the Table)
4.3.1.2 Saving Acquisition Sequence

Click (Save) button in the toolbar in [Acquisition Sequence Editor] dialog box, then [Save as
Acquisition Sequence] dialog box will be displayed.
28
Enter appropriate filename and click <Save> button in the dialog box.
CAUTION : The following message will be displayed if “Acquisition Time” in the

Acquisition Sequence and “Method Time” in the Control Mehotd are
not suitable.
Click <×> button in [Acquisition Sequence Editor] dialog box, then it will be closed.
Loading Acquisition Sequence

Show [Acquisition Sequence Monitor] view in the Data Acquisition window.
Figure 4.16 [Acquisition Sequence Monitor] View
Click (Load Acquisition Sequence) button in the toolbar in the Data Acquisition window, then [Open
Acquisition Sequence] dialog box will be displayed.

Click the filename of the Acquisition Sequence created beforehand to highlight and click
<Open> button. Then, the Acquisition Sequence will be displayed in the view.
29
Figure 4.17 Acquisition Sequence in [Acquisition Sequence Monitor] View
4.3.2.1 Setting End Mode

Click (End Mode) button in the toolbar in [Acquisition Sequence Monitor] view, then the popup
menu will be displayed.

Specify the condition of the flowing when the Acquisition Sequence has been finished as
follows.
STOP: stops all pumps.

PUMP: backs to the initial conditions in the Control Method set in the last row.
HOLD: keeps the last conditions in the Control Method set in the last row.
Click (Power Control) button in the tool bar in [Acquisition Sequence Monitor] view, then [Power
Control] dialog box will be displayed.
Figure 4.18 [Power Control] Dialog Box
The condition of the instruments in the HPLC system when the Acquisition Sequence has been
finished can be specified.
30
For LC-4000 series instruments, specify “Power Off” in [Autosampler], [Pump], [Oven],
[Detector], and [BPR] lists. Then, corresponding instruments will be turned off automatically for
the power saving.
Specify “Oven Off” in [Oven] list, then all heaters of ovens will be turned off.
Specify “Lamp Off” in [Detector] list, then lamps of detectors will be turned off (except a part of
lamps).
Check [Enable Settings] check box.
Click <OK> button in [Power Control] dialog box, then it will be closed.
Running Acquisition Sequence
Note: The Conditioning can be performed just before the Acquisition Sequence is
started. Click (PUMP) button in the middle of the Data Acquisition window,
then all modules will start to work and ChromNAV will start to monitor
baselines with the initial conditions in the Control Method set in the first row in
the Acquisition Sequence.
Click (START) button in the middle of the Data Acquisition window, then the autosampler will
start to load the first sample.

The data acquisition and the time programs in the Control Method will start when the
autosampler has injected. [System Status] will be also changed from “Pump” to “Run”.
A little before the data acquisition and the Control Method in the first row in the Acquisition
Sequence, the autosampler will start to load the second sample.
Then, the autosampler will inject when the Control Method in the first row has been finished,
and the data acquisition and the time program in the Control Method in the second row in the
Acquisition Sequence will start.
If the manual injector is used for the injector instead of the autosampler, [System Status] will be
changed from “Pump” to “Run/Wait” and the data acquisition and the time programs will not
start automatically when (START) button is clicked.
It will be changed from “Run/Wait” to “Run” and they will start when the sample is injected by
the manual injector.
[System Status] will be changed from “Run” to “Run/Wait” again at the second row to wait for
the next injection when the data acquisition and the Control Method in the first row has been
finished.
31
The current baselines (chromatograms) will be displayed in [Chromatogram Monitor] view and
[PDA Monitor] view.
Each status in each sequence row will be shown by different color in [Acquisition Sequence
Monitor] view.
The rows not to be run will be colored by green.

The row to be prepared will be colored by yellow.
The current (running) row will be colored by red.
The rows to be finished will be colored by gray.
Figure 4.19 [Acquisition Sequence Monitor] View during the Run
4.3.3.1 Editing Acquisition Sequence during the Run

In [Acquisition Sequence Monitor] view, only rows colored by green can be edited during the
run.
The background color will disappear and the [ * ] marks will be attached in the row number
column for all modified rows. In this situation, their modifications have not applied yet.
Figure 4.20 Editing Acquisition Sequence during the Run (Not Saved)
32
Click (Save Acquisition Sequence) button in the toolbar in the Data Acquisition window, then the
current Acquisition Sequence will be overwritten with all modifications. The background color
will be backed to green, and all [ * ] marks will disappear.
Figure 4.21 Editing Acquisition Sequence during the Run (Saved to be applied)
CAUTION : If their modifications have been left without overwriting, [System

Status] will be changed from “Run” to “Run/Pause” and ChromNAV
will stop the progress and wait for the overwriting to be applied when
it has finished the previous row to the modified row.
Click (Save Acquisition Sequence) button in the toolbar in the Data
Acquisition window, then all modification will be applied, [System
Status] will be backed to “Run” again, and ChromNAV restart the
progress.
4.3.3.2 Stopping Pump after Finishing

If the End Mode is set to “Pump” or “Hold”, the pump flowing will continue with “End/Pump” or
“End/Hold” in [System Status] when the Acquisition Sequence has finished.
Click (STOP) button in the toolbar in the Data Acquisition window, then the pump flowing will
stop and [System Status] is changed to “Stop”.
Data Acquisition by Manual Injector

Another data acquisition mode to repeat the same measurement with the same analysis
conditions (ex. Control Method) for multiple samples. It is suitable for the HPLC system with a
manual injector.
To activate the “Single Run” mode, select [View] > [Change Acquisition Mode] > [Single Run
Mode] in the menu in the Data Acquisition window.
33
Figure 4.22 [Single Run Monitor] View
Setting Single Run Configuration

ChromNAV will store all chromatogram files in a copy file of the Acquisition Sequence created
when the Acquisition Sequence has been run. The copy file is called as “Executed Sequence”.
In the Single Run mode, any Acquisition Sequence is not used. But, ChromNAV will create a
virtual “Executed Sequence” and store all chromatogram files in it for the same manner as one
in the Acquisition Sequence mode.
In [Sequence Name] input box, enter appropriate filename for the virtual “Executed
Sequence”.
In [Sample #] input box, enter appropriate number (1 to 9999 by a positive integer) to be

identified. In case of the autosampler, enter the position of the vial to be injected. It may be
useful the Sample # will be incremented by one automatically in each injection if “1” is entered
in [Increment] input box.
In [Chromatogram Name] input box, enter appropriate filename for the chromatograms to be
acquired. Take care a part of symbolic characters cannot be used.
Click <…> button in [Chromatogram Name] input box, then [Chromatogram Name] dialog box
will be displayed. Click <OK> button without any modifications, then the same name with
numeric characters as ID will be entered automatically in [Chromatogram Name] input box. It
may be useful ID will be incremented by one automatically in each injection if “1” is entered in
[ID] input box.
Click <…> button in [Control Method] input box, then the popup menu will be displayed.
Select [Open] in the menu, then [Open Control Method] will be displayed
Click the filename of the Control Method (analytical conditions) created beforehand to highlight
and click <Open> button. Then, the filename will be displayed in [Control Method] column.
34
Enter an appropriate value by min in [Acq. Time] column.
To lengthen the Acquisition Time, take care of the following relationship;

Refer to the description of “Method Time” in [Control Method Editor] dialog box.
Enter the correct value by µL in [Injection Volume] column. It will be recorded in the
chromatogram file.
Starting Single Run
Click (START) button in the middle of the Data Acquisition window, then [System Status] will
be also changed from “Pump” to “Run/Wait”.

The data acquisition and the time programs in the Control Method will start when the sample
has been injected by the manual injector. [System Status] will be also changed from “Run/Wait”
to “Run”.
If the autosampler is used for the injector instead of the manual injector, [System Status] will be
changed from “Pump” to “Run” and the autosampler will start to load the first sample.
The data acquisition and the time programs in the Control Method will start when the
autosampler has injected.
[System Status] will be backed from “Run” to “Run Wait” when the Control Method in the first
row has been finished. Then, the next sample can be injected.
If the autosampler is used for the injector instead of the manual injector, [System Status] will be
backed from “Run” to “Pump”. Click (START) button again, then the autosampler will start to
load the next sample.
The current baselines (chromatograms) will be displayed in [Chromatogram Monitor] view and
[PDA Monitor] view.
A list of chromatogram filenames acquired in the current run will be displayed at the lower-right
field in [Single Run Monitor] view.
35
Figure 4.23 List of Chromatogram Names
Note: In Single Run mode, up to 999 chromatograms can be acquired and stored in
the same Executed Sequence.
4.4.2.1 Editing Configuration during the Run

In [Single Run Monitor] view, configuration (parameters) can be modified during the run.
Click (EDIT) button in the middle of the Data Acquisition window, then the message, “Are you
sure you stop data acquisition?”, will be displayed. Click <Yes> button, then ChromNAV will
stop the data acquisition in the current Single Run and [System Status] will be changed to
“Pump”.
Parameters such as [Sample #], [Chromatogram Name], [Control Method], [Acq. Time], or
[Injection Volume] can be changed. Click (START) button again to restart the current Single
Run with the new parameters.
Note: In this operation, the Sequence Name (Executed Sequence Name) cannot
be modified.
4.4.2.2 Exiting Single Run
Click (STOP) button in the middle of the Data Acquisition window, then the message, “Are you
sure you stop data acquisition?”, will be displayed. Click <Yes> button, then the current Single
Run will be finished.
36
5. Data Analysis
The data analysis is performed in the Data Analysis window. ChromNAV provides various and
useful functions for the data analysis. In HPLC, the following three processes are performed
well as typical functions in the data analysis.
Peak Integration
Peak Identification
Quantitative Analysis (creating calibration curves and calculating quantities)
Of course, it is also important to printout chromatograms with calculation results.

These data analysis can be performed not only to each chromatogram manually, but to
multiple chromatograms automatically.
Here, well-used and simple operation is described to explain the basis of the data analysis in
ChromNAV.
Figure 5.1 Data Acquisition Window
Opening Chromatogram
Click (Open Chromatogram) button in the toolbar in the Data Analysis window, then [Open
Chromatogram] dialog box will be displayed.
37
Figure 5.2 [Open Chromatogram] Dialog Box
In [Executed Sequence] list in the left pane in the dialog box, all Executed Sequences
(including “virtual” Executed Sequence created in the Single Run mode) will be displayed.
Click any Executed Sequence name to highlight, then all chromatogram files included in the
Executed Sequence will be displayed in the lower field in the left pane in the dialog box.
Click any chromatogram filename to highlight, its preview and information will be displayed in
the right pane in the dialog box. While still pressing Shift key, click any chromatogram and
different chromatogram, then multiple chromatogram files can be selected simultaneously.
Click <Open> button in the dialog box, then all chromatogram files to be selected will be
displayed in the Data Analysis window.
Note: Up to 32 chromatogram files can be opened simultaneously in the Data

Analysis window.
Analog channels (CH1 – CH4), digital channels (CH5 – CH8), and virtual channels (CH9 -
CH16) will be displayed in [Chromatogram] view.
3D chromatogram and virtual channels (CH9 – CH16) will be displayed in [PDA] view.
About Active Chromatogram

All opened chromatogram filenames will be displayed using a tree in [Loaded Chromatograms]
field in the middle of the Navigation Window.
Double click any chromatogram filename, then the name will changed to the bold type. For this
manual, it is called as an “Active Chromatogram”. The Active Chromatogram will be displayed
in the right pane in [Chromatogram] view and [PDA] view.
38
Double click different filename in [Loaded Chromatogram] field, then the Active Chromatogram
will be replaced.
Figure 5.3 Active Chromatogram
Chromatogram Information
Click the right button in any chromatogram filename in [Loaded Chromatogram] field, then the
popup menu will be displayed. A part of chromatogram information such as properties can be
browsed.
Chromatogram information will be changed if it is an Active Chromatogram. Executed

Sequences displayed in the same field show their properties. Information to be shown is as
follows. Except a part of information, they can be edited. Click (Save Chromatogram) button in the
toolbar, then the chromatogram file is overwritten to apply their modifications.
[Active Chromatogram]
Properties
Sample Information
Chromatogram Description
Additional Information
Channel Names and Units
Column Information
Browse On-flow Spectra
[Other Chromatograms]
Properties
[Executed Sequences]
Properties of the Acquisition Sequence
39
Displaying Chromatogram
In [Chromatogram] view, several displaying modes of chromatograms can be available and
chosen. Some of them, multiple chromatograms in multiple chromatogram files (not only an
Active Chromatogram but other chromatograms) can be displayed simultaneously.
In a part of displaying modes, the data channel to be displayed can be chosen by [Channel] list
in the toolbar in [Chromatogram] view.
[Paged] Mode:
Shows specified data channel in the Active Chromatogram.
[Stacked – Active Chromatogram] Mode:

Shows all data channels in the Active Chromatogram in stacked graphs.
[Overlaid – Active Chromatogram] Mode

Shows all data channels in the Active Chromatogram overlaid in a graph.
[Stacked – Same Channel] Mode:

Shows specified data channel in all opened chromatograms in stacked graphs.
[Stacked – Each Channel] Mode:

Shows the same data channel in all opened chromatograms overlaid in a graph and all data
channels in stacked graphs.
[Stacked – All Chromatograms] Mode:

Shows all data channels in each chromatogram in each graph in stacked graphs.
[Overlaid – Each Channel] Mode:

Shows specified data channel in all opened chromatograms overlaid in a graph.
40
Figure 5.4 [Stacked – All Chromatograms] Mode
Peak Integration
In ChromNAV, two ways are available for the peak integration.
Automatic Peak Processing

One way is to set parameters in the “Peak Method”, and run it in the “Data Processing Method”
to the chromatogram in order to find and integrate peaks automatically.
Manual Peak Processing

Find and integrate peaks, shift peak edge positions, shift baseline start/end positions, and
delete peaks manually in [Manual Peak Processing] dialog box.
Normally, find and integrate peaks by the Automatic Peak Processing (Peak Method). The
manual peak processing may be able to find the peaks if any peaks cannot be found by the
automatic peak processing with various parameter values several times.
CAUTION : The automatic peak processing will delete all peaks found by the
manual peak processing.
Automatic Peak Processing
5.2.1.1 Setting Peak Method

Click (Edit Peak Method) button in the toolbar in the Data Analysis window. Then, [Peak Method
Editor] dialog box will be displayed.
41
Figure 5.5 [Peak Method Editor] Dialog Box
The Active Chromatogram will be displayed in the upper field in the dialog box when any
chromatograms have been opened in the Data Analysis window.
Two tabs, [General] and [Peak], will be displayed in the lower-left side in the dialog box. The
peak integration will be done with parameters in [General] tab. Parameters in [Peak] tab will be
used to calculate various peak parameters such as NTP, Resolution, Symmetry Factor, etc.
[Time Program] table will be displayed in the lower-right side in the dialog box. Various time
program parameters can be used to assist parameters in [General] tab for the peak integration.
Several important parameters in [General] tab are described as follows;
[Slope Sensitivity]
Enter the value of slope of the baseline (chromatogram) to find peak start and end positions.
[Smoothing Width]
Enter the value to smooth chromatogram by reducing noises. The higher value will smooth
more strongly.
[Min. Area]
Enter the value of peak area by µV·sec as the threshold to ignore peaks having smaller values
of peak areas than the threshold.
[Min. Height]
Enter the value of peak height by µV as the threshold to ignore peaks having smaller values of
peak heights than the threshold.
42
5.2.1.2 Verifying Peak Method
Click (Check) button in the toolbar in the dialog box. Then ChromNAV will try to find peaks in
the Active Chromatogram using parameters in [General] tab and [Time Program] table, and
show the results.
Figure 5.6 Verifying Peak Method
Note: Parameters in the Peak Method can be verified to check peak integration
results in the Active Chromatogram shown in the upper field in the dialog box.
Therefore, the test chromatogram using such as standard sample should be
specified for the Active Chromatogram.
In this test, one small peak was detected around 1.6 min except three target peaks.
Adjust parameters not to detect small peaks such as solvent peaks around the holdup time and
baseline noises. Here, two ways well-used are described;
Adjusting values of [Min. Area] and [Min. Height]:

Increase the value of [Min. Area] by ten times. Click (Check) button again, then the small peak
around 1.6 min was deleted.
43
Figure 5.7 Deleting Unnecessary Peak (by [Min. Area])
Using parameters [Time Program] table:

In the first row in [Time Program] table, specify “Lock” in [Functions] column, and enter “0.0000”
in [Start] column and “2.0000” in [End] column. It means “ChromNAV never finds any peaks
between 0.0000 min and 2.0000 min”. Click (Check) button again, then the small peak around
1.6 min was deleted.
Figure 5.8 Deleting Unnecessary Peak (by [Lock])
5.2.1.3 Saving Peak Method

Click (Save) button in the tool bar in the dialog box, then [Save As Peak Method] dialog box
will be displayed. Enter an appropriate name in [Filename] input box and click <Save> button,
then the Peak Method will be saved.
CAUTION : Here, the Peak Method has not been applied in the Active
Chromatogram yet.
44
5.2.1.4 Applying Peak Method
Click (Apply) button in the toolbar in the dialog box, then the Peak Method will be applied to the
Active Chromatogram.
Click (Close) button in the toolbar in the dialog box, then the dialog box will be closed.
Three peaks will be detected in the Active Chromatogram in [Chromatogram] view.

Retention Times, Peak Areas, and Peak Heights, etc. will be shown in [Peak Information] table
in the lower field in the right pane in the Data Analysis window.
All Peak Names will be shown as “Unknown” because the peak identification has not been
performed yet.
Figure 5.9 Results of Automatic Peak Integration
CAUTION : Here, results has been already shown for the quantitative analysis by
the Area/Height Percentage Method. They will be shown in [Area %]
and [Height %] columns.
To label their peaks, the Peak Identification must be performed.
An asterisk will be attached at the front of the Active Chromatogram name in [Loaded
Chromatogram] field in the Navigation Window. It means “Any data analysis has been
performed in the Active Chromatogram, but it has not been saved because the chromatogram
file has not been overwritten yet”.
Figure 5.10 Asterisk with Active Chromatogram Name
45
Click (Save) button in the toolbar in the Data Analysis window. Then, the Active
Chromatogram will be overwritten and an asterisk mark will be deleted.
Manual Peak Processing

Click (Manual Peak Processing) button in the toolbar in [Chromatogram] view. Then, [Manual Peak
Processing] dialog box will be displayed with the Active Chromatogram
Figure 5.11 [Manual Peak Processing] Dialog Box
5.2.2.1 Adding Peak

Click (Add Peak) button in the toolbar in the dialog box, then the mouse pointer will be changed
to .
Move the mouse pointer to the corresponding place for the peak start position and click, then
the mouse pointer will be changed to .
Move the mouse pointer to the corresponding place for the peak end position and click, then
[New Peak] dialog box will be displayed.
Figure 5.12 [New Peak] Dialog Box
In the dialog box, corresponding retention times will be shown in [Peak Start] and [Peak End]
columns to be clicked.
46
ChromNAV will also recognize the data point having highest intensity (µV) as the “Peak Top”
position, and the retention time of the data point will be shown in [tR] column.
Click <OK> button in the dialog box, then the peak will be displayed in [Manual Peak
Processing] dialog box.
The mouse pointer will be changed to in order to add different peaks. Click the right button
to finish adding peaks, then the mouse pointer will be backed to the normal style.
Figure 5.13 Adding Peak
Note: For all Peaks detected by the manual peak processing, “Manual” will be
shown in [Peak Mark] column
5.2.2.2 Deleting Peak

Click (Delete Peak) button in the toolbar in [Manual Peak Processing] dialog box, the mouse
pointer will be changed to . Move the mouse pointer to the peak to be deleted and click,
then [Select Peak] dialog box will be displayed.
Figure 5.14 Deleting Peak
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Check all peaks to be deleted and click <OK> button, then the peaks will be deleted in [Manual
Peak Processing] dialog box.
The mouse pointer will be changed to in order to delete different peaks. Click the right
button to finish deleting peaks, then the mouse pointer will be backed to the normal style.
5.2.2.3 Applying Manual Peak Processing

Click (OK) button in the toolbar in [Manual Peak Processing] dialog box, then the dialog box
will be closed.
Peaks detected by the manual peak processing will be displayed in the Active Chromatogram
in [Chromatogram] view.
Retention Times, Peak Areas, and Peak Heights, etc. will be shown in [Peak Information] table
in the lower field in the right pane in the Data Analysis window.
All Peak Names will be shown as “Unknown” because the peak identification has not been
performed yet.
Figure 5.15 Results of Manual Peak Integration
To label their peaks, the Peak Identification must be performed.
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Click (Save Chromatogram) button in the toolbar in the Data Analysis window. Then, the Active
Peak Identification
For the quantitative analysis, all required peaks must be labeled (Peak Names). In case the
quantitative analysis is not required, it may be useful to label peaks in order to identify or
specify the peak for each.
Peak Identification can be performed by the “Peak ID Table”. For the quantitative analysis, the
quantitation method (Absolute Calibration Curve Method / Internal Standard Method) must be
chosen. Furthermore, the internal standard peaks must be specified in the internal standard
method.
Changing Peak Annotation

Change the peak information shown at each peak top position to check each peak name by the
peak identification.
Note: This operation is not mandatory for the peak identification.
Click (Set Preferences) button in the toolbar in the Data Analysis window. Then, [Preference]
dialog box will be displayed.

Click [Baseline & Mark] tab in the dialog box.
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Figure 5.17 [Baseline & Mark] Tab in [Preference] Dialog Box
Specify “Peak Name” in [Annotation1] list in [Annotation] input box. Click <OK> button, then the
dialog box will be closed.
“Unknown” will be displayed at all peak top positions in the Active Chromatogram in
[Chromatogram] view.
Figure 5.18 Changing Peak Annotation
Note: “Unknown” of the peak name means the peak has not been labeled.
So, “Unknown” cannot be used for the peak name in ChromNAV.
Setting Peak ID Table

Click (Edit Peak ID Table) button in the toolbar in the Data Analysis window. Then, [Peak ID Table
Editor] dialog box will be displayed.
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Figure 5.19 [Peak ID Table Editor] Dialog Box
The Active Chromatogram will be shown in the upper field in the dialog box when any
chromatogram files have been opened.
Note: Parameters in the Peak ID Table can be verified to check peak identification
results in the Active Chromatogram shown in the upper field in the dialog box.
Therefore, the test chromatogram using such as standard sample should be
specified for the Active Chromatogram.
Click (Auto write) button in the toolbar in the dialog box. Then, data channels and retention times
of all peaks will be imported from the Active Chromatogram, and they will be copied in [CH] and
[tR] columns in the table in the lower field in the dialog box.
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Figure 5.20 Coping Peak Information
All peaks will be labeled temporary names such as “Peak-XXX” in [Name] column in the table.
Change them to appropriate names according to component names of their peaks.
Set the time window to find each peak by min in [Window] column in the table.
ChromNAV will find a peak having its peak top position within each time window for the peak
identification. For example, when “2.5667 (min)” in [tR] column and “0.1000 (min)” in [Window]
column, ChromNAV will try to find any peak top within 2.4667 min – 2.6667 min.
CAUTION : In HPLC, retention times of peaks will be shifted in each injection

compared with the previous injection by various factors.
So, it is better to enter large value in [Window] column in order to
create the wider time window. But, too much wide window may not
identify correctly because it may include two or more peak tops.
In case of quantitative analysis, specify the quantitative method in [Peak ID Table] dialog box.
Here, the way to set the Peak ID Table for the internal standard method is described as follows
because it is a complicated procedure compared with another of the absolute calibration curve
method.
Specify “Internal Standard Method” in the most left side list in the toolbar in the middle of [Peak
ID Table Editor] dialog box. Then, [ISTD] column will be displayed in the table in the dialog box.
Check in the check box in [ISTD] column for the row of the internal standard, and specify “1” in
the list displayed in the right side of the check box.
CAUTION : Up to 16 internal standard peaks are available in ChromNAV. But,

when the same internal standard compound is detected at multiple
52
wavelengths (or multiple detectors), they will be different internal
standard peaks.
In all remaining rows (except rows for the internal standards), specify appropriate ISTD
number to refer in the list in [ISTD] column.
Figure 5.21 Peak Name, Time Window, Quantitation Method, and Setting in [ISTD] Column
Verifying Peak ID Table

Click (Check) button in the toolbar in the dialog box, then the popup menu will be displayed.
Select “Check Identification Only” in the menu. Then, ChromNAV will try to identify peaks in the
Active Chromatogram showed in the upper field in the dialog box using parameters in the
middle of the dialog box and in the table in the lower field in the dialog box, and show the
results in the chromatogram.
Figure 5.22 Verifying Peak Identification
Saving Peak ID Table

Click (Save) button in the tool bar in the dialog box, then [Save As Peak ID Table] dialog box
will be displayed. Enter an appropriate name in [Filename] input box and click <Save> button,
then the Peak ID Table will be saved.
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CAUTION : Here, the Peak ID Table has not been applied in the Active
Chromatogram yet.
Applying Peak ID Table

Click (Apply) button in the toolbar in the dialog box, then the popup menu will be displayed.
Select “Apply Identification Only” in the menu, then the Peak ID Table will be applied to the
Active Chromatogram.
Three peaks and one internal standard peak will be identified in the Active Chromatogram in
[Chromatogram] view.
Retention Times, Peak Areas, and Peak Heights, etc. will be shown in [Peak Information] table,
and appropriate Peak Names will be also shown in the lower field in the right pane in the Data
Analysis window.
Figure 5.23 Verifying Peak Identification
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Click (Save Chromatogram) button in the toolbar in the Data Analysis window. Then, the Active
Quantitative Analysis
For the quantitative analysis, it is necessary to create the calibration curve using the peak area
or the peak height with a concentration (or an amount) in the standard sample, and to calculate
the concentration (or amount) as the quantity using the peak area or the peak height in the
unknown sample with the calibration curve.
To create and manage the calibration curves, the “Calibration Method” must be created for
each quantitative analysis.
To calculate the peak area and the peak height, the Peak Method is used. Normally, different
Peak Method must be used for different data channel because the retention time, the intensity,
the broadening, etc. vary in each data channel (each wavelength or each detector). So, the
“Data Processing Method” is used to run the same data process (ex. the peak integration)
multiple times using multiple Methods (ex. the Peak Methods) in one data analysis.
To run the batch of data processing for multiple chromatogram files, the “Recalculation
Sequence” is used. The setting in the recalculation sequence table must be done manually, but
all data processing in it can be done automatically (from creating calibration curves to
calculating quantities).
Calibration Method
In the quantitative analysis, the same “Calibration Method” must be used to all standard and
unknown samples.
Click (Edit Calibration Method) button in the toolbar in the Data Analysis window. Then, [Calibration
Method Editor] will be displayed.
55
Figure 5.25 [Calibration Method Editor] Dialog Box
Click (Open ID Table) button in the toolbar in the dialog box, then [Open Peak ID Table] will be
displayed.
Click appropriate filename of the Peak ID Table to highlight and click <Open> button. Then, all
peak names imported from the Peak ID Table will be shown in the table in the left pane in the
dialog box.
Note: Peak names of internal standards will not be shown in the table.
Specify number of levels of standard samples in [# of STDs] list, then [STDn] columns in the
table will be increased or decreased according to the value in [# of STDs] list.
Enter concentrations (or amounts) in [STDn] columns, and enter the unit for concentrations (or
amounts) in [Unit] column.
Specify “Linear” or “Quadratic” in [Type] column for types of approximate equations.
Specify how to use the origin to create the approximate equation in [Zero] column as follows.
Ignore: Does not use the origin to create the calibration curve.
Include: Includes the origin to create the calibration curve.
Connect: Does not use the origin, but create the calibration curve passing the origin.
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Figure 5.26 Setting Calibration Method
Click (Save) button in the tool bar in the dialog box, then [Save As Calibration Method] dialog
box will be displayed. Enter an appropriate name in [Filename] input box and click <Save>
button, then the Calibration Method will be saved.
Report Style
To printout Chromatogram files or Method files, it is a simple way to click (Print) buttons in the
corresponding views or in the corresponding dialog boxes. But, they are fixed layouts and not
customized anything.
Reports can be created and customized in the “Report Style” or the “Sequence Report Style”.
Here, the way to create the reports in the “Report Style” and the way to printout created report
style are described.
In the “Report Style”, various report styles to print the data such as the contour map of the 3D
chromatogram, the on-peak spectra, the calibration curves, etc., to print parameters in the
Methods, or to print instruments’ information and any profiles such as the flow rate, the
gradient elution, the oven temperature.
Refer to the following procedure to create those report styles.
Click (Edit Report Style) button in the toolbar in the Data Analysis window. Then, [Report Style
Editor] window will be displayed.
57
Figure 5.27 [Report Style Editor] Window
[Chromatogram] Object:
Double click the [Chromatogram] icon in the [Style Objects] tab in the left pane in the window.
Then, the [Chromatogram] object will be displayed on the image of the report shown in the right
pane in the window.
Click [Others] tab in [Properties] frame in the left pane in the window, and specify “Peak
Number” in [Annotation] > [Label1] list in the tab.
Drag frames of the [Chromatogram] object on the report and adjust the size of the object.
[Chromatogram Info.] Object:

Double click the [Chromatogram Info.] icon in the [Style Objects] tab in the left pane in the
window. Then, the [Chromatogram Info.] object will be displayed below the [Chromatogram]
object on the image of the report.
Drag frames of the [Chromatogram Info.] object on the report and adjust the size of the object.
[Peak Info. Table] Object:

Double click the [Peak Info. Table] icon in the [Style Objects] tab in the left pane in the window.
Then, the [Peak Info. Table] object will be displayed below the [Chromatogram Info.] object on
the image of the report.
Click [Details] tab in [Properties] frame in the left pane in the window, and specify “Show” or
“Hide” for each peak information.
Drag frames of the [Peak Info. Table] object on the report and adjust the size of the object.
58
Figure 5.28 Image of Report Style
Click (Save) button in the toolbar in [Report Style Editor] window, then [Save As Report Style]
dialog box will be displayed. Enter an appropriate name in [Filename] input box and click
<Save> button, then the Report Style will be saved.
Click (Exit) button in the toolbar in the window, then the window will be closed.
Data Processing Method

The “Data Processing Method” is some kind of batch of data processing. Especially, the peak
integrations and printing the reports are included in it.
Click (Edit Data Processing Method) button in the toolbar in the Data Analysis window. Then, [Data
Processing Method Editor] dialog box will be displayed.
Figure 5.29 [Data Processing Method Editor] Dialog Box
Specify “Find Peak” in [Process] column and enter “1” in [CH] column in the first row in the table
in the dialog box.
59
Click <…> button in [Parameters] column in the first row in the table, then [Open Peak Method]
dialog box will be displayed. Click the filename of the Peak Method created beforehand to
highlight and click <Open> button. Then, the filename will be displayed in [Parameters]
column.
Specify “Print Report” in [Process] column and enter “1” in [CH] column in the second row in
the table.
Click <…> button in [Parameters] column in the second row in the table, then [Open Report
Style] dialog box will be displayed. Click the filename of the Report Style created beforehand to
highlight and click <Open> button. Then, the filename will be displayed in [Parameters]
column.
Figure 5.30 Setting Data Processing Method
CAUTION : Printing objects in the Report Style are separated into the two types
between requiring data channel numbers and not requiring any data
channels.
For example, [Chromatogram] object will require any data channels,
and [Control Method] object will not require anything.
For the Report Style configured only printing objects not requiring
any data channels, [CH] column must be blank.
Note: Multiple data channel numbers can be set in one [CH] column.
Enter “1-4”, then the corresponding process will be done to all four channels
from CH-1 to CH-4.
Enter “1, 4”, then the corresponding process will be done to CH-1 and CH-4
only.
Click (Save) button in the toolbar in [Data Processing Method Editor] dialog box, then [Save
As Data Processing Method] dialog box will be displayed. Enter an appropriate name in
[Filename] input box and click <Save> button, then the Data Processing Method will be saved.
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Recalculation Sequence
After all preparations have been finished, create the “Recalculation Sequence” with acquired
chromatogram files. The Recalculation Sequence will analyze all chromatograms, and create
calibration curves and calculate quantities as follows;
(1) For Standard Chromatograms
1) Integrates peaks by the Peak Method in the Data Processing Method.

2) Identifies peaks by the Peak ID Table.
3) Creates calibration curves by the Calibration Method.
4) Printouts the chromatogram reports by the Report Style in the Data Processing
Method.
(2) For Unknown Chromatograms

1) Integrates peaks by the Peak Method in the Data Processing Method.
2) Identifies peaks by the Peak ID Table.
3) Calculate quantities from calibration curves in the Calibration Method.
4) Printouts the chromatogram reports by the Report Style in the Data Processing
Method.
5.4.4.1 Creating Recalculation Sequence

Show [Recalculation Sequence] view in the Data Analysis window.
Figure 5.31 [Recalculation Sequence] View
Click (Open Executed Sequence) button in the toolbar in [Recalculation Sequence] view. Then, [Open
Executed Sequence] will be displayed.
61
Figure 5.32 [Open Recalculated Sequence] Dialog Box
Click an appropriate name of the Executed Sequence to highlight in [Executed Sequence]

table in the left pane in the dialog box, and click <Open> button. Then, all chromatogram files in
the Executed Sequence will be shown in [Chromatogram Name] column in each row in the
table in [Recalculation Sequence] view.
Figure 5.33 Opening Chromatograms from Executed Sequence
CAUTION : Chromatogram must be set from standard samples to unknown

samples in order in the table.
62
Here, [Sample #], [Volume], [Acq. Time], and [Control Method] columns cannot be edited and
they are colored by blue. They are information in chromatogram files and will be shown
automatically.
Set [Type] column. Specify appropriate number from “STD1” to “STD10” for corresponding
concentration (or amount) for each standard sample, and specify “UNK” for all unknown
samples.
Figure 5.34 Setting Sample Type
Drag [Peak ID Table] columns from the first row to the sixth row and click the right button, then
the popup menu will be displayed. Select “Open” in the menu, then [Open Peak ID Table]
dialog box will be displayed. Click the filename of the Peak ID Table created beforehand to
highlight and click <Open> button, then the filenames will be shown in [Peak ID Table]
columns.
Drag [Calibration Method] columns from the first row to the sixth row and click the right button,
then the popup menu will be displayed. Select “Open” in the menu, then [Open Calibration
Method] dialog box will be displayed. Click the filename of the Calibration Method created
beforehand to highlight and click <Open> button, then the filenames will be shown in
[Calibration Method] columns.
Specify “New” in [Mode] list in the first row, “Add” in the second to fourth rows, and leave it
blank in the fifth to sixth rows.
Drag [Data Processing Method] columns from the first row to the sixth row and click the right
button, then the popup menu will be displayed. Select “Open” in the menu, then [Open Data
Processing Method] dialog box will be displayed. Click the filename of the Data Processing
Method created beforehand to highlight and click <Open> button, then the filenames will be
shown in [Data Processing Method] columns.
For those operations, settings in the table in [Recalculation Sequence] view should be as
follows;
Figure 5.35 Setting Recalculation Sequence
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Click the right button in any [ISTD #1] column from the first row to the sixth row, then [Fit Block
– ISTD] dialog box will be displayed. Enter an appropriate value in [ISTD #1] input box and click
<OK> button. Enter each value in all [ISTD #1] input boxes in the first row to the sixth row.
Figure 5.36 Setting Internal Standard
5.4.4.2 Running Recalculation Sequence

Click (Run) button in the toolbar in [Recalculation Sequence] view. Then all data process in
the table will be run automatically.
If the same chromatogram files in [Recalculation Sequence] view has been opened and any
data process has been done to them, the following message may be displayed.
Figure 5.37 Confirmation Message for Running Recalculation Sequence
Click <Yes> button, then all data process without saving in their chromatogram files will be lost
and the Recalculation Sequence will be run.
Click <No> button, then the Recalculation Sequence will not be run.
Browsing Result of Data Analysis
5.4.5.1 Browsing Calibration Curve

Click (Edit Calibration Method) button in the toolbar in the Data Analysis window. Then, [Calibration
Method Editor] dialog box will be displayed.
Click (Open) button in the toolbar in the dialog box, then [Open Calibration Method] dialog box
will be displayed. Click the filename of the Calibration Method used in the Recalculation
Sequence and click <Open> button.
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Figure 5.38 Calibration Curve in Calibration Method
The calibration curve and its information will be shown in the right pane in the dialog box.
Confirm any warning message has not been shown in the middle field in the right pane.
Click different peak name in the table in the left pane. Then, corresponding calibration curve
and its information will be shown in the right pane.
Click (Close) button in the toolbar in the dialog box, then it will be closed.
5.4.5.2 Browsing Quantity

Show [Chromatogram] view in the Data Analysis window.
Click (Open) button in the toolbar in [Chromatogram] view. Then, [Open Chromatogram]
dialog box will be displayed. Select all chromatogram files used in the Recalculation Sequence
and click <OK> button, then they will be opened in the view.
Figure 5.39 Recalculation Result in [Chromatogram] View
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Confirm the peak integration and the peak identification have been done correctly for all
chromatograms.
In unknown chromatograms, check values in [Quantity] columns in the peak information table
in the right pane in the view.
Figure 5.40 Quantitative Calculation Result
Confirm all chromatogram reports have been printed out.
Figure 5.41 Result of Report Style
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6. Three-dimensional Chromatogram
Advantages of three-dimensional chromatogram (3D chromatogram) acquired by the PDA
detector are not only to extract any chromatograms at any wavelengths, but to extract any
spectra at any retention times.
Advanced data analysis such as the peak purity calculation, on-peak spectral searching, etc.
can be done using spectra extracted from the 3D chromatogram.
Extracting Chromatogram and Spectrum

Show [PDA] view in the Data Analysis window and click “General” tab in the view, then
[General] panel will be displayed.
In [Contour Map] field in the lower-left frame in the panel, the 3D chromatogram in the Active
Chromatogram will be shown.
In [Chromatogram] field in the upper-left frame in the panel, the virtual channel chromatograms
in the Active Chromatogram file will be shown.
In [Spectrum] field in the lower-right frame in the panel, any spectra will not be shown.
Figure 6.1 [General] Panel in [PDA] View
Click the right button in the contour map, then the popup menu will be displayed. Select “XY
Cursor” in the menu, then a crosshair cursor will be displayed in the contour map.
Drag the cursor, then the corresponding chromatogram at the wavelength the cursor indicates
will be shown in [Chromatogram] field and the corresponding spectrum at the retention time the
cursor indicates will be shown in [Spectrum] field.
Click the right button in the contour map, then the popup menu will be displayed. Select “Add to
Chromatogram Frame” or “Add to Spectrum Frame” in the menu, then the chromatogram or
the spectrum the cursor indicates will be fixed in [Chromatogram] or [Spectrum] field.
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Note: Initial scales of “Intensity” axes in the [Chromatogram] and [Spectrum] fields
may be too large. Click the right button in any fields, then popup menu will be
displayed. Select “Normalize” in the menu, then the “intensity” axis will be
normalized.
Figure 6.2 Adding Chromatogram and Spectrum with Normalized Scale
Assigning to Virtual Channel

Click (Extract and Set Virtual Channels) button in [General] panel in [PDA] view. Then, [Extract and Set
Virtual Channels] dialog box will be displayed.

In [Data Type] and [WL1] columns, for acquired virtual channels and chromatograms extracted
from the contour map, “Chromatogram” and corresponding wavelengths will be shown.
Figure 6.3 [Extract and Set Virtual Channels] Dialog Box
For extracted chromatograms, “None” will be shown in [CH] column. Specify any empty data
channel in [CH] list and click <OK> button. Then, the chromatogram can be assigned to the
data channel if any data channel in the Active Chromatogram is not in use.
68
Figure 6.4 Assign Extracted Chromatogram to the New Virtual Channel
Click (Save Chromatogram) button in the toolbar in [PDA] view, the Active Chromatogram will be
overwritten and the new virtual channels will be saved.
Detecting Spectral Peak

Click the right button on the spectrum, then the popup menu will be displayed. Select “Find
Peak” in the menu, then [Spectral Peak Find] dialog box will be displayed.
Figure 6.5 [Spectral Peak Find] Dialog Box
Enter the threshold of intensity by percent in [Peak Threshold] input box.

ChromNAV will regard a data point having the lowest intensity as “0 (%)”, and a data point
having the highest intensity as “100 (%)”. Then, it will look for all peak top and peak valley
positions in all data points above the threshold.
Figure 6.6 Spectrum and Spectral Peaks
Browsing Bird’s-eye View

Click “3D” tab in [PDA] view, then [3D] panel will be displayed. The 3D chromatogram in the
Active Chromatogram will be shown by the style of the bird’s-eye view.
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Figure 6.7 3D Chromatogram in [3D] Panel in [PDA] View
Drag in the 3D chromatogram, then the chromatogram will be rotated.
Click the right button in the 3D chromatogram, then the popup menu will be displayed.
Select “Zoom” in the menu, and drag downward, then 3D chromatogram will be expanded, also
drag upward, then it will be contracted.
Select “Shift” in the popup menu, and drag in any direction, then 3D chromatogram will be
shifted.
Comparing Contour Map

Click “Compare Contours” tab in [PDA] view, then [Compare Contours] panel will be displayed.
The 3D chromatogram in the Active Chromatogram will be shown by the style of the contour
map view.
Figure 6.8 [Compare Contours] Panel in [PDA] View
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The 3D chromatogram in the Active Chromatogram will be shown in the lower contour map.
Another 3D chromatogram can be opened in the upper contour map to be compared.
Click the right button in the upper contour map, then the popup menu will be displayed. Select
“Open Chromatogram” in the menu, then [Open Chromatogram] dialog box will be displayed.
Click any chromatogram filename having the 3D chromatogram to highlight and click <Open>
button. Then, the 3D chromatogram in opened chromatogram file will be shown in the upper
contour map.
Click the right button in the view, then the popup menu will be displayed. Select “XY Cursor” in
the menu, then two crosshair cursors will be shown as one in the upper contour map and
another in the lower contour map.
Drag any cursor, then it will be moved and another cursor will be also moved. They are
synchronized and they will always indicate the same location in two contour maps.
Figure 6.9 Compare Contour Map by Cursor
Ratio Chromatogram
In well-separated chromatogram at any wavelength, one peak is formed by one component.
But, two or more components closed each other may form like one peak when they have not
been separated well.
When the chromatogram acquired at some wavelength is compared with others at different
wavelengths, the peak will become larger or smaller because the absorption of the component
varies by the wavelength. But, the degree of the slope (increased/decreased, steep/gentle,
etc.) between peaks at different wavelengths should correlate each other if the peak is formed
by one pure component.
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The ratio chromatogram will be created by dividing one chromatogram at any wavelength by
another at different wavelength.
All ratios of data points within one peak will be almost the same and the shape of the peak in
the ratio chromatogram will be plateau for the peak formed by one compound.
On the other hand, their ratios will vary and the shape of the peak in the ratio chromatogram
will not be plateau (like slant, convex, concave, etc.) if the peak formed by multiple compounds.
Click “Ratio Chromatogram” tab in [PDA] view, then [Ratio Chromatogram] panel will be
displayed. Three [Chromatogram] fields will be displayed vertically in the panel.
Figure 6.10 [Ratio Chromatogram] Panel in [PDA] View
Click the right button in [Ratio Chromatogram] panel, then the popup menu will be displayed.
Select “Select Chromatogram” in the menu, then [Add Ratio Chromatogram] dialog box will be
displayed.
Figure 6.11 [Add Ratio Chromatogram] Dialog Box
Enter appropriate wavelength as the numerator in [(N)] input box and another as the
denominator in [(D)] input box.
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The threshold level to calculate the ratio must be used for all data points because a very huge
value may be answered to interfere with checking ratio peaks if both intensities of data points
between the numerator and denominator are too low and almost zero. ChromNAV will not
calculate all data points having lower intensities than the value of [Threshold] column in the
chromatogram as the numerator and answer “0” for them.
Each height (level) of the ratio peak will be much different with others. Choose appropriate one
in [Factor] field to specify the scale in the intensity axis.
Click <OK> button, then the dialog box will be closed. In [Ratio Chromatogram] panel, The ratio
chromatogram will be displayed in the upper [Chromatogram] field, the chromatogram as the
numerator will be displayed in the middle of [Chromatogram] field, and the chromatogram as
the denominator will be displayed in the lower [Chromatogram] field.
Figure 6.12 Calculation Results of Ratio Chromatogram
The scale of the intensity axis can be changed to check smaller ratio peaks if necessary.
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Figure 6.13 Calculation Results of Ratio Chromatogram (Zoomed)
For example, a ratio peak at around 7.3 min is almost flat, and it means this peak is formed by
one compound.
On the other hand, another at around 6.3 min is not flat and becomes concave in the later half
of the peak, and it means this peak may be formed and overlapped by two or more compounds.
But, in this peak, ratio may not be able to be calculated correctly because both peaks of one as
the numerator and another as the denominator are not so high enough to calculate the ratio.
Therefore, two wavelengths having enough high intensities for the target peaks must be
chosen to calculate the ratio chromatogram.
On-Peak Spectrum and Spectral Library

Click “on-Peak Spectra” tab in [PDA] view, then [on-Peak Spectra] panel will be displayed.
Multiple [Spectrum] fields will be displayed in the upper side, and [Chromatogram] field will be
displayed in the lower side in the view.
The first virtual channel in the Active Chromatogram will be displayed in [Chromatogram] field.
Specify any data channel in [Channel] list in the toolbar in the view, the virtual channel shown
in the view can be changed.
Any spectrum at any retention time in the chromatogram shown in the lower side can be
extracted in any [Spectrum] filed in upper side in the view. Generally it is useful to extract
spectra at peak top positions in the chromatogram.
The spectral library to store extracted spectra can be created. If on-peak spectra (spectra at
peak top positions) extracted from the standard chromatogram are stored in the library as
standard spectra, ChromNAV can search similar spectra in the library with on-peak spectrum
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extracted from the unknown chromatogram and show several candidates by the degree of
coincidence.
Figure 6.14 [on-Peak Spectra] Panel in [PDA] View
Extracting On-Peak Spectra

According to procedures of data analysis described in the previous chapter, integrate peaks
beforehand in the chromatogram shown in [Chromatogram] field. It is better to identify them.
Figure 6.15 Peak Find and Peak Identification in Virtual Channel Chromatogram
Click right button in the chromatogram, then the popup menu will be displayed. Select “Add All
Peak-Top Spectra” in the menu, then all spectra of all peak-top positions will be displayed from
the most left spectrum field in order.
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Figure 6.16 Extractions of On-Peak Spectra
Note: If number of on-peak spectra are more than number of spectrum fields, select
[View] > [Number of Spec. Views] in the menu in [On-Peak Spectra] Panel in
[PDA] View to increase number of spectrum fields.
Creating Spectral Library

Select [File] > [Spectral Library] in the menu in [PDA] view. Then, [Edit Spectral Library] dialog
box will be displayed.
Figure 6.17 [Edit Spectral Library] Dialog Box
Click (New) button in the toolbar in the dialog box, then [Create Spectral Library] dialog box
will be displayed.
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Figure 6.18 [Create Spectral Library] Dialog Box
Enter appropriate filename in [Library Name] input box, and click <Create> button. Then, the
dialog box will be closed and the new library name will be displayed in the title bar in [Edit
Spectral Library] dialog box.
Click (Close) button in the dialog box, then it will be closed.
Note: Here, only the “container” of the spectral library is created.
6.5.2.1 Registering On-Peak Spectrum in Library

Click right button in any [Spectrum] field in [PDA] view, then the popup menu will be displayed.
Select [Add to Spectral Library] > [All Spectra] in the menu, then [Add Spectra] dialog box will
be displayed.
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Figure 6.19 [Add Spectra] Dialog Box
Click appropriate filename of the spectral library created beforehand to highlight and click
<Add> button. Then, the dialog box will be closed and [Edit Spectral Library] dialog box will be
displayed again.
Figure 6.20 Registration of on-Peak Spectra in the Library
The filename of the spectral library will be displayed in the title bar in the dialog box. All
on-peak spectra extracted in [on-Peak Spectra] panel will be displayed.
Click (Save) button in the toolbar in the dialog box, then the current spectral library will be
overwritten. Click (Close) button in the toolbar, then the dialog box will be closed.
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6.5.2.2 Creating Spectral Search Method
Click (Edit Spectral Search Method) button in the toolbar in the Data Analysis window. Then, [Spectral
Search Method Editor] dialog box will be displayed.
Figure 6.21 [Spectral Search Method Editor] Dialog Box
Check the filename of the spectral library to be used for the searching in the right side in the
dialog box. Multiple spectral libraries can be checked if necessary.
Several parameters will be also displayed in the left side in the dialog box. Here, try to edit
[Search Result Options] parameters.
Enter an appropriate value as the correlation in [Criterion of Correlation] input box. It may not
show any candidate spectra in libraries if much higher value is entered.
Specify number of candidate spectra for each spectrum to be searched in [Max. No. of
Candidates] input box. The candidate spectra will be displayed from the spectrum having
highest correlation in order.
Click (Save) button in the toolbar in the dialog box, then [Save as Spectral Search Method] will
be displayed. Enter appropriate filename in [Filename] input box and click <Save> button.
Click (Close) button in the toolbar in [Spectral Search Method Editor] dialog box, then the
dialog box will be closed.
Searching in the Library 1
CAUTION : In spectra acquired in the HPLC system, spectral peaks may be

shifted or their forms may be vary by various external factors such as
types of mobile phase solvents, components of their solvents, etc.
Therefore, the analytical condisions between acquiring standard
spectra and the spectrum to be searched should be the same as
possible.
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ChromNAV can search spectral libraries for the unknown spectrum showed in [General] or
[on-Peak Spectra] panel in [PDA] view, and identify by correlations between it and each
candidate spectrum.
Click right button in the corresponding [Spectrum] field, then the popup menu will be displayed.
Select [Spectral Library Search] in the menu and specify the spectrum to be searched shown in
the field. Then, [Execute Spectral Search Method] dialog box will be displayed.
Figure 6.22 [Execute Spectral Search Method] Dialog Box
Click the filename of the spectral library created beforehand to highlight and click <Execute>
button. Then, [Search Result] dialog box will be displayed.
Figure 6.23 [Search Result] Dialog Box
In this example, the spectrum was identified as “Pyrene” shown in the first row in [List of
Spectra] table because the correlation is very high and both of retention times are almost the
same.
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Searching in the Library 2
In [on-Peak Spectra] panel in [PDA] view, multiple on-peak spectra can be searched libraries
simultaneously.
Figure 6.24 Unknown Chromatogram and On-Peak Spectra
Click (Spectral Search for Detected Peaks) button in the toolbar in [on-Peak Spectra] panel in [PDA] view.
Then, [Spectral Search for Detected Peaks] dialog box will be displayed.
Figure 6.25 [Spectral Search for Detected Peaks] Dialog Box
Click (Open Spectral Search Method) button in the tool bar in the dialog box, then [Open Spectral
Search Method] dialog box will be displayed.
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Figure 6.26 [Open Spectral Search Method] Dialog Box
Click the filename of Spectral Search Method created beforehand to highlight and click
<Open> button. Then, the dialog box will be closed, and the filename will be displayed in
[Spectral Search Method] column in [Spectral Search for Detected Peaks] dialog box.
Figure 6.27 Spectral Search Method Name to be Used
Specify appropriate data channel number in [Channel] lit in the toolbar in the dialog box.
Click (Execute Searching) button in the toolbar in the dialog box. Then, search results for all
on-peak spectra will be displayed.
Figure 6.28 Search Results of Multiple on-Peak Spectra
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The spectrum having highest correlation compared with each on-peak spectrum is checked
among its candidates. The identified spectrum can be unchecked if the search results is not
reliable in case that the correlation is not so high.
Click (Create Peak ID Table) button in the toolbar in the dialog box. Then, [Peak ID Table Editor]
dialog box will be displayed, and all names of candidates (checked) for all on-peak spectra will
be imported in the peak ID table with their data channels and retention times automatically.
Click (Save) button in the toolbar in [Peak ID Table Editor] dialog box, then [Save as Peak ID
Table] dialog box will be displayed. Enter appropriate filename in [Filename] input box and click
<Save> button if necessary.
Peak Purity Calculation

In well-separated chromatogram at any wavelength, one peak is formed by one component.
But, two or more components closed each other may form like one peak when they have not
been separated well.
When the spectrum at peak-top position is compared with another at any retention time within
the same peak, they should correlate each other if the peak is formed by one component.
Furthermore, all spectra at all retention times within one peak should correlate each other in
the one component peak.
The peak purity calculation is one solution to check if the peak is formed by one component
using two or more spectra at different retention times within the peak. It is more reliable and
useful than the ratio chromatogram.
Click “Peak Purity” tab in [PDA] view, then [Peak Purity] panel will be displayed.
[Chromatogram] fields in upper side, [Spectrum] and [Peak] fields in the middle side, and the
calculation results in the lower side will be displayed in the panel.
There are two ways to calculate peak purities. One way is ChromNAV compares the spectrum
at the peak top position with another at “the front side” in the peak, and compares the spectrum
at the peak top position with another at “the tail side” in the peak by the correlations. The actual
places of “the front side” and “the tail side” can be chosen in the list.
Another way is ChromNAV compares the spectrum at the peak top position with all spectra at
all retention time within the peak by the correlations. The results will be displayed as colors
according to the correlations.
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Figure 6.29 [Peak Purity] Panel in [PDA] View
According to procedures of data analysis described in the previous chapter, integrate peaks
beforehand in the chromatogram shown in [Chromatogram] field. It is better to identify them.
Creating Peak Purity Method

Click (Edit Peak Purity Method) button in the toolbar in the Data Analysis window. [Peak Purity
Method Editor] dialog box will be displayed.
Figure 6.30 [Peak Purity Method Editor] Dialog Box
Here, the way to compare the spectrum at the peak top position with another at “the front side”
in the peak and compare the spectrum at the peak top position with another at “the tail side” in
the peak by the correlations are described.
In [Spectra Applied for Purity Calculation] field in the left-bottom side in the dialog box, click to
choose “Front & Tail Spectra”, and specify “4 Sigma” in the list.
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Click (Save) button in the toolbar in the dialog box, then [Save as Peak Purity Method] dialog
box will be displayed. Enter appropriate filename in [Filename] input box and click <Save>
button. Click (Close) button in the toolbar, then the dialog box will be closed.
Calculating Peak Purity

Click (Peak Purity) button in [Peak Purity] panel in [PDA] view, then [Execute Peak Purity
Method] dialog box will be displayed.
Figure 6.31 [Execute Peak Purity Method] Dialog Box
Click the filename of Peak Purity Method created beforehand to highlight in [Filename] column,
and click <Execute> button in the dialog box.
In the peak information table in the lower side in [Peak Purity] panel, the calculation results will
be displayed in [Purity Front] and [Purity Tail] columns.
The corresponding peak will be displayed with its peak top, “the front side”, “the tail side”, and
their three spectra will be displayed in the middle side in [Peak Purity] panel.
Figure 6.32 Peak Purity Calculation Results
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7. Various Features
Changing Analytical Conditions during the Run

During the conditioning (Monitor Baseline), or the data acquisition ([Acquisition Sequence]
mode or [Single Run] mode), analytical conditions (Control Method) can be changed
temporarily.
The gradient profile of the pumps (Time Program in Control Method) can be also changed and
overwritten during the run.
Temporary Change of Analytical Conditions

Click corresponding button in [System Monitor] view or the system monitor in Navigation
Window, then [Change Parameter] dialog box will be displayed.
Figure 7.1 [Change Parameter] Dialog Box
Change required parameters and click (Apply) button in the dialog box. Then, the dialog box
will be closed and their parameters will be changed immediately.
Note: Parameters changed by this function will be initialized automatically when the
control method of the next data acquisition has been started.
Changing and Overwriting Gradient Profile
CAUTION : In the chapter of “Data Acquisition”, it describes any parameters and

Methods cannot be modified in the current row colored by red and in
the next row ChromNAV has been started loading colored by yellow.
But, only this function can apply to not only later rows but red and
yellow rows immediately and overwrites Control Methods having the
same names automatically in them.
Click button in the pump monitor in [System Monitor] view in the Data Acquisition window,
then [Change Time Program] dialog box will be displayed. Normally it is used when the profile
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of the gradient elution is modified during the run to elute remaining peaks earlier for any reason
(ex. the method development).
Figure 7.2 [Change Time Program] Dialog Box
Change the gradient profile in [Change Time Program] dialog box.

Click (Apply and Close) button in the toolbar in the dialog box, then the dialog box will be closed
and the gradient profile in the current run will be changed and the current Control Method will
be overwritten.
Note: Changing time program events in the pumps will be applied immediately. If
the same Control Method is set in any later sequence rows, they will be
overwritten automatically.
Email Notification
The actual status of the running data acquisition by the [Acquisition Sequence] mode or the
[Single Run] mode can be sent by the email. The items of status can be notified are as follows;
Error
Start of the acquisition sequence (or the single run)
Start of the data acquisition
Finish of the data acquisition
Finish of the acquisition sequence (or the single run)
Switch to the end mode
Click the start button in Windows and select [All Programs] > [JASCO] > [ChromNAV] >
[ChromNAV Mail Manager], then [Logon] dialog box will be displayed.
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Figure 7.3 [Logon] Dialog Box
Log on using the username and password as [Control Center] window, then [ChromNAV Email
Settings] dialog box will be displayed.
Figure 7.4 [ChromNAV Email Settinigs] Dialog Box
Up to 10 email addresses can be registered in [Mailing List] table. Check [Send] for addresses
to receive emails.
Set appropriate values to parameters in [SMTP Setting] and [Security and Authentification].
Click <OK> button, then the dialog box will be closed.
Click (Email Notification) button in the toolbar in [Acquisition Sequence Monitor] view or [Single
Run Monitor] view in the Data Acquisition window, then [Email Notification] dialog box will be
displayed.
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Figure 7.5 [Email Notification] Dialog Box
Check [Notify by Email] and specify the username in [Email Receipt Destination] list. Check
events to be notified in [Contents] field.
Click <OK> button, then the dialog box will be closed. The email notification will perform
according to settings in [ChromNAV Email Settings] dialog box and [Email Notification] dialog
box when the data acquisition starts in [Acquisition Sequence] mode or [Single Run] mode.
Method Template
In ChromNAV, all initial values in all parameters in Methods are optimized for the general use,
but they are not always appropriate values for all applications. So, sometimes some of them
may be changed to much different values to be used according to the type of application.
ChromNAV can save any method to be edited and saved beforehand as Method Template. All
values set in Method Template will be the new “initial” values for the method.
Here, the way to create Method Template of Peak Method as an example.
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Figure 7.6 Peak Integration Results by Initial Parameter Values
As above figure, several solvent shocks around the holdup time and unnecessary small peaks
are found and integrated when all parameters are initial values.
So, change one parameter value and add one time program parameter to improve results as
follows.
Change [Slope Sensitivity] to 10 times value (100.00 [µV/sec]).

Change [Min. Area] to 20 times value (200000.00 [µV·sec]).
Add “Lock” from 0.0000 [min] to 3.0000 [min] in [Time Program] table.
Then, all unnecessary peaks are not found with the new parameter values as below figure.
Figure 7.7 Optimization of Parameter Values in Peak Method
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Click (Save) button in the toolbar in [Peak Method Editor] dialog box, and save the new Peak
Method.
After that, (Save As Template) button will become available in the dialog box. Click the button, then
the confirmation message will be displayed. Click <Yes> button, then all parameter values in
the new Peak Method will be saved as Method Template of Peak Method.
Close [Peak Method Editor] dialog box and open again. Three values, “Slope Sensitivity”, “Min
Area”, and “Lock”, saved as Method Template are shown as initial values.
Figure 7.8 Example of Method Template
Note: Method Templates will be saved in the current Project. It cannot be saved in
any other Projects.
Application Template
Application Template is very useful feature especially when analytical conditions are
determined and not changed for long time or when HPLC system configuration is fixed and not
changed for long time, etc.
Not only Method Templates, but specifying shown or hidden for all views, customizing toolbars
and a part of tables, changing initial values in preferences in both of the Data Acquisition
window and Data Analysis window, browsing external documents, can be provided.
It means ChromNAV can be customized for each user according to their applications and their
HPLC system configurations.
Application Template may be provided by JASCO for any JASCO original application system.
Application Template can be also created from any Project.
All items, which can be customized by Application Template, are shown as follows.
Refer to online help to know the way to set each item.
The initial view displaying at first when [ChromNAV] window has been launched.
Specifying shown or hidden for each view and view panel.
Customizing toolbars.
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Customizing the acquisition sequence table in [Acquisition Sequence Editor] dialog
box.
Customizing the acquisition sequence table in [Acquisition Sequence Monitor] view.
The Acquisition Sequence set in [Acquisition Sequence Monitor] view automatically
when [ChromNAV] window has been launched.
Showing or hiding parameter sets in [Single Run Monitor] view.
All initial values of parameters in [Single Run Monitor] view when [ChromNAV]
window has been launched.
All initial values of parameters in [Default Scales for Monitoring] dialog box in
[Chromatogram Monitor] view.
All initial values of parameters in [Default Scales for Monitoring] dialog box in [PDA
Monitor] view.
(Optional) All initial values of parameters in [Default Scales for Monitoring] dialog box
in [Collection Monitor] view.
Preferences in the Data Acquisition window.
Customizing the peak information table.
(Optional) Customizing the MW calculation results table.
(Optional) Customizing the collection results table.
Showing or hiding not identified peaks (named as “unknown”).
Customizing the recalculation sequence table in [Recalculation Sequence] view.
The last used filenames of Peak Methods (for each data channel), Peak ID Table, and
Calibration Method in [Peak Process] dialog box.
Five most recently used filenames of Data Processing Methods in [Execute Data
Processing Method] button in multiple views in the Data Analysis window.
Five most recently used filenames of Peak Purity Methods in [Peak Purity] button in
[Peak Purity] panel in [PDA] view.
Five most recently used filenames of Post Run Methods in [Execute Post Run
Method] button in [Recalculate Sequence] view.
(Optional) Five most recently used filenames of MW Calculation Methods in
[Calculate MW] button in [Recalculate Sequence] view.
Five most recently used filenames of Report Styles in [Print Report Style] button in
multiple views in the Data Analysis window.
Five most recently used filenames of Sequence Report Styles in [Print Sequence
Report Style] button in multiple views in the Data Analysis window.
All initial values of parameters in [Statistic Calculation Table] dialog box in [Statistic
Calculator] dialog box.
All initial values of parameters in [Acceptable Criterion] dialog box in [Statistic
Calculator] dialog box.
Preferences in the Data Analysis window.
All settings in [Extend Menu Setting] dialog box.
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Creating Application Template from Project
Click [Management Tools] tab in the left pane in [Control Center] window, and click [Application
Template] icon in the left pane. Then, [Application Template] screen will be displayed in the
right pane and the list of Application Templates will be displayed in it.
window, then [New Application Template] dialog box will be displayed.
Figure 7.9 [New Application Template] Dialog Box
[GPC] or [FC] check boxes will be displayed when an optional Molecular Mass Distribution
Calculation Program or an optional Fraction Collector Controller has been installed. Check
[GPC] for an optional Molecular Mass Distribution Calculation Program and [FC] for an optional
Fraction Collector Controller.
All corresponding Projects will be displayed in the list in lower side in the dialog box. Click any
Project in the list to highlight to be referred, then the Project name will be displayed in [Base
Project Name] column.
Enter an appropriate name in [Application Template Name] input box and enter any comments
in [Description] input box.
Click <New> button in the dialog box. Then the new icon of Application Template will be
displayed in the right pane in [Control Center] window.
Creating Project from Application Template

Click [Management Tools] tab in the left pane in [Control Center] window, and click [Project]
icon in the left pane. Then, [Project] screen will be displayed in the right pane and the list of
Projects will be displayed in it.
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window, then [New Project] dialog box will be displayed.
Figure 7.10 [New Project] Dialog Box
[GPC] or [FC] check boxes will be displayed when an optional Molecular Mass Distribution
Calculation Program or an optional Fraction Collector Controller has been installed. Check
[GPC] for an optional Molecular Mass Distribution Calculation Program and [FC] for an optional
Fraction Collector Controller.
Specify the name of Application Template to be referred in [Application Template] list.

Enter the appropriate name of the new Project in [Project Name] input box, and enter any
comments in [Description] input box if necessary.
Click <New> button in the dialog box. Then, the dialog box will be closed and the new icon of
the new Project will be displayed in the right pane in [Control Center] window.
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8. Maintenance
Module Diagnosis Information

ChromNAV records information of all modules configuring the HPLC system in all
chromatogram files such as model names, serial numbers, firmware versions, consumption
degrees of consumables, pressure and temperature profiles, etc. when their chromatograms
were acquired.
For consumption degrees of consumables, each criterion can be set and the warning massage
or the error can be occurred when any consumptions degree is compared with its criterion.
Click [Management Tools] tab in the left pane in [Control Center] window, and click [HPLC
System] icon in the left pane. Then, [HPLC System] screen will be displayed in the right pane
and the list of HPLC Systems will be displayed in it.
Click right button in the icon of corresponding HPLC system, then popup menu will be
displayed. Select [Set Module Diagnosis] in the menu, then [Set Module Diagnosis] dialog box
will be displayed.
Figure 8.1 [Set Module Diagnosis] Dialog Box
Each value in [Standard Value] column is a “criterion” determining if the warning is occurred.
The type of the warning can be chosen in [Warning Level] column.
All information stored in the chromatogram file can be browsed in [Diagnosis] view in the Data
Analysis window.
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Figure 8.2 [Diagnosis] View
Application Log
ChromNAV records operation logs such as opening Project, closing Project, starting data
acquisition, finishing data acquisition, analyzing chromatogram, etc. in the current Project.
Click [Management Tools] tab in the left pane in [Control Center] window, and click [Application
Log] icon in the left pane. Then, [Application Log] screen will be displayed in the right pane and
the list of Projects will be displayed in it.
Click corresponding icon of Project, then its application log will be displayed in the table in the
lower side in the right pane.
Figure 8.3 [Application Log] Screen
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Replacing Project and Copying Methods
Operations in ChromNAV may become slower if the same Project has been used for long time
and number of data and Methods has been increased in the database (Project).
In such a case, creating the new Project and replacing the original Project with the new Project
are recommended to solve the phenomenon.
Required Methods existing in the original Project are not stored in the new Project, but they can
be copied from the original Project to the new Project in [Project Manager] window.
Select [Operation] > [New] in the menu or click (New) button in the toolbar in the [Control
Center] window, then [New Project] dialog box will be displayed and create the new Project in
it.
Click (Start Project Manager) button in the toolbar. Then, [Project Manager] window will be
displayed.
Figure 8.4 [Project Manager] Window
Select [File] > [Project] > [Open] in the menu in [Project Manager] window, then [Open Project]
dialog box will be displayed. Click the name of the new Project (Destination Project) to highlight
and click <OK> button.
Select [File] > [Reference Project] > [Open] in the menu in [Project Manager] window, then
[Open Reference Project] dialog box will be displayed. Click the name of the original Project
(Origin Project) to highlight and click <OK> button.
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Figure 8.5 Project and Reference Project
The new Project (Destination Project) will be displayed in the middle pane, and the original
Project (Origin Project) will be displayed in the right pane in [Project Manager] window. In the
left pane in the window, icons of all Methods and the executed sequence will be shown.
Click the icon to be copied in the left pane, then all files of the corresponding Methods (or
executed sequences) will be displayed in the right pane (Origin Project) and in the middle pane
(Destination Project). Click the filename to be copied in the right pane. Multiple filenames can
be chosen simultaneously using Shift key or Ctrl key.
Click (Import) button in the toolbar in the window, then [Import List] dialog box will be
displayed.
Figure 8.6 [Import List] Dialog Box
Filenames shown in the [Name] column in the dialog box can be changed if necessary.
Click <OK> button, then files will be copied to the new Project and shown in the middle pane.
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Figure 8.7 Example of Copying Methods (Peak Method)
CAUTION : Several types of Methods include “nested” different Methods.

ChromNAV will also copy all “nested” Methods when such Methods
are copied. If any Methods having the same name as Methods to be
copied or “nested” Methods, the following message will be displayed.
Normally, it is useful to click <No> button in order to copy and
overwrite such Methods. But, click <Yes> button not to overwrite
Methods in the new Project, then their Methods will not be copied.
Figure 8.8 Confirmation Message to be Overwritten
CAUTION : Any related Methods will not be copied with chromatogram files when
the executed sequences are copied. But, all results of data
processing will be also copied in their chromatograms
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Figure 8.9 Copying Executed Sequence
Select [File] > [Close All] in the menu in [Project Manager] window, then the original Project
(Origin Project) and the new Project (Destination Project) will be closed.
Select [File] > [Exit] in the menu, then [Project Manager] window will be closed.
Backup and Restoration of Project

Not used Projects for long time storing old data and Methods can be deleted temporarily after
the backup. They can be used again after the restoration from the backup file.
Backing up Project
Select [Operation] > [Back up] in the menu in the [Control Center] window, then [Back up
100
Figure 8.10 [Back up Project] Dialog Box
Click any Project name to be backed up to highlight in [Project Name] column and click <Back
up> button in the dialog box, then the backup will be started.
The following message will be displayed when the backup has been finished. Click <Yes>
button, then the Project will be deleted from ChromNAV.
Figure 8.11 Message after Backup
The backup file will be stored in the folder specified in [Location] column in [Back up Project]
Dialog Box. The extension of the file is “.pjbk”.
Note: The backup filename will be encrypted by GUID for the security reason. The
file can be identified by any file information such as “Last Updated” in the
explorer.
The backed up Projects can be protected and the empty volume in the storage can be
increased if they are transferred to any optical disks or USB flash drives.
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Restoring Project
Transfer the backup file to the corresponding folder ([D:\ChromNAV2\backup\] folder in the
default) if it was transferred to the different folder or any external place such as the optical disk.
icon in the left pane. Then, [Project] screen will be displayed in the right pane.
Select [Operation] > [Restore] in the menu in the [Control Center] window, then [Restore
Figure 8.12 [Restore Project] Dialog Box
Click any Project file to be restored and click <Restore> button. Then, the icon of the Project
will be displayed in [Project] screen in [Control Center] window.
Backup and Restoration of ChromNAV Environments

Not only Projects but important information and configuration of ChromNAV can be backed up
and restored. The list of them is shown as follows;
Users
System Logs
Spectral Libraries
Projects
Application Logs
HPLC System Configurations
Application Templates
102
The backup of their environments is helpful in emergencies, for example, in case that the OS
must be formatted and reinstalled or in case that the PC must be replaced with the new one,
etc.
Backing up ChromNAV Environments

Click the start button in Windows and select [All Programs] > [JASCO] > [ChromNAV] >
[ChromNAV System Archiver]. Then, [ChromNAV System Archiver] wizard will be displayed.
Figure 8.13 [ChromNAV System Archiver] Wizard
Choose <Back up> button and click <Next> button.

In the next page, specify the location to create the backup folder and the name of backup folder
and click <Next> button.
In the next page, several check boxes will be displayed to specify the type of information to be
backed up. Check appropriate check boxes to be backed up.
Note: [Project, Application Log], [Spectral Library], and [Application Template] are
not checked in the default because their information will not deleted if
ChromNAV is uninstalled. Furthermore, it will take long time to back up their
information. Especially, in case of upgrading ChromNAV, it is better to back
up with initial configuration (checking [User Information, Authority
Information, HPLC System Information, System Log] only).
Click <Next> button, then the backup will be started.

[Result] dialog box will be displayed then the backup has been finished. Click <OK> button and
click <Finish> button, then [ChromNAV System Archiver] wizard will be closed.
Restoring ChromNAV Environments

Click the start button in Windows and select [All Programs] > [JASCO] > [ChromNAV System
Archiver]. Then, [ChromNAV System Archiver] wizard will be displayed.
103
Choose <Restore> button and click <Next> button.
In the next page, specify the location of the backup folder and click <Next> button.
In the next page, Check appropriate check boxes to be restored and click <Next> button, then
the restoration will be started.
[Result] dialog box will be displayed then the restoration has been finished. Click <OK> button
and click <Finish> button, then [ChromNAV System Archiver] wizard will be closed.
Checking Software Version of ChromNAV

Select [Help] > [About ChromNAV] in the menu in [Control Center] window or [ChromNAV]
window. Then, [About ChromNAV] dialog box will be displayed.
Figure 8.14 [About ChromNAV] Dialog Box
The software version of ChromNAV (inclufding build number) and optional add-in programs will
be shown. Click <OK> button, then the dialog box will be closed.
Upgrading Projects
The red exclamation marks may be displayed on the icons of the Projects in [Control Center]
window after ChromNAV has been upgraded. It means their Projects are not compatible with
the new version of ChromNAV.
Figure 8.15 Not Compatible Project (right one)
In such a case, their project must be upgraded for the version of ChromNAV.
104
icon in the left pane. Then, [Project] screen will be displayed in the right pane.
Select [Operation] > [Upgrade] in the menu in the window, then [Upgrade Project] will be
displayed.
Figure 8.16 [Upgrade Project] Dialog Box
Click the project name to be upgraded. Multiple project names can be selected with Shift key
or Ctrl key.
Click <Upgrade> button in the dialog box, then their Projects will be upgraded and red
exclamation marks will be removed.
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106
JASCO Corporation
2967-5, Ishikawa-machi, Hachioji-shi
TOKYO, JAPAN
Printed in Japan

0302-2138C ChromNAV InstructionManual 2

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0302-2138C ChromNAV InstructionManual 2

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ChromNAV

P/N:0302-2138C November 2016

Copying software for purposes other than backup

THIS WARRANTY DOES NOT APPLY TO DEFECTS RESULTING FROM THE

(1) IMPROPER OR INADEQUATE INSTALLATION

(1) Tungsten lamp, and other light sources

(3) Various kinds of information from various data acquisition views

(4) Acquisition sequence mode and single run mode

(5) Providing the low running cost

(8) Customizing for your application

About Project in ChromNAV

Figure 1.1 Image of Project

[ Peak Method], [ Report Style], or [ MW Calculation Method] may be nested in

[ Sequence Report Style] may be nested in [ Post Run Method].

Filename and Caption

Unavailable characters for filenames are as follws;

Unavailable characters for captions are as follows;

CAUTION : Do not connect any USB modules (PDA detectors or Fraction

Adjust settings and parameters in Windows as ChromNAV works appropriately.

Installation of the ChromNAV Package

Launching Control Center

Figure 3.1 [Logon] Dialog Box

window, then [New User] dialog box will be displayed.

Space or “. (Period)” as the first character

3.2.1.1 Logon without Password

Center] window, then [New Project] dialog box will be displayed.

Figure 3.5 [New Project] Dialog Box

Registering LC-Net II/ADC

window, then [Register LC-Net II/ADC] dialog box will be displayed.

Figure 3.6 [Register LC-Net II/ADC] Dialog Box

CAUTION : If a red-cross mark shows on the icon of the LC-Net II/ADC, it

Registering of HPLC System

window, then [HPLC System Registration] dialog box will be displayed.

Figure 3.7 [HPLC System Registration] Dialog Box

Enter any name in [HPLC System Name] input box.

ChromNAV Main Window

Figure 3.8 [Open Project] Dialog Box

Figure 3.11 Navigation Window

Figure 3.12 [Print Setup] Dialog Box

Figure 4.1 Data Acquisition Window

Type of Data Acquisition

[Acquisition Sequence] Mode

[Single Run] Mode

Figure 4.3 Control Buttons in Data Acquisition Window

Setting Analytical Condition

4.2.1.1 Setting in [CONFIG] Panel

CAUTION : “Method Time” is not data acquisition time.

To shorten Method Time, take care of the following relationship;

When any PDA detector has configured in the HPLC system:

Specify “Partially Fill” or “Full Loop” in [Injection Method] list.

CAUTION : In “Partially Fill” method, the Injection Volume must be within

CAUTION : Normally, “Direct” method cannot be used. It is necessary to

Enter the correct value in [Loop Volume] by µL.

4.2.1.3 Setting in [PUMP] Panel

Enter initial values in [Composition A] to [Composition D] by percent in case of the gradient

Click [Time Program] tab.

Here, an example to set the gradient elution programs.

Figure 4.5 Example of Time Program Settings

4.2.1.4 Setting in [OVEN] Panel

Enter an appropriate value by °C in [Temperature] input box.

4.2.1.5 Setting in [PDA] Panel

Click [Channel] tab.

Set any Digital Channels or Virtual Channels to be acquired if necessary. Specify