Eksigent® Control Software

Software User Guide

D5031167 A
February 2012
This document is provided to customers who have purchased
AB Sciex equipment to use in the operation of such AB Sciex
equipment. This document is copyright protected and any reproduction
of this document or any part of this document is strictly prohibited,
except as AB Sciex may authorize in writing.
Software that may be described in this document is furnished under a
license agreement. It is against the law to copy, modify, or distribute
the software on any medium, except as specifically allowed in the
license agreement. Furthermore, the license agreement may prohibit
the software from being disassembled, reverse engineered, or
decompiled for any purpose.
Portions of this document may make reference to other manufacturers
and/or their products, which may contain parts whose names are
registered as trademarks and/or function as trademarks of their
respective owners. Any such use is intended only to designate those
manufacturers' products as supplied by AB Sciex for incorporation into
its equipment and does not imply any right and/or license to use or
permit others to use such manufacturers' and/or their product names
as trademarks.
AB Sciex makes no warranties or representations as to the fitness of
this equipment for any particular purpose and assumes no
responsibility or contingent liability, including indirect or consequential
damages, for any use to which the purchaser may put the equipment
described herein, or for any adverse circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.

The trademarks mentioned herein are the property of

AB Sciex Pte. Ltd. or their respective owners. Eksigent is a division of
AB Sciex, LLC.
AB SCIEX™ is being used under license.

Eksigent
5875 Arnold Road, Dublin, CA 94568.
AB Sciex LP is ISO 9001 registered.
© 2012 AB SCIEX.
Printed in Canada.
Contents

Chapter 1 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Install the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
To install the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Configure Software Drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Configure the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chapter 2 Acquisition Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Components of the Acquisition Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
System Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Analysis Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Chapter 3 Run Manager. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
The Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Devices Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Run Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Contents of the Run Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Edit the Run Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
The Sample Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Status of Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Selecting a Vial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Method Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Run Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Chapter 4 Peak Viewer Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Peak Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Sample Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Peak Viewer Sample Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Monitoring Peak Trends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Peak Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Plot Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Peaks Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
Plots Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61

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Chapter 5 Autosampler Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Configuring the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Chapter 6 LC Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Creating and Editing Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Summary Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Selected Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Method Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Column Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Run Conditions Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Pre-Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Sample Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Post-Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Flow Profile Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Flow Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Profile Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Programmable Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Flow Table Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Detector Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Detector Wavelength Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74
Chapter 7 2D Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Creating and Editing 2-D Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
The Summary Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Method Steps Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Chapter 8 Analysis Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Peak Detection Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Quantitation Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Options Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
Peak Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
The Capacity Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Peak Asymmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Calculation Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Chapter 9 Integration Time Events. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Peak Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Detection Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Detection Threshold Asymmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Minimum Peak Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Minimum Peak Height . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Minimum Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Shoulder Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Integration Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94

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Negative Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94

Valley To Valley . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
Front Skim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .96
Back Skim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Manual Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Forward Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99
Backward Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100
Lowest Point Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101
Reset Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .102
Reset Baseline at Valley . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Force Peak Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104
Force Peak Stop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104
Split Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Merge Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Force Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
Manual Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
Reference Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
Incompatible Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .108
Chapter 10 Quantitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Peak Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
Terms and Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
Types of Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
Types of Fits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Linear Fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Nonlinear Fits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Scaling Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
External Standard Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
Internal Standard Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .126
Automated Calibration Table Generation through the Run Manager . . . . . . . .127
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Chapter 11 User Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
User Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Configure the User Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
User Manager Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
Manage Electronic Signature Reasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
Chapter 12 Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Role of the Electronic Signatures Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Components of the Electronic Signatures Dialog . . . . . . . . . . . . . . . . . . . . . . .141
Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .142
Signing Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143
Revoke Signatures on Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .144
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

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1
Install the Software
The application software and important instrument calibration values are supplied on disk. The
instructions presented in this chapter should be followed to install the software and calibration
information on your computer.

Note: This software should be installed by an individual with Administrator privileges.

To install the software

1. Close all open applications
2. Insert the software disk in the drive. The current software verison is shown, refer to
Figure 1-1.

Figure 1-1 The initial software setup dialog

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3. Click Next for license agreement dialog, refer to Figure 1-2.

Figure 1-2 Software Setup License Agreement dialog

4. Click Next to specify the target installation directory.i

Tip! Choose the default directory (Eksigent) unless there is a conflict.

5. Click Next to select desktop icon and/or a Quick Launch icon settings, refer to
Figure 1-3.

Figure 1-3 Software Setup Icon Creation Dialog

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6. To create additional icons for launching the software, select one or both options
shown in the Additional Tasks Setup dialog.
7. Click Next to open the Ready to Install dialog, refer to Figure 1-4.

Figure 1-4 The Ready to Install Dialog

8. Press Install to continue with the installation.
A status dialog will indicate the progress of the installation, refer to Figure 1-5.

Figure 1-5 Software Setup Installing Status dialog

After the software has been installed, a validation routine will be performed to verify
the integrity of the installed files.

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A status dialog will indicate the progress of the validation, refer to Figure 1-6.

Figure 1-6 Automated Installation Validation Progress Bar

If an error is determined during the validation routine, a message will be presented to
indicate the appropriate action.

Note: This validation can be run at any time from the list of programs that
is accessed via the Programs menu, refer to Figure 1-7.

Figure 1-7 Programs Associated with Eksigent Software

After the validation routine is complete, the Wizard Completion dialog is shown, refer
to Figure 1-8.

Figure 1-8 Wizard Completion Dialog

Item Description
1 View Release Notes option will present information that was generated
after the manual was completed.
2 Validate Installation option will perform the validation described as a result
of step 8 on page 9.
3 Configure Software Drivers option is used to indicate the drivers that
should be used, refer to Configure Software Drivers on page 11.

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Configure Software Drivers

Software drivers allow the Eksigent® software to be controlled by third party programs. You can
select the appropriate drivers through the Driver Configuration Utility dialog which is accessed
from the Wizard Completion dialog or the Program menu. The plug-in configuration can be run at
any time from the Programs group menu.

Figure 1-9 Device Plug-In Setup Utility Dialog

For installs on a new system or an attempt to restore a system to original factory-installed
calibration settings, insert the disk with the original calibration values and click Calibration Disk.
Otherwise, click OK to complete software installation.

Configure the System

After the software has been successfully installed, configure the HPLC system using the
Instrument Configuration dialog. This dialog is used to select which hardware components are
installed, set the communications protocol, and choose certain system options. The performance
parameters set in this window are described in more detail in Instrument Configuration on
page 29.

To configure the device

1. Connect the instrument to a serial port on the PC.
2. Power up the HPLC instrument.
3. Launch the Eksigent control software from your computer Programs menu or from
the desktop icon.

Note: If the software does not detect the instrument, a warning message
will appear. In this case check that the instrument is turned on and that the
serial cable is properly connected. The default serial port connection on the
computer is COM1.

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4. Select Instrument Configuration from the System menu to present the Instrument
Configuration dialog, refer to Figure 1-10.

Figure 1-10 Instrument Configuration dialog

5. Make any necessary changes. A detailed discussion of this dialog is presented in
Configure the System on page 11.

Note: If there is no communication between the PC and the instrument, it

is likely that the COM port entry should be changed.

6. Press the OK button to accept the new settings and restart the software.

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2
Overview
The application software consists of three primary modules:
• The Acquisition Window, which is used to establish operational parameters and
monitor an acquisition
• The Run Manager, which is used to setup and queue a series of acquisitions
• The Peak Viewer, which is used to view and analyze data after acquisition
These three modules control the acquisition of each sample, manage individual sample
information, and process the resulting data for the configured LC device.
When the software is started, the Acquisition window (Figure 2-1) is displayed. All areas of the
software can be accessed from this screen, including the Run Manager and the Peak Viewer.

Figure 2-1 Acquisition Window

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Components of the Acquisition Window

The Acquisition window displays the currently acquired sample data and provides access to a
broad range of device configuration and diagnostic information. The main screen has the
following sections:
• Status Area on page 14
• Control Buttons on page 15
• Spectral Absorbance Region on page 15
• Main Plot Region on page 15
• Peak Table (UV Detector Systems only) on page 16
• Contour Plot Region (UV Detector Systems only) on page 16

Status Area
The Status area displays information about the current run, including the flow rate, run time,
current method, sample information, pump state, injection valve position, the location in the
sequence, and the file name used to save the data is saved after the run is completed, refer to
Figure 2-2.

Figure 2-2 The Status Area

The content of the Status area can be customized by right-clicking on the area and selecting
items from the status area options presented in the menu, refer to Figure 2-3.

Figure 2-3 Status Information Options

If a status bar is chosen, it shows a graphical representation of the selected parameters such as
the current mobile phase flow rates (Qa and Qb), the total flow rate (Qc), the internal flowmeter
pressures (Pa and Pb), the column pressure (if installed, Pc and Pd) and the pump power as a
percentage of maximum pump power for each channel.
The units for flow rate and pressure can be changed by selecting the corresponding items from
the menu or directly by clicking the labels at the bottom of each status bar. Flow units can be

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displayed in nL/min or µL/min. Pressure units can be displayed in psi or bar. The current column
temperature will also be displayed if a column heater is installed.

Control Buttons
The Run Manager button provides access to the Run Manager where sample and method
information is entered to create sample sequences, for more information refer to Chapter 3.
When an acquisition is in progress, the Pause button maintains the conditions of the device at
their current values indefinitely. Pressing this button during a run will maintain the elution
conditions continuing to acquire data. After being pressed, the Pause button changes to Resume
and is used to continue the LC method.
The Stop button stops the LC method and then stops the sequence table at its current position.
For multi-channel devices, only the currently active channel is stopped. The device channel is
placed into the Standby state and the pumps are turned off.
The Extend Run icon provides a menu to extend or shorten the LC method run time. You can add
time to the run indefinitely, but you cannot shorten the run time to less than the original LC
method run time.
The Direct Control icon provides a shortcut to the Direct Control dialog.
The Acquisition Information icon opens a dialog that displays information about the sample run
and other acquisition information saved with the data file.

Spectral Absorbance Region

If your system is equipped with a UV Detector, the spectral absorbance region will display a real-
time UV absorbance spectrum. During a sample run, this region is continuously updated with the
most recently acquired spectrum. If the pointer is within the spectral contour plot region, the
spectral absorbance region shows the spectrum collected at the point in time nearest to the
pointer.
The vertical dashed lines in the spectral absorbance area indicate the absorbance wavelength
range used to calculate absorbance for the chromatogram. These values are initially defined in
the LC Method Editor, refer to Method Editors on page 49. The wavelength range can be
modified graphically by using the pointer to drag the dashed lines to a new wavelength range. To
modify only the upper or lower wavelength setting, hold the Ctrl key dragging the relevant dashed
line.
The axes limits for the spectral absorbance region are defined by the upper and lower
wavelength ranges (X-axis) of the spectrometer and the current chromatogram axis limits
(Y-axis).

Main Plot Region

The main plot data region can display the detector's UV absorbance signal as a function of time
(UV Detector systems only), the mobile phase gradient profile, the measured flow rate and the
system pressure. External detector information can also be displayed using the external A/D
signal input.
The plot scale can be modified by clicking the upper or lower X or Y-axis limits and entering a
new value. In addition, it is possible to graphically zoom into a specific range by dragging the
pointer over the region of interest. A zoom window will be drawn for reference and the zoom
action will occur when the mouse button is released. Click the right mouse button to open a menu
containing Zoom Last and Zoom Out functions.
The X-axis time units can be changed from minutes to seconds by clicking the X-axis label.

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The main plot data region can also be used to add integration timed events graphically by right-
clicking and selecting Add Integration Event from the menu. The list of all available events will be
displayed. The start and stop time can be selected directly from the plot area by moving the
pointer and clicking the left mouse button.
If peak results are present, moving the pointer over the peak baseline displays a move icon that
allows manual adjustment of the peak baselines. Dragging the baseline point to a new location
will display the Peak Detection Tab of the Analysis Method window with a new Manual Baseline
event added to the integration timed event table.

Peak Table (UV Detector Systems only)

Peak results are shown in the peak table. The table columns can be customized by selecting the
Choose Peak Table Columns option of the Analysis menu. If a corresponding column is selected,
peak names can be assigned and edited directly.

Contour Plot Region (UV Detector Systems only)

For systems equipped with a UV detector, the contour plot region displays spectral absorbance
data versus time over the entire spectrometer wavelength range. This spectral data appears
directly below the chromatogram window and has the same time X-axis range and units. The Y-
axis values are determined by the spectrometer wavelength range. The absorbance values in the
contour plot (Z-axis) are color-coded according to a user-selected color palette.
After data is collected, moving the pointer over the contour plot region will update the spectral
absorbance region with the absorbance spectrum at the indicated acquisition time.

Menus
Table 2-1 to Table 2-5 list the various commands that are provided from the menus found in the
Acquisition dialog. Each menu contains a list of options consisting of commands and sub-menus
used to operate the system.
Table 2-1 File Menu
Command Function
Open Opens and displays a previously saved data file, refer to Open on
page 18.
Save As Saves a data file to the hard disk. Also allows you to save the current
data in formats that are compatible with other program, refer to Save As
on page 18.
Output Options Displays the Output Options dialog, allowing access to the file output
parameters, refer to Output Options on page 19.
Peak Viewer Displays the Open dialog to select a file or list of files. When a file is
selected, then the Peak Viewer dialog will appear to allow viewing each
file, refer to Peak Preview on page 20.
Print Preview Displays the Report dialog, refer to Print Preview on page 21.
Print Prints a report summarizing the current data, refer to Print on page 22.
Autosave Instructs the system to automatically save the data file at the end of an
analysis.

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Table 2-1 File Menu (Continued)

Command Function
Autoprint Prints a report summarizing the current data at the end of a run
Exit Displays the Close Program dialog.

Table 2-2 The View Menu

Command Function
UV Detector Toolbox Opens the UV Detector dialog which allows for manual control of the
detection settings, refer to UV Detector Toolbox on page 23.
PeakPark Toolbox Opens the PeakPark toolbox which allows fir setting peak parking
options, refer to Peak Park Toolbox on page 22.
Smoothing Toolbox Opens the Smoothing window which provides access to the post-
acquisition data spline values, refer to Smoothing Toolbox on page 24.
System Logs Displays the System Logs submenu to access audit trails of system
messages, and warnings, refer to System Logs on page 25.

Table 2-3 System Menu

Command Function
Hardware Diagnostics Displays the Hardware Diagnostics dialog, refer to Hardware
Diagnostics on page 27.
Instrument Displays the Instrument Configuration dialog, refer to Instrument
Configuration Configuration on page 29.
Notification Options Displays the Notification Options dialog, refer to Notification Options on
page 33.
Appearance Settings Displays the Appearance Settings dialog for customizing the data
display, refer to Appearance Settings Dialog on page 33.
Mobile Phases Displays the Mobile Phases dialog to describe the mobile-phases and
controlling the purge/flush functions, refer to Mobile Phases Dialog on
page 35.
Direct Control Displays the Direct Control dialog, which allows for manual control of
the pumping system and injection valve, refer to Direct Control on
page 37.
User Authentication Displays the User Logon dialog, refer to User Authentication on
page 38.
User Manager Displays the User Logon dialog followed by the User Manager dialog,
refer to User Manager on page 38.
Electronic Signatures Displays the Electronic Signatures dialog, refer to Electronic
Signatures on page 38.

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Table 2-4 The Analysis Menu

Command Function
Settings Displays the Analysis Settings dialog, which contains peak detection
parameters, refer to Chapter 8.

Table 2-5 The Help Menu

Command Function
Help Displays the interactive help system
Check for Updates Displays the default Internet browser and selects a web page to show
the latest version of software
Email Tech Support Displays the default e-mail client software and fills in the address and
system information to be sent to Eksigent Technical Support
www.eksigent.com Accesses the Eksigent website with the default Internet browser
About Displays installed software and firmware versions

File Menu
Open
The Open command is used to open a previously stored data file (.txt,.dat) in the main acquisition
window. Only a single file can viewed at any one time. The Peak Viewer utility should be used to
view multiple files or to open files while an acquisition is in progress, refer to Peaks Menu on
page 59.

Save As
The Save As... command is used to store acquired data in a .txt, .xls, .dat, or .cdf (AIA/ANDI)
format. A bitmap image of the spectral absorbance contour can also be independently exported
using this command.

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Output Options
The Output Options dialog (Figure 2-4) is used to specify the preferred data file formats, paths,
and naming inventions to be used when the AutoSave option is selected.

Figure 2-4 Output Options Dialog

Output
The Output folder field is used to indicate the default folder where Autosave data will be stored.
Additional sub-folders can be created with the output filename entry (refer to below). If the folder
does not exist, you will be prompted with a choice for creating that folder.
Use the Output filename(s) field to specify filename attributes for each data set after the run has
completed. You can customize the file naming convention by using one or more tags. These may
include the method name, sample name, date, time, vial number, incremental counter, and so
forth. The default filename format uses a dynamically created date subfolder and creates a
unique filename based on the time:
\<date>\ EK< channel>_<time>
Many other unique filenames can be generated from the various tags. Click Help for more
information on the available tags or use the drop-down box to insert new tags.
When you create your naming convention, an example filename is shown. If Prompt to save is
selected, a prompt for naming the data file is shown at the completion of each run (this is not
recommended for when there is more than one sample in the Run Manager). Tags that use
information from the Run Table is shown in the example filename as either blank or as the value
last used with that tag.
Autosave automatically generates a data file name and saves the file in the folder specified in the
Output folder. If this command is not selected, you will be prompted to save the data file after
each sample run. The use of the Autosave option is highly recommended.

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If a unique filename is not specified in the Output filename(s) edit box and Autosave is selected,
a unique filename is created if the current filename already exists in the specified folder.

Autosave Output Format

The Autosave Output Format region allows you to specify which data file types should be
automatically created. File types include Text, ANDI, binary .dat, and a peak table (text format)
that can be appended.
Text files contain the chromatogram, flow and pressure data, and are tab-delimited. Text files
have .txt file extensions.
ANDI files contain a single chromatogram and AIA-defined information only. ANDI files have the
.cdf file extension.
Binary .dat files contain system settings, flow, pressure data, and complete absorbance spectral
data for systems with spectrometers.
The Appendable peak table format is a tab-delimited text file that contains sample and peak
information only. The file is named PeakTable.xls and is located in the specified sample file
folder. The information from subsequent sample runs will be appended to this file, so the analysis
results of an entire sample set are created in a single file for importing into spreadsheet/database
applications.

Ownership Tags
Operator Name: Name of the person who is running the experiment or test that generated the
current data set.
Data Set Origin: Name of the organization where the current data set originated. Data Set
Origin information can include the organization's address, telephone number, e-mail nodes, and
the names of individual contributors, including the system operator(s), and any other appropriate
information.
Data Set Owner: Name of the owner of a proprietary data set. The person or organization
named here is responsible for this field's accuracy. Data copyrights should be indicated here.

Peak Preview
The Peak Preview function provides access to the Peak Viewer for loading and analyzing larger
sets of sample data. Refer to Peaks Menu on page 59.

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Print Preview
The Print Preview function is used to preview the appearance of a report before it is printed. Print
previews are generated in the Report dialog (Figure 2-5). The Report Window is shown with a
representation of the report for the currently loaded data.

Figure 2-5 Print Preview

You can choose between portrait and landscape mode for the orientation of the report by
selecting the corresponding option at the top of the Report window.
To generate a PDF or HTML copy of this report, check either the PDF or HTML box at the top of
the Report window.
• Double-click on the report to zoom in.
• Right-double-click on the report to zoom out.
• Use the horizontal and vertical scroll bars to scroll the report.
• Left click, hold, and drag on the report. The report will scroll in the direction that is
dragged. During this procedure, a hand graphic is used as the icon.
• Click the magnifying glass to toggle between two best-fit views (one best-fit to the
vertical and one best-fit to the horizontal).
• Click on the down-arrow to the right of the magnifying glass to select some
predefined viewing styles and magnification. The available viewing styles are Whole
Page, Page height, Two Pages, and Thumbnail. The available magnifications are
150, 100, 75, 50, and 25%.

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• Click the printer icon to print the report. A Print dialog will appear to allow
modification of print settings.
To exit the print preview, simply close the window. The selected report format will be used the
next time the Report Window is launched.

Print
The report for the currently loaded data can be printed directly without using the Print Preview or
the Print dialog by pressing Print. The report for the currently loaded data will be sent directly to
the default printer specified for that computer and the most recently chosen report format will be
used.

View Menu
Peak Park Toolbox
Eksigent® LC devices can rapidly reduce the total column flow rate to allow for extended MS/MS
analysis at a particular point in the chromatogram. This procedure, which is commonly called
peak parking, is controlled using the Peak Part Toolbox (Figure 2-6). Adjustments to the
composition of the flow profile are paused during the parked period and resume after parking is
discontinued.

Figure 2-6 PeakPark Tool Box

The Park Now button should be clicked during a sample acquisition to rapidly set the total LC
flow rate to the value indicated in the Flowrate field. When this feature is selected, the button
changes to Unpark and can be pressed again to resume the method condition at the original flow
rate.
As an alternative, the LC device Park In external trigger signal can be used to initiate/resume
peak parking using external device control (for example a mass spectrometer using contact
closure control).
The Flowrate field indicates the total pump flow rate during parking conditions. When peak
parking is activated, the pumps will provide this flow rate while maintaining the current mobile
phase composition.
The Flowrate reference option determines the reference method that is to be used to rapidly
stabilize the LC flow rate at the new lowered value.

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• The Column flow rate reference method uses the measured column pressure at the
start of the PeakPark operation to estimate the current column flow resistance. This
value, with the real-time measured column pressure is used during the peak-park
transition to stabilize the column at the new flow rate. This method is typically the
fastest method to attain the target peak-park flow rate values.
• The Mobile Phases flow rate reference method uses the flow rates measured
directly from the individual mobile phase (A and B) flowmeters while the pump flow
rates are decreasing. This method is typically slower to lower the total flow rate
through the column, but more accurately maintains the mobile phase mixture
fraction.
Timing check boxes can be used to ignore external triggers or peak-park for a fixed duration after
the initial trigger event. This option is useful when noisy trigger signals are present (from the
mass spectrometer) and ensures that the device will stay in park mode for a configurable
acquisition period.

UV Detector Toolbox
If the system includes a UV absorbance spectrometer, the UV Detector Toolbox can be used to
view the current UV detector settings and make adjustments as necessary.

Note: This window is typically used for diagnostic purposes, as each LC method
contains detector settings that are specific to that method. As a result, many of the
settings in this toolbox are not accessible during acquisition as they are being controlled
by the parameters specified in the LC method.

Figure 2-7 UV Detector Toolbox

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For more detailed information and descriptions of the parameters in this dialog, refer to Chapter
6.

Absorbance
The Absorbance field is used to set the required Wavelength and Bandwidth.

Mode
The Mode field is used to indicate if single beam or double beam measurements are required.

Baseline Field
The Baseline field is used to indicate the parameters for collection of the baseline. If the Real-
time collection option is selected, you can indicate the wavelength and bandwidth.

Reference/ Background
The Reference/Background options allow you to turn on or off the Automatic background and
reference acquisition. If this option is selected, the detector background and reference signal will
be acquired prior to every LC method acquisition. When it is disabled, the Acquire Reference and
Acquire Background buttons can be used to manually acquire those signals. In this case, each
LC method acquisition starts immediately and the current background and reference information
(in memory) are used.
The Sync. options allow you to determine how to synchronize the detector acquisition. The Sync.
with Injection start option indicates that the detector should start acquiring data (time = 0) when
the injection valve moves to the inject position. The Sync. with gradient start option indicates that
the detector should start acquiring data (time = 0) when the injection has completed and the
gradient (flow profile) begins. This mode is useful when comparing retention time reproducibility
with varying injection volumes (binary gradient LC methods with metered injections.)

Plots
The Plots field allows the user to format the plot.

Monitor Detector
The Monitor Detector button provides access to UV Detector Plot for diagnostic purposes.

Smoothing Toolbox
The Smoothing Toolbox (Figure 2-8) allows you to apply a cubic spline fit to their chromatogram
after acquisition is completed and can be employed with systems with a spectrometer. The error
band defines the looseness of fit in Y units, where a larger number applies more smoothing.

Figure 2-8 Smoothing Toolbox

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System Logs
The System Logs submenu allows you to display a variety of log files, which are audit trails that
record all pertinent system information, including ordinary usage statistics, system warning
messages, and experiment status logs. Log files are designed to prevent malicious tampering
with their contents to make sure of the long-term validity of the system audit trail. Each log file is
archived on a regular basis. Click any of the available logs under the System Logs menu to open
the log dialog.

Figure 2-9 Viewing Instrument Logs

A typical log (the Alerts log) is shown in Figure 2-10.

Figure 2-10 The Alerts Log

To view the contents of a log in the log window, click any available log in the left-hand column.
The entries of that log are shown in the pane to the right. Alternatively, the Select Log button can
also be used to select a log. Clicking will launch an Open File dialog where a log file can be
selected.
To sort the log contents, click on any column heading. The log entries will be sorted based on that
column. Ascending sort is always used when the column is first clicked. To use descending sort,
click the column heading again.
Log entries may often appear in alternating lines of black and blue. The coloring scheme is to
help locate identical entries within a field. The color of the entries is based on the column on
which the sort is applied. For example, the log entries in Figure 2-10 are sorted based on date.
Starting at the top, the color will alternate when a different value is detected. The first line is
always black. On the second line, the date value is different, so the color alternates to blue. On
the third line, the date value is the same as the second, so the color stays blue. On the fourth
line, the date value changes again, so the color alternates back to black. This pattern continues
to the end of the entries.
The Log Information field displays some basic information about the selected log. These include
creation date, last modified date, and the file location of the log file.
To exit the log dialog, click OK in the lower right corner.

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The contents of any log can be exported to a PDF file or to an Excel spreadsheet (.xls). Choose
the desired format in the Log Information field and Export frame and press Export.
If the Excel option is selected, a Windows Export to dialog opens. Type a name for the log in File
name and then click Save.
If the PDF option button is clicked, a PDF preview window is shown. Use the Portrait or
Landscape buttons to change the page orientation. Click Save to open a Save As dialog to save
the PDF file. The page navigation arrows can be used to navigate through multiple-page PDF
documents. The magnifying glass icon can be used to switch between two best-fit views of the
document. To print the PDF, click the printer icon, which will launch a Print dialog.
The Alerts Log (Figure 2-10) contains a list of any warnings and messages automatically
generated by the system but which do not need immediate attention. The Alerts Log will open
automatically when a system check discloses a potential issue and displays the issue as an Alert
event. The log includes information such as the Login name of the current user, the date of each
occurrence of the Alert event and a detailed description of the event.
The System Configuration log (Figure 2-14) contains a list of user actions that affect the device
such as calibration options.

Figure 2-11 System Configuration Log

The Sample Queue log (Figure 2-12) contains a list of samples that have been processed for
acquisition by the Run Manager. The column on left side of the table indicates what action has
been taken on each sample.

Figure 2-12 Sample Queue Log

The Channel 1 log (Figure 2-13) contains a list of user actions that affect Channel 1 conditions,
such as flow rate. For multi-channel instruments, channel log information is available for each
additional channel.

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Figure 2-13 Individual Channel Log

System Menu
Hardware Diagnostics
The Hardware Diagnostics dialog (Figure 2-14) allows for calibration of the LC hardware,
examine instrument usage statistics, and perform automated diagnostic routines.
.

Figure 2-14 Hardware Diagnostics Flow Calibration

Select The Remind Me to Run Diagnostic Tests Once a Month check which provides the option
of presenting an Alert message once a month to run diagnostic tests.

Flow Calibration Tab

The Auto-Diagnose region allows you to select any of three auto-diagnostics. The system will
sequence through selected diagnostics automatically when you click Start Diagnostics.

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• Re-Initialize Transducers is a calibration function that reads and sets the steady-
state, zero-pressure reading on the internal system transducers.
• Check For Leaks/Blockage is a diagnostic function that sequences the pumps at
different flow rates, determines whether pressures and flow rates reach expected
levels, and reports any problems. It is recommended to use a column or flow
restrictor at the device outlet.
• Check Flow Stability is a diagnostic function that will temporarily flush the system at
a pre-determined flow rate and report flow stability.

The Flow Metering and Control region is a calibration function that guides you
through the following steps:
• Calibrate Flowmeter displays the Flowmeter Calibration dialog (Figure 2-14), which
guides you through flow calibration steps.
• Auto Tune Controllers starts a pressurized calibration function that automatically
adjusts flow controller parameters to optimize stability. These parameters are saved
and used to control the pumps during data collection.
• Pump Response Time allows you to adjust how quickly the pump responds to
setpoint changes and flow disturbances. Sliding the bar to the right increases the
responsiveness. This setting affects flow control stability. This setting does not alter
Auto Tune Controllers diagnostic results.

Usage Information
• Total Sample Injections displays the total number of injections performed. This
number is useful for tracking instrument usage. Pressing the CLR clears the counter.
• Total Flowmeter Usage displays the total number of hours of flowmeter usage. This
number is useful for tracking instrument usage. Pressing the CLR clears the counter.
• Flowmeter Serial documents the identity of the instrument flowmeter. Pressing the
CLR clears the field.
• Filter Usage documents the volume of fluid that has passed through the cell guard
filter. Clear the field by pressing CLR when you change the filter.

Calibration Values Tab

The Calibration Values tab is shown in Figure 2-15.

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Figure 2-15 Calibration Values Tab

Flow Region
The Flow region on the Calibration Values tab (Figure 2-15) displays fluid-independent and fluid-
dependent K values used for flow control. The actual K values may slightly change every few
seconds because they are calculated based on measured temperature.

Pressure Sensors
The Pressure Sensors region displays the pressure sensor calibration values.

PID Region
The PID region shows calibration values relating to the pump control parameters.

Instrument Configuration
System Tab
The Instrument Configuration dialog is used to set hardware configuration options. Usually these
are set during the initial installation, but they may be set at any time should the system
configuration change.

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Figure 2-16 Instrument Configuration - System Tab

Eksigent Device is used to configure the software for the appropriate Eksigent LC instrument
COM Port allows you to select the serial port used to connect to the LC instrument.
Injection Valve allows you to configure the software for the presence or absence of an injection
valve. For most systems, this field should be set to Internal.
System shut down is an option that shuts down power to critical electronic components after a
specified period of inactivity. The system shut down option allows you to program a series of
unattended runs and, following successful completion will execute a method designed to reduce
the wear on the lamp, pump seals, pump check valves and heater element.
Display flow profile setpoint values is an option to display setpoints for the flow rate values in
the status area of the main screen. If the check box is unselected (default), the measured flow
rate values will be shown in the status area.
The Export Settings button is used to copy system settings to a file. This file can be used to
transfer instrument settings to another computer.

Device I/O Tab

The Device I/O tab is shown in Figure 2-17.

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Figure 2-17 Instrument Configuration - Device I/O

Signal Input Polarity

• Run Trig In active low is an option that triggers the start of a run when the Run
Trigger is brought low (TTL or contact closure). This option allows the use of an
external device, such as an autosampler, to trigger the start of a run. If no external
device is attached, this option should remain selected to avoid false signals.
• Park Trig In active low is an option that starts the Peak Parking feature when the
Park Trigger input is brought low (TTL or contact closure). This option allows the use
of an external detector to reduce the flow when a peak is detected to allow more time
to resolve the data. If no external device is attached, this option should remain
selected to avoid false signals.

Signal Output Polarity

• Ready Trig Out active low is an option that brings the Ready output contact low
(TTL or contact closure), when the device is waiting for the next sample. During a
run, the Ready output contact is held at TTL high (or contact open). Use this option
to signal an external device, such as an autosampler, that the LC pump is ready for
the next sample.
• Park Trig Out active low is an option that brings the Park output contact low (TTL or
contact closure) when the LC device is running in Peak Park mode.
• Gradient Trig Out active low is an option that brings the Gradient output contact low
(TTL or contact closure) when the LC device is running and a gradient is in progress.

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Input A/D Range

Aux A/D Range radio buttons allow you to set the input signal range of an auxiliary analog device
as measured on the device's A/D converter. The maximum dynamic range is ±10V. Over-voltage
protection is provided up to 15V.

Output D/A Range

Scale (mV/mAU) indicates the multiplier used on the chromatogram signal (systems with
spectrometers) to create the analog signal out of the device. This signal can be used in
conjunction with an external data acquisition system. The default value is 1 mAU/mV.
Offset (mV) indicates the offset added to the analog out signal specified above.

Advanced Tab
The Advanced Tab is shown in Figure 2-18.

Figure 2-18 Instrument Configuration - Advanced

Flow Stabilization Limits

• Stabilize flow conditions is an option that allows you to program the system to start
the pumps and stabilize the column flow within a specified flow rate range before
allowing the LC method to begin. The LC method flow profile will not start until the
column flow is stabilized within the specified flow stabilization limit. It is
recommended to program a pre-run flush into each LC method to equilibrate the
column. If a LC method is started with the pumps off (no equilibration), the actual
method start will be delayed until the stabilization criteria is met, which may result in
timing incompatibilities with external devices.
• Stop device if Pc exceeds allows you to set an output column pressure sensor (Pc)
pressure value that will stop data collection if outlet pressure exceeds a specified
limit. High values of Pc can indicate a clogged column, post-column filter, or flow cell.

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• Stop device if pump power remains at 100% allows you to set a time duration that
will stop the pumps and data collection if pump power remains at 100% for a
specified period of time. Pump power can remain at 100% for unusually long
durations if pump flow-control logic is attempting to compensate for leaks or
blockages in the flow path.
• Rapid Inject pressure limit is used to protect the system from over-pressure during a
Rapid Inject process. This value is usually lower than the absolute column pressure
limit. The system flow rate is reduced as the system pressure approaches this limit
and is maintained just below the designated limit until the injection is complete. After
injection, the flow rate returns to the value specified in the analytical method.

Notification Options
The Notification Options dialog allows you to set e-mail notification options.E-mail Notification
Options

E-mail Settings
If you want notification of various events via e-mail, select the Notify by E-mail option and
indicate the address and server. The Test button is used to verify that communication has been
established.

Notification Events
• LC device error allows you to choose to receive e-mail if the LC device reports an
error.
• Autosampler error allows you to choose to receive e-mail if the autosampler device
reports an error.
• RunTable complete allows you to choose to receive e-mail when the instrument has
completed acquiring all samples specified in the Run Manager sequence.

Notification Frequency
The Notification Frequency region allows you to select whether to receive e-mail notifications
immediately, hourly, daily, or not at all.

Appearance Settings Dialog

The Appearance Settings dialog (Figure 2-19) allows you to determine the attributes of data
plotted in the Main window.

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Figure 2-19 Appearance Settings Window

Flow Data
Qa (nL/min) allows toggling a display of mobile phase A's measured flow rate in the main
window and selecting which color will be used in the display.
Qb (nL/min) allows toggling a display of mobile phase B's measured flow rate in the main
window and selecting which color will be used in the display.
Qtotal (nL/min) allows toggling a display of total flow in the main window and selecting which
color will be used in the display.
Profile A toggles a display of the gradient profile of mobile phase A in the main window and
selecting which color will be used in the display.
Profile B toggles a display of the gradient profile of mobile phase B in the main window and
selecting which color will be used in the display.
%A allows toggling a display of mobile phase A's measured mixture % (from flow rate) in the
main window and selecting which color will be used in the display.
%B allows toggling a display of mobile phase B's measured mixture % (from flow rate) in the
main window and selecting which color will be used in the display.

Pressure
Column (Pc, psi) allows toggling a display of the measured column pressure in the main window
and selecting which color will be used to display the information.
Amp A (Pa, psi) allows toggling a display of the measured internal pressure of mobile phase A in
the main window and selecting which color will be used to display the information.
Amp B (Pb, psi) allows toggling a display of the measured internal pressure of mobile phase B in
the main window and selecting which color will be used to display the information.

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Absorbance
UV Signal (mAU) allows toggling a display of the detector's signal channel and selecting the
color which will be used to display (systems with spectrometers).
UV Reference allows toggling a display of the detector's reference channel and selecting the
color which will be used to display (systems with spectrometers).

A/D Channel
Aux A/D (mV), scale X allows you to choose whether to display the analog signal from an
auxiliary device and to choose the color of the display. You can also designate a multiplier to be
used to magnify the analog signal plot.

Left/Right Axis T
The colors of various plot window attributes can be modified by changing the Background,
Gridlines, and Axis Label colors.

Plot Axes
Automatically adjust time axis allows you to choose whether to allow the scale of the time axis to
vary automatically to fit the amount of data available for display.

Contours and Shading

The menu in the Contours and Shading region allows you to choose a color scheme for the
display of spectral data.

Mobile Phases Dialog

The Mobile Phases dialog (Figure 2-20) allows you to configure the A and B operating fluids,
document any additives, and reset the usage counters. Accurate flow viscosity correction, flow
rate measurement, and flow stability depends upon correct identification of mobile phase fluid
compositions in the Mobile Phases dialog.

Figure 2-20 Mobile Phases Dialog - Basic

The Binary Mixture fields are used to specify the mobile phase in each reservoir. In the example
shown in Figure 2-20, mobile phase A is composed of 100% aqueous solution and 0%
acetonitrile while mobile phase B is composed of 95 % aqueous solution and 5 % acetonitrile.

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The Comment/Modifiers fields allow you to document mobile phase buffering additives, dates, lot
numbers, and other details relating to the composition of mobile phase A and B.
The Channel value (upper right corner) indicates the LC device channel to apply the current
mobile phase settings (multi-channel systems only.)
The More button accesses additional fields. For more information, refer to Mobile Phases Dialog
on page 35.

Mobile Phase Change

Automatically purge initiates a sequence that thoroughly purges both A and B pumps following
a change of mobile phase.
Automatically flush initiates a sequence designed to thoroughly flush the fluid path from the
pump through to the injection valve.
The More button expands the Mobile Phase dialog (Figure 2-21) to show fields that allow you to
change parameters to manually adjust the purge and flush functions.

Figure 2-21 Mobile Phases Dialog - Advanced

The Manual Purge Settings field specifies the number of pump volumes to be purged with
mobile phase following a mobile phase change. Side A and Side B designates which pumps
should be purged following the mobile phase change. Purge Now initiates an immediate purge
of the pumps.
The Manual Flush Settings field specifies the volume and flow rate of mobile phase that should
be used to flush the fluid path between the pump and the injection valve following a mobile phase
change. The Flush Now button initiates an immediate flushing of the pumps.
The Cancel button ignores any changes made to the mobile phase settings and returns you to
the main screen.
The OK button exits the Mobile Phases dialog. If the mobile phases have changed, an automatic
purge or flush sequence may be initiated according to the above settings.

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Direct Control
The Direct Control dialog (Figure 2-22) allows you to start the pumps at a specific flow rate.
Direct Control is useful for operations such as system flushing, equilibrating and tuning an
electrospray interface.

Figure 2-22 Direct Control Window

Pump Manual Control

Conserved Flow allows you to specify mobile phase composition and the total flow rate.
Independent Flow allows you to independently specify the actual flow rate of each individual
mobile phase. The combined flow rate is calculated and displayed.
Monitor Baseline enables data collection while in direct control mode. When Start is clicked, an
equivalent method (of 1 hour duration) will start. The results will be plotted real-time in the main
plot window. When the method ends or is stopped, the data will be saved in the relevant data file
(if the Autosave option has been selected).
Start initiates the specified pump direct control options. When changing the settings, click Start
again for changes to take effect.
Stop stops the pumps.

Valve Direct Control

Load Position changes the state of the internal valve to the Load position. The header of the
Valve Manual Control region changes to reflect the current position of the valve.
Inject Position changes the state of the internal valve to the Inject position. The header of the
Valve Manual Control region changes to reflect the current position of the valve.

Lamp Direct Control

The On button turns on the lamp. The header of the Lamp Direct Control region changes to
reflect the current state of the lamp.
The Off button turns off the lamp.

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User Authentication
User authentication is used to set user access to the software. This allows applying varying
permissions to several users. For more information, refer to Chapter 10.

User Manager
The User Manager Dialog is used to set different permissions for various users. It is described
in Chapter 11 and is only relevant if User Authentication is enabled.

Electronic Signatures
Electronic Signatures are used to view, apply, and revoke electronic signatures from data files.
For more information, refer to Chapter 12.

Analysis Settings
The Analysis menu is used to adjust the parameters that control the analysis process. These
parameters are used by the peak finding algorithm when identifying, placing, and integrating the
peaks found in the chromatogram. The analysis menu can also be configured to automatically
analyze a chromatogram after acquisition is complete.
The Analysis Settings dialog allows you to set peak integration parameters. These settings
determine which peaks the integration routines are recognized during peak finding.

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3
Overview
The Run Manager button on the Acquisition window opens the Run Manager dialog (Figure 3-1)
which allows you to queue a series of samples and acquire them using the specified instrument
methods. The sequence of samples can be saved as a file, recalled, run, copied, modified, and
saved as a new file.

Figure 3-1 Run Manager Dialog

The Menu
Table 3-1 to Table 3-5 shows the lists of the menus available on the Run Manager dialog. Each
menu contains a list of options consisting of commands and sub-menus used to operate the Run
Manager.
Table 3-1 File Menu
Command Function
Open Opens selected Run Table sequence file, refer to File Menu on page 41.
Save Saves the current sequence as a run file, refer to File Menu on page 41.

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Table 3-1 File Menu (Continued)

Command Function
Save As Saves the current sequence as a specific file, refer to File Menu on
page 41.
Import Allows you to import data into the table, refer to File Menu on page 41.
Expert Allows you to export data from the table, refer to File Menu on page 41.
Print Print the table contents, refer to File Menu on page 41.
Exit Ends the current run table sequence and exits the Run Manager dialog,
refer to File Menu on page 41.

Table 3-2 Edit Menu

Command Function
Cut Removes the current selection and copies it into the Windows clipboard,
refer to Edit Menu on page 41.
Copy Copies the current selection into the windows clipboard, refer to Edit
Menu on page 41.
Paste Pastes the previous cut or copied selection, refer to Edit Menu on
page 41.
Delete Deletes the current selection in the run table, refer to Edit Menu on
page 41.
Undo Undoes the previous command, refer to Edit Menu on page 41.
Insert Row Inserts a single blank row in the Run table, refer to Edit Menu on page 41.
Insert Rows Inserts a specified number of blank rows in the Run table, refer to Edit
Menu on page 41.
Insert Copied Rows Inserts a set of copied rows in the Run table, refer to Edit Menu on
page 41.
Reset Rows Clears the status of selected rows in the Run table, refer to Edit Menu on
page 41.
Reset Table Clears the status of every row in the Run table to restart the sequence
from the beginning when Start is clicked, refer to Edit Menu on page 41.
Erase Table Removes all entries from the Run table, refer to Edit Menu on page 41.
Choose Columns Displays Choose Columns dialog, refer to Edit Menu on page 41.

Table 3-3 View Menu

Command Function
Acquisition Window Displays the Main window, refer to View Menu on page 42.

Table 3-4 Devices Menu

Command Function
LC Device Settings Displays the instrument Configuration window, refer to Devices
Menu on page 42.

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Table 3-4 Devices Menu (Continued)

Command Function
LC Wait for Contact Forces the LC to wait for external contact closure before starting
Closure acquisition, refer to Devices Menu on page 42.
Autosampler type Selects or removes the autosampler device, refer to Devices Menu
on page 42.
Autosampler device Displays the Autosampler settings, refer to Devices Menu on
settings page 42.
Skip Missing vials When selected, the run table sequence will skip the row if a vial is
missing from the tray (rather than stop with an error), refer to
Devices Menu on page 42.
Inject Ahead When selected, permits the autosampler to run ahead to the next
method in the table when finished.
Spotter type Select the Spotter device.
Spotter Device Settings Modify the spotter device settings, refer to Devices Menu on
page 42.
AutoNumber Spot Automatically control the location of spots to optimize plate usage,
Position refer to Devices Menu on page 42.

Table 3-5 Help Menu

Command Function
Help View the Help file
About View the About dialog

File Menu
Use the options on the File menu to select any run table files stored on the computer.
Open: Open the desired file
Save: Save the sequence of samples to a Run Table file.
Save as: Opens the Save As dialog that is used to save a run table file to a different file name.
Import: Imports data into the run table from one of 4 different file types - a proprietary file type for
the grid which allows saving format information as well as data, a comma-delimited text file, a
tab-delimited text file, and an Excel file.
Export: Save the run table data in one of 4 different file types - a proprietary file type for the grid
which allows saving format information as well as data, a comma-delimited text file, a tab-
delimited text file, and an Excel file.
Print: Print the contents of the Run Table.

Edit Menu
Cut: Removes the selected Run Table cells and copies them to the windows clipboard.
Copy: Copies the selected Run Table cells to the windows clipboard.

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Paste: Add copied or cut cells into the Run Table.

Delete: Removes the contents of the currently selected Run Table cells.
Undo: Restores the table to its state prior to the previous command.
Insert Row: Inserts a single row at the currently selected Run Table row.
Insert Rows: Opens a dialog used to insert a set number of rows into the Run Table.
Insert Copied Rows: Copies rows from the Windows Clipboard into the Run Table.
Reset Row(s): Clears the status of the selected row(s).
Reset Table: Resets the status for the entire Run Table. This allows you to restart the queued
sequence of events.
Erase Table: Clears the entire contents of the Run Table.
Choose Columns: Opens the Choose Columns dialog. This dialog is used to show, hide, and
move the available columns in the run table.

Figure 3-2 Run Manager Column Selection

View Menu
Acquisition Dialog: Opens the main acquisition dialog with the chromatogram plot and status
area.

Devices Menu
LC Device Settings: Opens the Instrument Configuration dialog (Figure 2-16), that allows
configuration of the LC device and setting the various configuration parameters of the device.
LC Wait for Contact Closure: Delays the start of the LC method until it receives an external
contact closure signal. This allows the start of the acquisition to be synchronized to an external
signal.
You can select the desired autosampler (or remove one) by choosing Autosampler Types. The
autosamplers which are currently supported are described in Chapter 5.

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Autosampler Device Settings: Opens the Autosampler Configuration dialog. This is used to
configure autosamplers which may be delivered with the instrument. Currently supported
autosamplers are described in Chapter 5.
Skip Missing Vials: If selected, will allow the table sequence to continue running if the
requested vial is missing from the autosampler tray. The sample row will be skipped and marked
with an error. If not selected, an error will occur and the sequence will stop (no subsequent
sample rows are processed).
Inject Ahead, If selected, permits the autosampler to run ahead to the next line in the table and
start the next autosampler method before the current LC method is complete. This is primarily
useful for high-throughput applications with short LC method durations.
Click on the Spotter Device Settings opens the spotter configuration dialog.
When you select AutoNumber Spot Positions, the Run Manager is configured to control the
location of spots automatically to optimize the use of the plate.

Run Table

Contents of the Run Table

The sample grid in the Run Table allows linking together an autosampler method, a sample tray,
a sample vial, an analysis method, sample method overrides, and sample information such as
injection amount, sample name, ID, type, and any other comments. Each sample is represented
by a single row. The various columns in Table 3-6 contain the following information:
Table 3-6 Run Manager Columns
Command Function
Seq. # The row number of the sample in sequence.
Run Indicates which samples are to be processed in the sequence.
(unchecked rows will be skipped).
Run Interval Time field for entering a sampling run interval. Time format is
hh:mm:ss. The specified time is the time between the start of each
acquisition. Blank values are treated as no interval.
Run Replicates Text field for specifying the number of replicates for each row in the
run table. Blank values are treated as a single run.
Autosampler Method This menu selects the autosampler method.
Autosampler Tray This menu selects the tray location of the sample vial or well.
Autosampler Vial This menu selects the vial to be sampled.
Autosampler Aspirate This edit box specifies an override value for the aspirate volume in
(µL) the autosampler method (leave blank to use the value specified in
the LC method).
Autosampler Dispense This edit box specifies an override value for the dispense volume in
(µL) the autosampler method. Leave blank to use the value specified in
the LC method.
LC Method This menu selects the LC method for the LC device acquisition.

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Table 3-6 Run Manager Columns (Continued)

Command Function
LC Flow Rate This edit box specifies an override value for the total flow rate in the
LC method. Leave blank to use the value specified in the LC
method.
LC Injection Vol. (nL) This edit box specifies an override value for the injection volume
(nL) in the LC method. Leave blank to use the value specified in the
LC method.
LC Channel This menu selects the LC channel for the LC device. Used for multi-
channel LC devices only. An asterisk (*) indicates any available
channel may be used. For high-throughput applications with
identical columns on each channel, this option allows the fastest
processing of all the samples in the list, as no specific channel is
required to be available for any particular sample
LC. Inj Type This menu selects an override value for the injection type used in
the LC method. Leave blank to use the value specified in the LC
method.
LC Column Temp (°C) This edit box specifies an override for the column temperature (°C)
in the LC method. Leave blank to use the value specified in the LC
method.
Sample Name Text field for labeling the sample.
Sample Type Text field for describing the sample type.
Sample Amount Text field for entering the amount of sample.
Sample ID Text field for assigning an ID to the sample.
Analysis Method This menu selects the post-acquisition analysis method.
Spotter plate # This menu selects the plate number for spotting deposition.
Spotter Time/Drop (ms) Frequency of spotting.
Spotter Time (min) Duration of the spotting operation.
Other Comments Text field for entering additional comments about the sample.
Other status The current status of the sample row being acquired.
Other Flag Tag Text field for specifying a tag for use in generating the data file
name. You should only use characters allowed for valid filenames.
Other Data File Name Text field for displaying the data file name.

When an acquisition is in progress, the color of the sample row indicates the state of its progress:
• Light green - the sample is preparing to run (equilibrating)
• Dark green - the sample is running
• Red - the sample has stopped.
• Yellow - an error occurred.
• Gray - the sample has completed
After acquisition has been completed, the table can be set to the pre-run state using the Reset
Table button. The sequence will begin with the first sample row the next time it is started.

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Edit the Run Table

To edit a cell
Cells in the table can be navigated with the arrow keys on the keyboard or by selecting cells with
the pointer.
The actions allowed in each cell in the table are dependent on the column type. Depending on
the column data, the typical cell types are:
• menus, where the selection is made from a list.
• Edit boxes that allow numbers and decimal points (for floating point numbers).
• Text editors that allow any character.
If a cell uses a menu, the menu can be activated by double-clicking the cell. If the cell already is
open, the menu can be activated by clicking Enter or pressing Space. Once an item in the menu
is selected, the value will be displayed in the table. Accept this value by either moving to another
cell or by clicking Enter.

Figure 3-3 Activated Cell with List Box

If a cell uses a text box or edit box, the cell can be activated by double-click the cell. If the cell
already has focus, the edit box can be activated by typing numbers or characters. To accept the
value, click another cell or pressing the Enter key.

Figure 3-4 Activated Cell with Text Edit Box

Typical Cut, Copy, Paste, and Delete operations can be applied to any cell.

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To select multiple cells

To select any range of cells in the Run table, click on cell and drag an area to select it. Releasing
the mouse button will finish the cell selection.
Entire rows can be selected by dragging the row label (Seq #).

Figure 3-5 Run Manager Multi-Cell Selection

A multiple cell selection can also be performed by holding Shift and using the arrow keys to
select a cell range.
If you click in the Seq # column header, then the entire run table will be selected.
Select the entire run table by clicking the Select All menu item either on the Edit submenu, from
the right-click menu, or using Ctrl + A. This feature works only if any cell in the Run Table is
highlighted.
Once you have selected one or more rows, right-click to open a context menu to Cut, Copy,
Paste, Insert New Rows, Insert Copied Rows, Insert Series of Rows, or Delete selected
rows.
Cut, Copy, and Delete will operate on the highlighted selected rows. Paste will place copied or
cut rows to where the cell is currently active.
A single copied row can be pasted into multiple rows by selecting the desired destination rows
prior to the Paste operation.

To move selected cells

A black border will be visible around the cell selection. This border can be grabbed and moved
using the pointer. Move the pointer over the selection border and an arrow icon with rectangle at
the base appears. Drag the border to move the selection to a new location within the Run Table
grid.
If the selected cell types do not match the cell types of the new location, an icon will indicate the
operation is not allowed.
This operation can be performed on entire rows by using the same method after the entire row is
selected. The move operation can also be completed by dragging the row label (Seq #).
When an acquisition is in progress or if the sample row is being used in some operation, the rows
will be locked for editing. If the rows are locked, they can not be moved and/or edited.

The Auto-Complete Command

Creating large sample lists can be greatly simplified by using the ability to drag a selection and
auto-complete subsequent rows based on the previous values of the selection.
After selecting cells, auto-complete is accomplished by grabbing the small square in the selection
border and dragging it down the column. For most selections, the handle is located at the bottom

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right of the selection border. For entire row selections, the handle is located at the bottom left of
the selection border.
Below is a list of various types of auto-complete operations used when auto-completing an
extend-dragged selection of column cells:
• Single cell new cells repeat the first selection.
• Multiple text cells new cells repeat the entire selection.
• Multiple numeric cells an attempt is made to identify any trend in the selection and
the trend is extrapolated. For example, if you select two cells containing 1 followed
by 2, auto-complete will insert 3, 4, 5, and so forth. into the following cells.
• Multiple drop-down list box cells (numeric & vials) same as numeric cells, but the
range is limited by the values in the list. Extending a selection beyond the last
number in the list box will wrap the pattern back to the values at the beginning of the
list.

Showing, Hiding Arranging and Sizing Columns

Right-clicking the column labels at the top of the table will display a context menu with the
Columns menu item This will open the Choose Columns dialog, that allows show, hide, and
arrange the order of columns in the Run Table. This option can also be selected from the Edit
menu.
Arrange columns by left-clicking on a column label and dragging the column to a new location.
To drag entire column categories, click the first row where the column categories (for example,
LC, Autosampler, and so forth) are located and drag whole categories of columns to a new
location. To drag individual columns, click on the second row label (for example, Tray, Vial) and
drag individual columns to new locations. When moving a column outside its category, the
category header will be added above the relocated column.
Resize columns by moving the pointer over the grid lines in the column labels. A resize cursor
icon will indicate a drag operation that will set the column height to a new size.

Column Sorting
Sort columns by clicking column labels in the second row (except for the Run column that sorts
by clicking on the column header in the first fixed row). A direction arrow will appear indicating
the direction of the sort.
Hierarchical sorting can be accomplished by sorting the desired columns in the desired order. If
the Run Table sequence is running a dialog will open before allowing the sort operation.

Freezing Rows and Columns

Freeze rows and columns in the Run Table so that they remain in the visible area while the rest of
the table area can be scrolled. Freeze rows at the top by moving the pointer over the border
between the fixed column label rows and the scrollable area until the pointer changes to a lock
mouse cursor. Left-click the mouse and drag the border down any number of rows to freeze. Any
movement or scrolling in the grid area will not affect the frozen rows.
Columns can be frozen at the left of the grid by moving the pointer over the border between the
fixed column and the scrollable area until the pointer changes to a lock mouse cursor. Drag the
border across any number of columns to freeze. Any movement or scrolling in the grid area will
not affect the frozen rows.

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The Sample Tray

Status of Samples
The Current Tray (Lower left corner of Figure 3-3) shows an image of the configured
autosampler tray type and indicates active sample vials and their states.
Vial state:
• Green - sample is currently running.
• Blue - valid method associated with this vial.
• Blue/Checked - the sample finished successfully.
• Red - an error occurred while running this vial or the sample was stopped.
• Yellow - vial is selected.
The Status area indicates the currently selected (or active) tray and a text description of the
current autosampler action or status. The displayed tray can be selected using the arrow buttons
next to the tray name in the Status area or by choosing a row in the table with the desired tray.
For autosamplers with tray cooling, the tray temperature will appear in the tray temperature area.
The Pause button is available to hold the autosampler in its current state/position. If an
autosampler method is running, the pause button will hold the method and stop the autosampler
in its current action. The Resume button will appear to allow the method to continue when the
system has been paused. This action is useful for changing sample trays while the autosampler
is running.

Selecting a Vial
You can use the tray graphic to select the vial for the current sample row by clicking the vial in the
tray image. If the active row in the sample table is valid, the vial number will be updated to reflect
the vial number selected in the graphic.

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It is possible to rapidly add many new samples to the sample table by clicking and dragging the
mouse on the tray to select multiple vials. A Vial Selection dialog (Figure 3-6) will be displayed to
indicate how the sample table rows will be filled. The newly created rows will duplicate the
information of the row number indicated in the Current Table Row text box, but include the newly
inserted vial numbers. The default entry is the currently selected row in the table.

Figure 3-6 Selecting Vials in the Current Tray

You have the option to Insert Rows with the newly selected vials or Overwrite Existing Rows in
the sample table. Inserting rows will insert new rows into the table beginning with the currently
active cell. Overwriting existing rows will add the new entries starting at the currently active table
cell and fill down over the existing entries.

Method Editors
The Autosampler Methods button displays the autosampler method editor, which allows you to
create and edit methods specifying the amount of sample to be drawn from the sample vial and
the parameters to be used for pre- or post-injection syringe cleaning. The editor displayed will
depend on the type of autosampler configured. CTC PAL Autosampler Control or NanoLC-AS1
Autosampler Control editors are currently supported.
The LC Method button opens a window for entering the parameters to be used for separating
and detecting the sample. This information includes flow rate, gradient profile, detection
wavelength, and so forth and is stored in a sample method. The method parameters available will
depend on the configuration of the LC device. 1D LC methods and 2D methods are available.
The Analysis Methods button opens an Analysis Method Settings dialog which allows you to set
the peak detection configuration parameters.
The Spotter Methods button provides access to method information for any configured spotter
devices.

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Run Manager

Run Sequence
The Sequential option is the only option available for single channel instruments. This mode runs
the samples in the order they appear in the table, row by row. For example, the sequence starts
with row 1 and proceeds to row 2, row 3, and so forth. After each row finishes, the next row
begins.
The As Available and Synchronized Multi-channel options are available to multi-channeled
devices.
The As Available option starts each row when its assigned LC channel becomes available. A row
will not start until all previous rows with the assigned channel number are finished processing.
For high-throughput applications, this option allows the fastest processing of all the samples in
the list.
The Synchronized Multi-channel option requires that all channels of a device start
simultaneously. As a consequence, the LC methods on every channel must finish before the next
series of samples will begin synchronously.
Start/Stop begins the sample sequence defined by the rows entered in the table. When a
sequence begins, current changes to the run table are validated and saved. The button changes
from Start to Stop to end the run table sequence, if desired. If the table contains rows with
samples that have been previously stopped during acquisition, a prompt to re-start these
samples will appear each time the sample table is re-started.
Flush/Equilibrate when Idle is an option that keeps the pumps running to minimize equilibration
delay at the start of each run. Selecting this option also ensures column heater equilibration to
the temperature specified in the method. This option applies only to LC methods with pre-flush
settings.

Figure 3-7 Run Manager Sequence Selection

After all acquisitions are complete, the table can be set back to the initial state by clicking Reset
Table. The sequence will begin with the first sample row the next time it is started.
The Elapsed Time indicator displays the approximate time elapsed since the run table started.
The Queued Time indicator displays the approximate time required to run all of the active
samples in the run table. This time is an approximation based on the LC methods only and does
not include additional time required for autosampler methods.

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4
The Peak Viewer Utility can be opened from the Main Acquisition dialog by selecting Peak
Viewer on the File menu. The Open dialog will appear to browse and locate files either in the
Eksigent® data or text format. Locate the file(s) of interest and select Open to load the data into
the Peak Viewer.
The Peak Viewer utility can also be started directly from the installed Program Group menu.

Figure 4-1 Peak Viewer dialog

Plot
The Plot dialog can be configured to display one or multiple data sets simultaneously. For
systems with spectrometers, the chromatogram (UV absorbance data) will be displayed. All other
systems will display the AUX A/D signal (for use with external detectors).
The peak table displays the current peak analysis results for each data set and can be used to
edit (remove) peak information directly. A sample report, peak statistics, and peak trends are also
accessible from the peak table.

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Peak Viewer Utility

Peak Table
When the program starts, the peak table indicates data source information related to the loaded
data files and any peak information stored in the data file (resulting from automated analysis
following the acquisition). If the data has not been previously analyzed or if there are no peaks
detected, the table will be empty except for the data source information. Click Find Peaks to
access data files for re-analysis at any time.
The contents of the table can be adjusted using the Show menu and selecting from the available
peak parameters, including Retention Time, Area,% Area, Plates, Height, Asymmetry, Base
Width, and so forth. Once selected, the table will be updated to show the relevant parameters.
The data source information can be customized either by right-clicking the mouse and selecting
Annotations from the Peaks menu.
The table can be sorted by clicking the relevant column header labeled with the peak number.
The rows will be sorted by ascending or descending order in that column each time the column
heading is clicked. For example, to sort the information by peak area, select Show Area and
press the relevant peak number at the top of the table.
Data in the table can be selected in multiple ways:
• Use the mouse to click-drag and select a range of cells.
• Entire rows can be selected by pressing the row label (first column).
• Holding the Shift key while clicking allows selection of a range of cells or rows.
• Holding the Ctrl key while clicking allows selecting multiple cells or rows in any order.
Any range of information in the table can be copied to the Windows clipboard by selecting cells,
right-clicking the mouse and selecting Copy. The cell contents will be available to be pasted into
any other application.
Individual erroneous peaks can be removed by selecting the peak in the table and either pressing
the Delete key on the keyboard or right-clicking the mouse and selecting Delete.
Peak information in the table can be marked (color coded) in order to more easily identify trends
in the data. To mark the data, enter a value into the Mark Values entry field and select a sign
(greater, lesser, equal) to mark all values in the table that meet the specified criteria. A slight color
gradient will be used to differentiate the range of values.

Sample Report
At any time, a text sample report is available that includes a list of peak attributes for every
individual open data file. The report can be accessed by selecting the Sample Report tab above
the peak table. It contains a section for each file indicated by the data source information
displayed in the peak table and a set of peak attributes for each peak in the file. The set of peak
attributes can be customized from the Report Contents tab of the Peaks > Annotations menu
item.

Figure 4-2 Peak Viewer Sample Report

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Peak Viewer Sample Report

Individual peak attributes can be edited by graphically editing the chromatogram, by deleting a
peak from the table, or by re-analyzing the data. Any changes to the current peak information will
cause the report to be automatically updated to reflect the results of the new analysis.
The contents of the report can be copied to the Windows clipboard by selecting text within the
report, right-clicking the mouse, and selecting Copy. This can also be accomplished by selecting
the text and pressing Ctrl-C on the keyboard.
The peak table, sample report and statistics can be printed to the default printer using the Print
command on the File menu and exported to a file using the Export command on the File menu.

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Peak Viewer Utility

Statistics
Statistics are generated from all of the open files and for the peak attribute currently displayed in
the peak table. The statistics table, which displays the mean, median, relative standard deviation
(RSD), maximum and minimum value generated for each peak number is at the top half of the
Statistics tab. The chart below the table indicates the mean and the one and three sigma range
for the current peak attribute with the data source number on the abscissa. A chart can be
generated for each individual peak by selecting the corresponding row in the statistics table. In
case of a numerical data source label, (e.g. relative retention time), the abscissa displays the
actual numerical value. The statistics table and chart is useful for examining the reproducibility of
any of the peak attributes within a set of data files. The table and chart are regenerated following
any modifications to the peak attributes in the table or chromatograms.

Figure 4-3 Peak Viewer Statistics

Monitoring Peak Trends

When monitoring a process, dilution, or other related set of samples it is useful to examine the
temporal trends of particular peaks or groups of peaks. Peak trends are generated for the
selected peak attribute for all loaded sample files.
The trend table at the top of the Trend tab gives you the option to trend by peak attribute, or by a
custom formula. The chart in the lower left area displays the actual trend lines for each selected
peak, and the chart in the lower right area shows an overlay of all chromatograms.

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To create peak trends via custom formulas, check the Custom Formula option and enter the
formulas in the third column of the trend table. For example, to create a trend which is the
average of Peak 1 and Peak 2 enter:
½ (Peak1 + Peak2)
The value used for Peak1 is the currently selected peak attribute (for example, Area, Retention
Time, and so forth) To apply the formula and display the result, check the box in the first row. You
can also edit the name of the peak trend in the second row which will then be displayed as the
legend.
The X-axis uses the currently select sample Annotation method. All charts and table entries can
be copied to the clipboard by right-clicking and selecting Copy.

Figure 4-4 Peak Viewer Peak Trends

Peak Analysis
Click Find Peaks to analyze available data files. By default the analysis parameters stored in the
data files are used for the analysis. To edit parameters, click Settings. This opens the Analysis
Settings Editor dialog, for more information refer to Chapter 8. The new peak information will be
updated in the peak table, the plots and the report.
To analyze all open files, select all files in the table before pressing Find Peaks. If no files (rows)
are selected in the table, a prompt will indicate that all files will be analyzed.

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Peak Viewer Utility

To analyze particular files, select each file (by row) of interest and click Find Peaks. Only the
selected files will be processed.
The results in the data file will not be permanently altered. However, the new peak attributes can
be stored to disk by selecting the file(s) in the table and choosing Save Changes from the File
menu.
For more information, refer to Peak Detection Tab on page 82.

Plot Area
The chromatogram or external detector signal for each data file is displayed individually in the
plot area. The plot area can be modified to display multiple plots simultaneously by selecting Tile
on the View menu and selecting the number of plot windows to display.

Figure 4-5 Plot Area Options

The contents of the plot area can be copied to the Windows Clipboard by right-clicking the plot
area and selecting Copy.
If multiple chromatograms have been overlaid, the overlaid data can be removed individually by
selecting a data set with the pointer and choosing Remove > Overlay or all at once by selecting
Remove > Overlays.
Individual peaks can be highlighted by moving the pointer close to or across the peak area. To
remove a peak from the peak table highlight the peak and select the sub menu item Remove >
Peak.
Integration timed events can be added graphically from the Add Integration Event menu item.
After re-analyzing the chromatogram the results will be updated in the peak table, sample report,
and statistics.
The plot axes can be modified directly by clicking the X or Y axis limits (maximum or minimum
value) to activate a text box that allows entering the new axis limit values. The new limits will take
effect after pressing the return key or clicking away from the axis area.
You can quickly zoom into and out of a region of interest by click-dragging a region directly on the
plot. A rectangle will be displayed indicating the region of interest. Releasing the mouse will
redraw the plot using the new axis limits.
Double-clicking the plot area will re-scale the plot to fit the entire data contents in the plot window.
Clicking the X-axis time units will toggle the axis units from seconds to minutes.
If peaks are present, moving the mouse over the peak baseline displays a move icon that allows
you to manually adjust the peak baselines. Click the baseline point and drag it to a new location.
The Autoscale properties available from this menu will automatically adjust the axis limits to
display the entire data set based on maximum and minimum values in the data set. Use Zoom
Out or Zoom Last to undo the previous zoom region or axis settings.

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 Peak Viewer Utility

The Plot Properties dialog can also be accessed from this menu, where peak labels and plot area
display settings can be adjusted.

Menus
File Menu
Table 4-1 presents the Commands on the File menu.
Table 4-1 The File Menu Commands
Command Function
Open The Open selection is used to load new data sets into the peak viewer.
The existing peak information and plots will be removed and the new file
data will be used to populate the peak viewer. No changes to the
previously loaded data will be stored.
Add files The Add Files selection is used to add new data files to the current data
set. The new data will be added to the end of the peak table (and plots
windows)
Save Changes To save changes to the peak information for the open data files, select
Save Changes. Modifications to the peak information will be stored to the
data files.
Only the selected files will be updated. If no files are selected, a prompt
will appear to save all files.
Export The Export function is used to export the current peak table, sample
report and statistics information in various Windows file formats (Excel,
tab-delimited text, and so forth).
Print Preview The Print Preview function allows you to preview the appearance of a
report before it is printed. The format of the report is similar to the one
generated in the Acquisition window. It contains file, sample and method
information, a plot of the chromatogram and the set of peak results
displayed in the sample report.
Print Print allows printing the selected plots, current peak table, sample report,
statistics and trends information to the default printer.
Print All This prints all information for the data set, including the peak table, the
sample report, statistics, trends and plots.
Monitoring This function can be used to monitor samples in real time as they are
completed from the run table. When selected, the results of each sample
will be automatically loaded into the Peak Viewer software, followed by
an update of all charts, trends, and reports. If not already open, it also
loads the Run Manager window which allows you to queue and acquire a
series of samples.
Monitor Folder As an alternative to monitoring the run table, this function observes a
specified folder for new files (in the text output format). After detecting a
new file, it will be opened and analyzed automatically by the Peak Viewer
software, followed by an update of all charts and reports.
Skip First Sample If this item is checked, the first file after start monitoring the run table or a
folder will be skipped.

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Peak Viewer Utility

Table 4-1 The File Menu Commands (Continued)

Command Function
Exit Close the Peak Viewer utility

Edit Menu
Table 4-2 presents the commands on the Edit table.
Table 4-2 The Edit Table
Command Function
Copy Table This copies the selected section of the currently displayed table to the
Selection clipboard. Sections of the peak table can be selected freely by clicking
and dragging in the table to highlight the cells of interest. For the
summary report and statistics table, you can click on rows to select the
entire row.
Copy Plot Selection This copies the current selected plot to the clipboard. To select a plot,
click the desired plot or click anywhere in the peak table row for the data
file.
This can also be accomplished by selecting the plot, right-click the
mouse, and select Copy.
Select All This function selects the entire table which is currently displayed.

View Menu
The View menu is presented in Table 4-3.
Table 4-3 The View Menu
Command Function
Full Screen This sets the plot area to display a single data set. The current active
data file (selected via plot window or peak table grid) will be used to fill
the entire plot area. Full Screen is the default setting when the Peak
Viewer Utility starts.
Tile This rearranges the plot area to display multiple data sets in a tiled
window format. Use the right scroll-bar to scroll through the plots. Any
data files added to the data set will be appended at the end. An example
is shown in Figure 4-6.

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Figure 4-6 Displaying Multiple Chromatograms

Peaks Menu
The Peaks Menu commands are shown in Table 4-4.
Table 4-4 The Peaks Menu Commands
Command Function
Analysis Settings This provides access to the Analysis Method Editor, for more information
refer to Chapter 8. Click Settings as an alternate way to open the
Analysis Method Editor.
Import Analysis This imports analysis settings from an existing analysis method file and
Settings apply the settings to each selected file.
If no files (rows) in the table are selected, a prompt will appear to apply
the settings to all files.
Find Peaks The Find Peaks function analyzes the current data set. Each selected file
will be processed in sequence using the Analysis Settings stored in the
file.
If no files (rows) in the table are selected, a prompt will appear to process
all files.

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Peak Viewer Utility

Table 4-4 The Peaks Menu Commands (Continued)

Command Function
Annotations Displays the Annotations dialog, refer to Figure 4-7.
Data Source Displays the Data Source tab of the Annotations dialog, which contains a
list of labels that can be applied to identify the data source for items
displayed in the peak table, the statistics and trend charts, refer to
Figure 4-7.
Report Comments The Report Contents tab of the Annotations dialog, which contains the list
of peak attributes that can be displayed in the sample report. Any
combination of peak attributes can be added to the report by selecting
the corresponding check boxes, refer to Figure 4-8.
Peak Labels The Peak Labels tab of the Annotations dialog, which contains the list of
peak attributes that can be displayed as peak labels in the chromatogram
plots. The list is identical to the options in the Report Contents tab.

Figure 4-7 Plot Labels Options

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Figure 4-8 Report Contents Options

Plots Menu
The commands on the Plots menu are described in Table 4-5.
Table 4-5 The Plots Menu
Command Function
Properties The peak labels can be adjusted in the Peak Labels tab so that any peak
attribute can be labeled on the plot next to each peak, refer to Peak Label
Options on page 62.
Overlay Selection The Overlay Selection is used to present two or more chromatograms on
a common set of axes. For more information, refer to Overlaying
Chromatograms on page 63.
Make All Plots When selected, the Make All Plots Identical option will cause all
Identical displayed plots to have the same attributes. The axes limits, plot labels,
colors, and so forth, will be adjusted on all the plot windows to be
identical to the currently selected plot. While selected, any further actions
to modify the plot window will affect all other displayed plot windows. For
example, zooming in a region of one chromatogram will also cause the
axes limits for all other chromatograms to be adjusted as well.
Auto Scale All Plots Auto Scale All Plots will disable the Make All Plots Identical feature and
will automatically scale all plot windows to fit the entire contents of their
individual chromatograms. It is possible that the resulting plot axes limits
will vary among each loaded data file.

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Peak Viewer Utility

Peak Label Options

Multiple peak attributes can be added to the label by selecting multiple check boxes. The
orientation of the labels can be changed by selecting a corresponding angle from the Orientation
menu, refer to Figure 4-9.

Figure 4-9 Peak Label Options

The colors used to draw the plot area and grid lines can also be adjusted in the Properties tab by
double-clicking the relevant color dialog, refer to Figure 4-10.

Figure 4-10 Color and Grid Line Options

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Overlaying Chromatograms
To overlay chromatograms, select the data file rows in the peak table by holding Shift to select
multiple sequential rows, hold Ctrl to select multiple rows in any order, or use the pointer to drag
an area to highlight in a range. From the menu, choose Overlay Selection. The topmost data file
in the peak table selection will be used as the active chromatogram and the plot window will be
updated with overlays of the data from the selected data files. The overlays can be removed by
selecting Remove Overlays; this can also be done using the corresponding right-click plot
window menu item. For an example, refer to Figure 4-11.

Figure 4-11 Overlaying Chromatogram Data

Make All Plots Identical

When selected, the Make All Plots Identical option will cause all displayed plots to have the same
attributes. The axes limits, plot labels, colors, and so forth, will be adjusted on all the plot
windows to be identical to the currently selected plot. While selected, any further actions to
modify the plot window will affect all other displayed plot windows. For example, zooming in a
region of one chromatogram will also cause the axes limits for all other chromatograms to be
adjusted as well.

Auto Scale All Plots

Auto Scale All Plots will disable the Make All Plots Identical feature and will automatically scale
all plot windows to fit the entire contents of their individual chromatograms. It is possible that the
resulting plot axes limits will vary among each loaded data file.

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Peak Viewer Utility

Math on/Between Sets

This menu item opens the Math on/between Data Sets dialog, refer to Figure 4-12.

Figure 4-12 Math on/between Data Sets dialog

To perform a math operation, click to select the desired data set from the Available Data list. Click
the upper arrow to display the data set under Selected Data Sets. Type an arithmetic operator in
the Operator text box and either type a numerical value or select another data set from the
Available Data list and press the lower arrow. If using a data set an additional offset can be
applied by entering a non-zero value in the Time Offset field. Click Apply to perform the
operation. The plot window will be updated to show the resulting data sets. If Re-Analyze Peaks
is selected, the software will automatically analyze the modified chromatograms. Click Undo to
restore the original data.

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Autosampler Control
5
Configuring the Autosampler
To configure the software to be controlled within the Run Manager; select Devices >
Autosampler Type > <customer autosampler type here>, refer to Figure 5-1.

Figure 5-1 Selecting the AS1 Autosampler

After the autosampler hardware is selected, the Run Manager will attempt to communicate with
the device using the default settings. Refer to your hardware user guide for more information on
configuring the device and creating device methods.

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6
Creating and Editing Methods
LC Methods are created and edited using the Method Editor, which is accessed by clicking on the
Method Editor button in the Run Manager Window. The Method Editor window contains a
Selected Method region and up to 5 tabs: Summary, Run Conditions, Flow Profile, Flow Table,
and Detection. For more information, refer to the application specific method creation
documentaton included with the hardware.

Note: Depending on the configuration of the LC device, it may not be equipped with an
absorbance detector.

Summary Tab
The Summary tab will be presented when the Method editor is opened and is used to enter
descriptive information about the column used for a particular run (Figure 6-1). In addition, it
summarizes the information from the other tabs in the LC Method Editor dialog.

Figure 6-1 LC Method Editor Dialog - Summary

Selected Method
The Name field in the selected method region indicates the name of the LC method used. The
menu allows for selecting an existing method for viewing and editing. Save writes all the current

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LC Method Editor

values from the Method Editor dialog tabs to the LC method file using the file name specified in
the Name field. Change the name and click Save to create a new method.

Method Identification
The Method ID field is a comment field that allows you to assign an identification number to the
LC method.

Column Identification
The Column Information region contains a series of fields which can be used to describe the
column used for a run. The entry of this information is optional.
The Manufacturer field is the name of the manufacturer of the column to be used for the LC
method.
The Type field is the description of column to be used in the current run. An example might be
C18, CN, and so forth.
The Serial Number field is the serial number of the column to be used with the method. The
Particle Size field is the particle size of the column stationary phase and the Diameter field is the
column inner diameter.
The Length field is the length of the column to be used with the LC method.
The Sample Injection, Flow Profile and Detection fields present information about system
conditions, and are not editable via this tab.

Detection
For devices that include a spectrometer, the Detection region displays the details of detection
data to be collected during the run of the LC method. Information includes data rate, wavelength
range and data file size.

Run Conditions Tab

Information in the Run Conditions tab is used to specify pre-run, sample injection, and post-run
conditions (Figure 6-2). The size of the sample injection and the temperature of the run are
determined here.

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Figure 6-2 LC Method Editor Dialog - Run Conditions Tab

Pre-Run
Flush column allows you to equilibrate the column prior to the run for a defined duration and flow
rate using the method initial mobile phase composition. The specified duration is the minimum
time that the column will equilibrate before acquisition begins. If the specified duration elapses
and the acquisition has not started (for example, column temperature has not stabilized), the
device will continue to equilibrate indefinitely.
For systems with column heaters, Stabilize column temperature sets the temperature (ºC) for the
column heater. Acquisition will not start until the column reaches the specified temperature within
0.1 ºC.

Sample Injection
The Sample Injection region allows you to choose between None, Standard, Metered, or Rapid
sample injection modes.
None indicates that the sample valve will not actuate during the acquisition.
Standard indicates that the sample valve will switch to the Inject position when the acquisition
begins and switch to the load position when the acquisition ends. As a result, the sample loop
remains in the flow path during the acquisition.
Metered injection mode offers the flexibility to vary the injection volume. The valve is switched to
the Inject position when the acquisition starts and the specified volume of sample is metered to
the column by the LC pumps at the specified conditions. After the specified volume is injected,
the sample valve switches to the load position so the sample loop is removed from the flow path
during the acquisition.

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Rapid injection mode operates similar to Metered injection mode, but the LC pumps steadily
increase the flow rate during the injection (maintaining the initial mixture fraction) in order to
quickly meter larger sample volume.

Post-Run
Flush column allows you to rinse the column after the run is complete for a defined duration and
flow rate using the method ending mobile phase composition.

Flow Profile Tab

The Flow Profile tab (Figure 6-3) allows you to graphically display and program mobile phase
composition changes for the acquisition using click and drag techniques.

Figure 6-3 LC Method Editor Window - Gradient Profile

Flow Mode
The Flow Mode region allows you to choose between conserved flow and independent flow
modes.
• Conserved flow maintains a constant total flow rate for the entire duration of the
acquisition while varying mobile phase composition.
• Independent flow mode allows you to specify the independent flow rates of each
mobile phase.

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Profile Editor
The Profile Editor region allows you to manually enter values for the mobile phase composition
profile by inserting values at different points in time.
Runtime is the total analysis time specified in minutes.
Total flow rate is the combined flow rate of both A and B mobile phases and is maintained
constant for the duration of the LC method run.

Note: Total flow rate is not shown for Independent Flow Mode.

The point selector scrolls through the programmed points of the profile.

Programmable Events
For device firmware versions X.39 or greater, Events are supported by the LC Method Editor
using the Flow Profile tab.
In the Flow Profile tab, a right mouse-click in the chart area displays the Event context menu,
from which one of 12 possible events may be selected (Figure 6-4). Up to 32 Events can be
inserted into the method. The event is inserted at the time located in the X axis where the right-
click was performed. The Event may be moved by dragging the pointer over the event flag icon.

Figure 6-4 Programmable Events

To delete an event, right-click on the event flag icon. Display event information after insertion, by
moving the pointer over the flag icon. A tool-tip will appear describing the event type.

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LC Method Editor

Flow Table Tab

The tabular representation of the Flow Profile is displayed on the Flow Table tab, refer to
Figure 6-5. The Flow Table allows data describing the LC method flow profile to be typed in. As
with the Flow Profile tab (Figure 6-4), the total flow rate is not shown in the Flow Table tab when
Independent Flow Mode is selected.

Figure 6-5 LC Method Editor Window - Flow Table

You can select a flow profile Event from the Event menu in the Event column. Any events added
in the table will also be reflected in the Flow Profile Editor Tab. Use the arrow and X to insert or
remove rows in the table.
The Flow Mode region is used to choose between conserved flow and independent flow modes.
• Conserved flow maintains a constant total flow rate for the entire duration of the
acquisition while varying mobile phase composition.
• Independent flow mode allows you to specify the independent flow rates of each
mobile phase.
The Profile Editor is used to indicate the total flow rate, which is the combined flow rate of both A
and B mobile phases and is maintained constant for the duration of the LC method run.

Note: Total flow rate is not shown for Independent Flow Mode.

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Detector Tab
The Detector tab is presented for instruments that include a spectrometer (Figure 6-6). This is
used to setup the spectral range that defines the main chromatogram as well as the rate at which
spectra are acquired.

Figure 6-6 Detector Tab

Data Acquisition
The Approximate acquisition rate in Hz field specifies the data acquisition rate used to collect the
absorbance signal. For instruments equipped with an absorption spectrometer, an entire
absorption spectrum is measured at each time point.
The Average reference/background acquisitions field specifies the number of data points
averaged together to calculate the spectrometer dark current and reference signals prior to
initiating acquisition. The default value is 4.

Detector Wavelength Range

The Lower limit and Upper limit are wavelengths used to define the range of spectral information
that is collected during the acquisition. The values range from a minimum of 200 nm to a
maximum of 380 nm.

Chromatogram
The Chromatogram region is used to indicate which mode of spectrometer acquisition to use.
Absorbance is the default selection as it is typically used for HPLC detection. However, for

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diagnostic purposes, you can select either UV light Transmission or Detector counts for
monitoring system performance.
The Absorbance region defines the parameters used to display the single wavelength
chromatogram in the Acquisition Window. Two fields specify the spectral window wavelength
range by defining a center wavelength and a spectral band height.
The Wavelength corresponds to the center wavelength of the spectral window. It can be set to
within 1 nm of the specified detector wavelength range (for example, 201-C379 nm) as long as
the band height setting keeps the spectral window within this range.
The Bandheight is adjusted to set the wavelength range used to generate the chromatogram.
Wider band height can be used to reduce baseline noise, but large band heights can compromise
detector response linearity. The band height value is limited by the acquisition wavelength range.
For example, if Wavelength is set to 205 nm, the Bandheight can be no greater than 10 nm. The
minimal permissible band height setting is 1 nm.

Mode
The Mode region allows you to select between Single beam and Dual beam mode of operation.
In Single beam operation, the detector uses a detector reference signal acquired at the start of
the acquisition for the entire chromatogram. In Dual beam operation, the reference signal is
continuously measured with an independent spectrometer. In both cases the reference signal
uses the center wavelength and band height specified above.
Checking the Realtime baseline correction check box enables real time baseline correction. In
this case a region of the spectrum, typically on the red (high wavelength) end is used to
normalize the rest of the spectrum. This is useful for removing refractive index front which may
occur on injection.
With Realtime baseline correction enabled you fill in a Monitor baseline and Bandheight which
together determine the spectral window used to normalize the rest of the spectrum. Using typical
values of 360 nm for the monitor baseline and 20 nm for the band height would have the effect of
dividing all other wavelengths in the spectrum by the average normalized intensity between 350-
370 nm. This normalization occurs at each time point in the run. Here again the spectral window
defined by the monitor baseline and band height must fit within the specified range of the
detector (200-380 nm).

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7
Creating and Editing 2-D Methods
Two-channel LC devices can be configured to control an automated 2-D system (Nano MDLC).
The Method Editor dialog which you see is dependent on the device configuration.
To create and edit 2-D methods, launch the 2-D Method Editor dialog (Figure 7-1) by clicking the
Method Editor located in the Run Manager. This dialog is used to enter the conditions for
separating the sample.

The Summary Tab

The Summary tab summarizes the steps used to run the method which were entered in the
Methods Step tab.

Figure 7-1 2-D Method Editor Dialog - Summary

Selected 2D Method
The Name field contains the name under which the analysis method is saved. Its menu allows
you to select an existing analysis method for viewing and editing. Change the name and click
Save to create a new method.
Assign an ID number to a method using the ID field.
Save writes all the current values from the Method Editor dialog to a method file using the file
name specified.

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2D Method Summary
The 2-D Method Summary region indicates the total number of steps, total duration of the run,
and the length of each reversed phase second-dimension gradient. These parameters are
entered in the Methods Step tab.

Sample Injection
The Sample Injection region allows you to choose between None, Standard, Metered or Rapid
sample injection modes.
• None indicates that the sample valve will not actuate during the acquisition.
• Standard indicates that the sample valve will switch to the Inject position when the
acquisition begins and switch to the load position when the acquisition ends. As a
result, the sample loop remains in the flow path during the acquisition.
• Metered injection mode offers the flexibility to vary the injection volume. The valve is
switched to the Inject position when the acquisition starts and the specified volume of
sample is metered to the column by the LC pumps at the specified conditions. After
the specified volume is injected, the sample valve switches to the load position so
the sample loop is removed from the flow path during the acquisition.
• Rapid injection mode operates similar to Metered injection mode, but the LC pumps
steadily increase the flow rate during the injection (maintaining the initial mixture
fraction) in order to quickly meter larger sample volume.

Method Steps Tab

The Method Steps tab (Figure 7-2) is used to enter the actual steps for the method. These steps
are used to determine the details of the salt content in the first dimension, the profile of the
second dimension, and the synchronization options.

Figure 7-2 2-D Method Editor Dialog - Method Steps

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Salt Elution
The Salt Elution Method Region determines the detail of the separation in the first dimension.
Initial % salt elution is the percent composition of the B phase to elute the first fraction.
Final % salt elution is the percent composition of the B phase to elute the final fraction.
Number of salt increments is the total number of first dimension steps in the method. For
example, a 2-step method would only have the initial salt elution and the final salt elution.

Reverse Phase Method

The Reverse Phase Method region is used to specify the details of the separation in the second
dimension. You can either select an existing reverse phase method from the menu or edit a
method using Edit Method. Either way each salt elution step will be followed by this method.
Edit Method brings up the LC Method Editor dialog, which provides access to all of the
parameters which describe the second dimension separation. For more information, refer to
Chapter 6.
The Delay starting RP methods until after first salt step completes box should be checked when
using simultaneous synchronization mode to ensure that the RP analysis starts after the first
fraction elutes.

Synchronization
The Synchronization region is used to determine how the two dimensions behave with respect to
one another.
Simultaneous Salt/RP steps is used to indicate that the two channels should run in parallel to
speed up the experiment. This requires that 2 traps or columns are installed in the 10-port valve.
While one salt fraction is eluting from the first trap onto the analytical column, the next salt
fraction will be eluting from the SCX column onto the second trap. When the Simultaneous Salt/
RP steps option is selected, the flow rates and duration for the Salt Elution and De-salt wash
(visible in the Advanced Options dialog) will automatically be adjusted to match the length of the
Reverse Phase method selected.
Alternating Salt/RP steps runs a salt step followed by a reversed phase step. Only one channel
will be active at any moment. When the Alternating Salt/RP steps option is selected, the flow
rates of the Salt Elution and desalt wash will automatically be set to the maximum (20 µL/min) to
allow for the shortest duration. These flow rates can be changed manually in the Advanced
Options dialog, refer to Figure 7-3.
Toggle valve after each step allows you to toggle the second dimension valve after each reverse
phase gradient is complete. This should be checked if two traps are configured on the second
dimension 10-port valve. Once one reverse phase gradient is complete, the valve will switch to
the other trap to start the gradient on the next fraction.
A checked Reset valve will make sure that the valve is returned to its starting load state at the
end of the method.
Export as 1 -D Methods opens a dialog which allows you to export the salt step and reverse
phase gradient methods as a series of 1-dimensional methods.
Advanced Options Presets opens up the Advanced Options dialog, refer to Figure 7-3.

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Advanced Options Dialog

The Advanced Options dialog (Figure 7-3) provides access to a wider variety of parameters for
the salt elution channel and for desalting than does the 2D Method Editor (Figure 7-2). This
includes defining the channel, flow rate, and flow profile.

Figure 7-3 2-D Method Advanced Options Window

Channel Definition
Salt Delivery Channel in the Channel Definition region selects the gradient pump channel (1 or 2)
and pump mobile phase (A or B) that contains the salt solution. The default setting is 1B.

Salt Elution - Manual Control

The Salt Elution - Manual Control region allows the flow rate and duration of each step to be set
manually. After entering the data and clicking OK, the calculated volume will be displayed in the
2D Method Editor dialog (Figure 7-2). This sets the elution volume of each fraction.
The Flow Rate and the Duration determine the Salt Elution Volume in the 2D Method Editor
dialog.
Table Editor brings up a tabular representation of the salt steps shown in the Table Editor Salt
Elution region. This can be used to adjust the composition of each salt step manually. Initially this
is setup automatically in the 2-D Method Editor window by specifying the initial and final
percentages of salt elution and by the number of steps. This initial setup merely divides the
starting and ending salt concentration by the number of steps minus one. Each step is linearly
different in salt than the last. You may change this to an arbitrary profile with this Table Editor.
Changes in either the initial or final salt step will be reflected in the 2-D Method dialog.
Elute with step function and Elute with ramp function determine whether each salt fraction is
delivered as a step or as a gradient. Selecting Elute with ramp function delivers a linear gradient
over the duration indicated.

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De-Salt Wash Manual Control

This region determines the Flow rate, Duration, and Wash mixture salt percentage. After entering
the parameters and clicking OK, the calculated wash volume will be displayed in the De-Salt
Wash Volume in the 2D Method Editor dialog.

Pre/Post Run Options

Setting Wash when idle instructs the instrument to continue washing the first dimension even
when there is nothing running. The conditions for this wash are indicated in the % initial flow rate
conditions box.

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Analysis Method Editor
8
Overview
The analysis module automatically analyzes chromatograms. The centerpiece of this module is
the automatic peak detection algorithm that locates likely peaks and performs peak integration to
extract the peak area and a set of physical peak properties such as retention time, peak height
and width.
The automatic peak detection algorithm is based on the first derivative, which is calculated from
the chromatogram. Following peak detection the algorithm determines the beginning and ending
time for each peak that define the default integration interval. Baselines are constructed that pass
through the absorbance level at the beginning and end of the respective integration interval.
Subsequent peak integration determines the area between the baseline and absorbance values
of each peak.
The analysis module comes with a set of default settings that are adequate for analysis of simple
chromatograms. More complex chromatograms may require more careful treatment of the data,
or special techniques to integrate specific peaks or group of peaks. This is achieved by utilizing a
set of integration timed events. They are provided to optimize peak detection and to customize
peak integration (for more information, refer to Chapter 9). Integration timed events can be added
to a method either graphically in the Acquisition window (for more information, refer to Chapter 2)
or in the Analysis Method window.
In addition to the automatic peak detection algorithm, Quantitation and peak identification may be
performed. Quantitation is the process of calculating concentrations of chemical compounds in
solutions. Quantitation utilizes a calibration table of known compounds and their corresponding
retention times.
The Analysis Method dialog (Figure 8-1) can be opened by selecting Analysis Methods in the
Run Manager dialog or by selecting Settings from the Analysis menu option in the Acquisition
dialog. The window is divided into three tabs: Peak Detection, Quantitation, and Options.

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Analysis Method Editor

Individual methods can be created, edited, and saved using Open, Save, Save As and Exit on
the File menu options.

Figure 8-1 Analysis Method Dialog

Peak Detection Tab

The Peak Detection tab shown in Figure 8-1 contains the integration timed events table. A
typical integration timed event consists of a start and stop time indicating the time interval for
which it applies and a parameter which may specify a threshold value (e.g. Detection Threshold)
or a more specific integration technique (e.g. Tangent for Front or Back Skim). Events may be
added or removed except for the first four rows that contain entries for the Detection Threshold,
the Detection Threshold Asymmetry, the Minimum Peak Height and the Minimum Peak Width.
Parameter values for these events may be adjusted and overwritten by subsequent events of the
same type. However, they are required by the peak detection algorithm during the entire duration
of the chromatogram. The analysis module provides a set of default values for these events that
have proven to work well for simple chromatograms and that may provide a good starting point
for the development of more complex analysis methods. For more information, refer to Chapter
9.

Quantitation Tab
The quantitation tab shown in Figure 8-2 consists of two parts: the calibration table and
calibration curve window. The calibration table contains all the necessary information to

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determine the concentration of unknown chemical compounds as well as sample specific

information.

Figure 8-2 Quantitation Tab

The Insert New Table Entry dialog (Figure 8-3) can be selected by pressing the arrow to the right
of the calibration table. The window can also be opened by or by selecting Insert New Table
Entry from the Advanced menu option in the Analysis Method Dialog.

Figure 8-3 Insert New Table Entry Dialog

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Analysis Method Editor

Options Tab
The Options tab shown in Figure 8-4 contains the settings for peak identification and
Quantitation. The options are divided into three sections:

Figure 8-4 The Options Tab of the Analysis Method Settings Dialog
Response - allows for the selection of the response to be used for solving for unknown
concentrations and generating calibration curves.
Peak Windows - presents the options for peak identification. For more information, refer to Peak
Identification on page 113.
Adding Standards - presents the options for updating the calibration table for automatic
calibration. For more information, refer to Chapter 11.
• New calibrants will replace previous values - allows for one replicate per level, each
new replicate will replace the last replicate.
• New calibrants are appended to previous values - allows for multiple replicates
If the response of the column drifts with time, it is important to perform a rolling average of
replicates by selecting the Average previous replicates check box. Rolling averages will replace
the oldest replicate with the latest replicate to account for any changes in response.
The Average previous number of replicates check box is selected if New calibrants are appended
to previous values is selected. If the check box is not selected, the table will contain all replicates.

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Peak Results
Analyzing a chromatogram leads to a set of results for each identified peak. The results include
qualitative and quantitative properties that characterize the peak location and shape, the column
performance and the amount of substance that created the peak. Peak results are displayed in
the peak table in the Acquisition dialog, refer to Chapter 2.
The table columns can be customized using the Choose Peak Table Columns options on the
Analysis menu. The items that can be selected are indicated in Table 8-1.
The following results are available for display:
Table 8-1 Peak Results
Peak Type Description
Peak Name The name of the peak as entered in the peak table.
Peak Number The peak number is assigned in ascending order according to the
retention time.
Retention Time (min) Position of the maximum peak absorbance, determined from a
quadratic curve fitted to peak data points around the absolute
maximum.
Peak Height (mAu) The maximum absorbance of a peak, determined from baseline-
corrected absorbance values.
Percent of Total Height Percentage from the sum of all peak heights.
(%)
Area (mAu.s) The area between the baseline and the absorbance data from the
begin to the end of the peak.
Percent of Total Area Percentage from the sum of all areas.
(%)
Base Width (sec) The area between the baseline and the absorbance data from the
beginning to the end of the peak.
Width at 5% Peak width determined at 5 percent of the peak height.
Width at 10% Peak width determined at 10 percent of the peak height.
Width at 50% Peak width determined at 50 percent of the peak height.
Asymmetry at 50% The ratio of front to back width at 50 percent of the peak height.
Asymmetry at 10% The ratio of front to back width at 10 percent of the peak height.
Asymmetry at 5% The ratio of front to back width at 5 percent of the peak height.
Tailing Factor Ratio of total width to twice the front width at 5 percent of the peak
height.
Number of Plates (N) Number of theoretical plates based on different methods* [USP, DAB,
JP, EMG].
Number of Plates per Number of theoretical plates per meter based on different methods*
meter (N/m) [USP, DAB, JP, EMG].
Resolution Resolution between the peak of interest and the peak preceding it
based on different methods* [USP, DAB, JP, EMG].
Signal to Noise Signal to Noise Ratio.

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Table 8-1 Peak Results (Continued)

Peak Type Description
Capacity Factor Ratio of time spent by substance in stationary phase to time spent by
substance in mobile phase.
Relative Retention Relative retention measured with respect to an unretained compound.

*The available calculation methods are United States Pharmacopoeia (USP), German Pharmaco-
poeia (DAB), Japanese Pharmacopoeia (JP) and the method based on the Exponential Modified
Gaussian (EMG) model.

The Capacity Factor

The capacity factor of a peak with retention time is calculated according to the formula in
Figure 8-5 where item 1 in Figure 8-5 is the retention time of an unretained or reference peak.

Figure 8-5 Capacity factor

The relative retention is calculated using the formula in Figure 8-6.

Figure 8-6 Relative retention formula

Reference peaks are defined by the corresponding integration timed event, refer to Chapter 9.

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Peak Asymmetry
Asymmetric peak shapes are characterized by different values for the front half width f and back,
or tail, half width b. As a quantitative measure of the peak asymmetry, the analysis module
provides values for the Asymmetry A
A=b/f
at 5, 10 and 50 percent of the peak height, and the Tailing Factor T which is calculated at 5
percent of the peak height:
T= (b+f)/2f

Figure 8-7 Asymmetric Peak with Front Width (f) and Back Width (b) indicated at 5, 10
and 50% of the Peak Height

Calculation Methods
The peak results include column performance parameters based on four different calculation
methods.

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Analysis Method Editor

United States Pharmacopoeia (USP) Calculation Method

Number of Plates N:

t = Retention time of peak

W = Base width determined by tangent method (Figure 8-8)

Figure 8-8 Tangent Method: The Base Width is Determined by the Intersection of the two
Tangents at the Inflection Points with the Peak Baseline
Resolution(R) between a peak of interest (peak 2) and the peak preceding it (peak 1):

Where:
t1,2 =Retention time of peak 1 and peak 2
W1,2 = Base width of peak 1 and 2 determined by tangent method

German Pharmacopoeia (DAB) Calculation Method

Number of Plates N:

t = Retention time of peak

W50% = Width of peak at 50% peak height
Resolution R between a peak of interest (peak 2) and the peak preceding it (peak 1):

Where:
t1,2 = Retention time of peak 1 (2)
W1(2), 50 = Width of peak 1(2) at 50% peak height

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Japanese Pharmacopoeia (JP) Calculation Method

Number of Plates N:

t = Retention time of peak

W50% = Width of peak at 50% peak height
Resolution R between a peak of interest (peak 2) and the peak preceding it (peak 1):

Where:
t1 ,2= Retention time of peak 1 and peak 2
W1 ,2 = Width of peak 1 and 2 at 50% peak height

Exponential Modified Gaussian (EMG) Calculation Method

Number of Plates N:

Where:
t = Retention time of peak
W10% = Width at 10% peak height
f10% = Front width of peak at 10% peak height
b10% = Back width of peak at 10% peak height
Resolution R between a peak of interest (peak 2) and the peak preceding it (peak 1):

With:
t1,2 = Retention time of peak 1 and 2
W1 ,2= Width of peak 1 and 2 at 10% peak height

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Integration Time Events
9
Overview
Analyzing a chromatogram is controlled by integration timed events. These events are provided
to improve peak detection and to customize integration of particular peaks or groups of peaks.
Integration timed events fall in two categories:
Peak Detection events control the peak location algorithm and determine if a feature in a
chromatogram should be reported as a peak. These include:
• Detection Threshold
• Detection Threshold Asymmetry
• Shoulder Detection
• Minimum Peak Width
• Minimum Peak Height
• Minimum Area
• Integration Off
• Negative Peaks
Peak Integration events control the peak integration by manipulating the baseline and the
analysis of fused peaks. These include:
• Valley To Valley
• Front/Back Skim
• Manual Baseline
• Forward/Backward Horizontal Baseline
• Lowest Point Horizontal Baseline
• Reset Baseline
• Reset Baseline At Valley
• Force Peak Start/Stop
• Split/Merge Peak
• Force Result
• Manual Peak
• Reference Peak

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Peak Detection

Detection Threshold
The Detection Threshold is applied to identify and locate peaks in a chromatogram. A non-zero
value is required by the software for the duration of the chromatogram. The threshold value is
specified as a percentage with respect to the highest value of the first derivative computed for the
entire chromatogram. A high value will suppress the detection of very slowly rising features and
small peaks while a low value will increase the number of small peaks that will be reported. The
default threshold value is 1%.
Table 9-1 Event Parameters
Event
Parameters
Start Time: Start using the specified value for the detection threshold
Stop Time: Stop using the specified value for the detection threshold
Parameter: Detection threshold

Detection Threshold Asymmetry

Most chromatographic peaks exhibit asymmetric shapes, characterized by slower falling tails.
This phenomenon is taken into account by the peak detection algorithm via the Detection
Threshold Asymmetry which relaxes the detection threshold in the tail region of a potential peak.
The threshold value is specified as a percentage indicating which fraction of the Detection
Threshold is applied to detect the back of a peak. A non-zero value is required by the software for
the entire duration of the chromatogram. The default threshold value is 20%.
Table 9-2 Event Parameters
Event
Parameters
Start Time: Start using the specified value for the detection threshold asymmetry
Stop Time: Stop using the specified value for the detection threshold asymmetry
Parameter: Detection threshold asymmetry

Minimum Peak Width

The Minimum Peak Width event sets a lower limit for the smallest width of a feature that will be
reported as a true peak by the detection algorithm. A positive value is required by the software for
the entire duration of the chromatogram. The width is specified in seconds, the default value is
one second.
Table 9-3 Event Parameters
Event
Parameters
Start Time: Start using the specified value for the minimum peak width
Stop Time: Stop using the specified value for the minimum peak width

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Table 9-3 Event Parameters (Continued)

Event
Parameters
Parameter: Minimum peak width

Minimum Peak Height

The Minimum Peak Height event sets a lower limit for the smallest peak height above baseline.
Features in the chromatogram with heights below this limit will not be reported as peaks. The
height is specified in units of mAU, the default value is zero.
Table 9-4 Event Parameters
Event
Parameters
Start Time: Start using the specified value for the minimum peak height
Stop Time: Stop using the specified value for the minimum peak height
Parameter: Minimum peak height

Minimum Area
The Minimum Area event sets a lower limit for the area that defines a peak. Features in a
chromatogram that lead to areas below this limit will not be reported as peaks. A positive value is
required by the software. The area is specified in units of mAU, the default value is zero.
Table 9-5 Event Parameters
Event
Parameters
Start Time: Start using the specified value for the minimum peak area
Stop Time: Stop using the specified value for the minimum peak area
Parameter: Minimum peak area

Shoulder Detection
Shoulders occur when two peaks are so close that no valley is formed in-between (for example,
Figure 9-1). The Shoulder Detection event enables the detection of shoulders attached to larger
peaks in a chromatogram. The shoulder detection algorithm is based on the second derivative.
The parameter indicates the sensitivity of the algorithm and is specified as a percentage with
respect to the highest value of the second derivative calculated for the entire chromatogram. A
higher value will decrease shoulder sensitivity, while lower values increase the sensitivity to
shoulder peaks. A zero value indicates that shoulder detection is turned off. Shoulder detection
will change peak boundaries and the integrated areas of parent peaks.
Table 9-6 Event Parameters
Event
Parameters
Start Time: Start using shoulder detection

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Table 9-6 Event Parameters (Continued)

Event
Parameters
Stop Time: Stop using shoulder detection
Parameter: Shoulder detection sensitivity

Figure 9-1 Fused Peaks without Shoulder Detection

Figure 9-2 Fused Peaks with Shoulder Detection Enabled

Integration Off
Integration Off disables peak detection and peak integration during the specified time interval.
Table 9-7 Event Parameters
Event
Parameters
Start Time: Start disabling peak detection and integration
Stop Time: Stop disabling peak detection and integration

Negative Peaks
The Negative Peaks event can be applied to integrate portions of the chromatogram that are
below the baseline (for example, Figure 9-3). As a consequence, features that appear as deep
valleys are reported as true peaks.

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 Integration Time Events

Table 9-8 Event Parameters

Event
Parameters
Start Time: Start detection of negative peaks
Stop Time: Stop detection of negative peaks

Figure 9-3 Default Baseline without Negative Peaks Enabled

Figure 9-4 Baseline with Negative Peaks Enabled between 5.5 and 8 Minutes

Valley To Valley
The Valley To Valley event is applied to groups of fused peaks. By default, a common baseline is
drawn for all fused peaks, with each peak separated by a vertical drop line. During a Valley To
Valley event the baseline is constructed by connecting the valleys in-between individual peaks.
Table 9-9 Event Parameters
Event
Parameters
Start Time: Start using valley to valley
Stop Time: Stop using valley to valley

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Integration Time Events

Figure 9-5 Default Baseline for a Series of Fused Peaks

Figure 9-6 Baseline after Valley To Valley Event

Front Skim
The Front Skim event is applied to resolve one or several small child peaks or shoulder peaks
attached to the front of a larger parent peak. To construct the baseline of the child peak, three
options are available:
• Tangent skim leads to a straight baseline for the child peak(s)
• Gaussian skim leads to a Gaussian curve for the baseline of the child peak(s)
• Exponential skim leads to an exponential curve for the baseline of the child peak(s)
Table 9-10 Event Parameters
Event
Parameters
Start Time: Start of the first child peak
Stop Time: Stop of the parent peak
Parameter: Tangent, Gaussian or Exponential

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Figure 9-7 Default Integration of Fused Peaks using Vertical Drop Lines

Figure 9-8 Front Skim Event with Tangent Option

Figure 9-9 Front Skim Event with Exponential Baseline

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Integration Time Events

Figure 9-10 Front Skim Event with Gaussian Baseline

Back Skim
The Back Skim event is applied to resolve one or several small child peaks or shoulder peaks
attached to the back of a larger parent peak. To construct the baseline of the child peak three
options are available:
• Tangent skim leads to a straight baseline for the child peak(s)
• Gaussian skim leads to a Gaussian curve for the baseline of the child peak(s)
• Exponential skim leads to an exponential curve for the baseline of the child peak(s)
Table 9-11 Event Parameters
Event
Parameters
Start Time: Start of the parent peak
Stop Time: Stop of the last child peak
Parameter: Tangent, Gaussian or Exponential

Manual Baseline
The Manual Baseline event is applied to change a baseline of a peak without changing the
integration parameters. By default a baseline is constructed based on the peak boundaries as
they arise for a single isolated peak or in a group of fused peaks. A manual baseline is drawn
without changing the baseline of other peaks in the chromatogram. It is constructed by
connecting the data point at the specified start time with the data point at the specified stop time.
If the specified start time of the manual baseline is earlier than the start of the original baseline
the original start time is maintained. Similarly, if the specified stop time of the manual baseline is
later than the original baseline stop the original stop time is maintained.
Table 9-12 Event Parameters
Event
Parameters
Start Time: Start of manual baseline
Stop Time: Stop of manual baseline

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Figure 9-11 Default Baseline

Figure 9-12 Manual Baseline between 4.65 and 5.3 Minutes

Forward Horizontal Baseline

The Forward Horizontal Baseline event forces a horizontal baseline in forward direction. The
base line is constructed by drawing a horizontal line from the data point which corresponds to the
start of the original baseline to the specified stop time. If the specified stop time is later than the
original baseline stop, the original stop time is maintained.
Table 9-13 Event Parameters
Event
Parameters
Start Time: Start of forward horizontal baseline
Stop Time: Stop of forward horizontal baseline

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Integration Time Events

Figure 9-13 Default Baseline

Figure 9-14 Forward Horizontal Baseline Event between 4.5 and 7.2 Minutes

Backward Horizontal Baseline

The Backward Horizontal Baseline event forces a horizontal baseline in backward direction. The
baseline is constructed by drawing a horizontal line starting at the data point which corresponds
to the stop of the original baseline to the specified start time. If the specified start time is earlier
than the start of the original baseline, the original start time is maintained.
Table 9-14 Event Parameters
Event
Parameters
Start Time: Start of backward horizontal baseline
Stop Time: Stop of backward horizontal baseline

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Figure 9-15 Default Baseline

Figure 9-16 Baseline after Backward Horizontal Baseline Event between 4.3 and 5.75
Minutes

Lowest Point Horizontal Baseline

The Lowest Point Horizontal Baseline event creates a horizontal baseline that intersects with the
absorbance minimum between the start and stop time of the event. The start and stop time of the
original baseline is maintained.
Table 9-15 Event Parameters
Event
Parameters
Start Time: Start of lowest point horizontal baseline
Stop Time: Stop of lowest point horizontal baseline

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Figure 9-17 Default Baseline

Figure 9-18 Baseline after Lowest Point Horizontal Baseline Event between 3.9 and 9.5
Minutes

Reset Baseline
The Reset Baseline event resets the baseline at the data point which corresponds to the
specified start time of the event.
Table 9-16 Event Parameters
Event
Parameters
Start Time: Start of reset baseline

Figure 9-19 Default Baseline

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Figure 9-20 Rest Baseline Event at 8.63 Minutes

Reset Baseline at Valley

The Reset Baseline at Valley event generates a baseline reset at the next valley detected after
the specified start time.
Table 9-17 Event Parameters
Event
Parameters
Start Time: Start of reset baseline at valley

Figure 9-21 Default Baseline

Figure 9-22 Baseline after Reset Baseline at Valley Event

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Force Peak Start

The Force Peak Start event is applied to force the start of the baseline at the specified start time.
If the start of the event is earlier than the start of the original baseline the event has no effect.
Table 9-18 Event Parameters
Event
Parameters
Start Time: Start of peak

Figure 9-23 Default Baseline

Figure 9-24 Baseline after Force Peak Start Event at 8.75 Minutes

Force Peak Stop

The Force Peak Stop event is applied to force the stop of the baseline at the specified stop time.
If the stop of the event is later than the stop of the original baseline, the event has no effect.
Table 9-19 Event Parameters
Event
Parameters
Start Time: Stop of peak

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Figure 9-25 Baseline for Peak in Figure 9-23 after Force Peak Stop Event at 9 Minutes

Split Peak
The Split Peak event divides a peak by inserting a perpendicular drop-line at the specified start
time of the event. The feature to the left and right of the drop line are reported as two separated
peaks. If the start time is not within the peak boundaries of a detected peak, the event is ignored.
Table 9-20 Event Parameters
Event
Parameters
Start Time: Indicate when to split a peak

Figure 9-26 Split Peak Event at 5 Minutes

Merge Peak
The Merge Peak event reports the series of peaks between the start and stop of the event as one
peak. The retention time of the merged peaks is determined by the highest peak in the series. If
only one peak is detected between the start and stop time the event is ignored.
Table 9-21 Event Parameters
Event
Parameters
Start Time: Start of merge peak
Stop Time: Start of merge peak

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Figure 9-27 Default Baseline

Figure 9-28 Baseline of Merged Peaks

Force Result
The Force Result event reports results for a peak in the specified time interval even if no peak
was detected. The event is useful to monitor peaks that are expected to emerge within a certain
time interval during a series of runs.
Table 9-22 Event Parameters
Event
Parameters
Start Time: Start of Force Result
Stop Time: Stop of Force Result

Manual Peak
The Manual Peak event defines a feature in a chromatogram as a peak that was previously not
detected. The event is convenient to force integration without changing other integration
parameters for a specific region of the chromatogram.
Table 9-23 Event Parameters
Event
Parameters
Start Time: Start of the manual peak

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Table 9-23 Event Parameters (Continued)

Event
Parameters
Stop Time: Stop of the manual peak

Figure 9-29 Default Baseline

Figure 9-30 Manual Peak Event between 9 and 17 Minutes

Reference Peak
The Reference Peak event defines the peak which is used to calculate the capacity factor and
relative retention. If no peak is detected in the time window defined by the start and stop of the
event, the capacity factor and the relative retention is set to zero. If more than one peak is
detected the retention time of the first peak is employed in the calculation. Only one Reference
Peak event can be entered into the integration timed event table.
Table 9-24 Event Parameters
Event
Parameters
Start Time: Start of the reference peak time window
Stop Time: Stop of the reference peak time window

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Incompatible Events
The analysis module restricts the simultaneous use of certain timed integration event
combinations. It is not possible to enter an event to the integration timed event table if conflicts
arise with existing events. Conflicts are determined by checking for overlap between two events
or in case of an event with only a start or stop time if it is contained within a time interval defined
by another event.

Note: If an event is listed as conflicting with itself it cannot be applied a second time
within the range for which it already exists.

Note: If an event which is listed as not conflicting with itself is entered multiple times,
the parameter (e.g. detection threshold) which was entered last is applied during the
overlapping time intervals.

Table 9-25 Incompatible events

Event Incompatible Event
Shoulder Detection Detection Negative Peaks
Integration Off Force Result
Negative Peaks Shoulder Detection
Negative Peaks
Valley To Valley
Front Skim
Back Skim
Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Manual Peak
Manual Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Force Peak Start
Force Peak Stop

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Table 9-25 Incompatible events (Continued)

Event Incompatible Event
Forward Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Backward Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Lowest Point Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak

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Table 9-25 Incompatible events (Continued)

Event Incompatible Event
Reset Baseline Manual Baseline
Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Reset Baseline At Manual Baseline
Valley Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Back Skim Back Skim
Front Skim
Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Manual Peak
Front SkimBack Skim
Front Skim
Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Manual Peak

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Table 9-25 Incompatible events (Continued)

Event Incompatible Event
Valley To Valley Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Manual Peak
Merge Peaks Manual Peak
Split Peak Manual Peak
Force Peak Start Manual Baseline
Manual Peak
Force Peak Stop Manual Baseline
Manual Peak
Force Result Integration Off
Manual Peak

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Quantitation
10
Introduction
Quantitation is the process of calculating the concentration of chemical compounds in samples
from the peak areas or peak heights. Quantitation requires peak identification and calibration.
Peak Identification - Indicating the presence of a compound on the basis of its retention time.
Calibration - A method that determines the relationship between the amount of a compound and
its measured response.
The Quantitation module allows users to calculate the amount of an unknown component from
the measured peak height or area. The type of calculation performed depends on the type of
standard. Two types of standards are available: External Standard (ESTD) and Internal Standard
(ISTD).

Peak Identification
Peak Identification is an integral part of quantitation. A peak cannot be quantified unless it is
identified. The identification must have the following information in the calibration table:
Name and Retention Time - The user must supply a name for each retention time in the
calibration table for identification.
Retention Time Window – The time window accounts for the variability or retention times by
providing an upper and lower bound for the search. Two types are available to the user.
• Absolute - The upper and lower bounds are user defined.
• Relative – The window is calculated by a percentage:

Peak Identification Rules - More than one peak can be located within the defined time window.
The identified peak is chosen from one of five possible rules:
Rule 1 - First Peak - the First Peak matching the criteria is found, refer to Figure 10-1.

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Figure 10-1 The First Peak is Found

rule 2 - Nearest - Finds peak located closest to center of window, refer to Figure 10-2.

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Figure 10-2 The Center Peak is Chosen

Rule 3 - Height - The peak with the largest height is found, refer to Figure 10-3.

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Figure 10-3 The Largest Peak is Found

Rule 4 - Last - The last peak is found, refer to Figure 10-4.

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Figure 10-4 The Third Peak is Found (the Last Peak in the Window)
Rule 5 - Best Match - finds the peak with most similar area relative to the indicated specification
in the calibration table.

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Figure 10-5 The Middle Peak is Chosen because its Area is closest to 1100 mA2 (the peak
area in the calibration table was 1100 mA2)

Calibration
Calibration is based on the principle that a relationship exists between the amount of a chemical
compound and its measured detector response. The relationship (calibration curve) can be linear
or nonlinear and the calibration curves are stored in the calibration table.

Terms and Definitions

Response Factor - ratio of the amount to response

Amount Ratio - ratio of the ESTD amount to ISTD amount

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Response Ratio - ratio of ESTD response to ISTD response

Multiplication Factor - a correction factor that is used to convert units (for example, conversion
factor for grams to kilograms is 1000)
Dilution Factor - a correction factor that accounts for serial dilution

Types of Calibration
A calibration curve is characterized by the number of levels (for example, different amounts of
analyte in each sample). Each level can be comprised of one or more replicates. The calibration
curve is generated from the averaging the replicate amounts and response for each level.
• Single Level Calibration - a calibration that uses a single point. It assumes the
response is linear throughout the entire concentration range and the curve passes
through the origin. For an example of a single level calibration, refer to Figure 10-6.

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Figure 10-6 Single Level Calibration Curve

• Multi-Level Calibration - a calibration that uses more than one calibrant. For an
example of a multi-level calibration, refer to Figure 10-7.

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Figure 10-7 Multi-Level Calibration

Types of Fits

Linear Fit
A linear response follows the Beer-Lambert Law. The response of a chemical compound is
directly proportional to the amount of that compound. The following equation is used:
aX + b = Y
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
A = slope
b = Y-intercept

Nonlinear Fits
If the response is nonlinear, the Quantitation module provides two polynomial fits: quadratic and
cubic.

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Quadratic Fit
Quadratic - minimum of three calibration levels
Y = aX2 + bX + c
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
a = coefficient 1
b = coefficient 2
c = Y-intercept

Cubic Fit
Cubic - minimum of four calibration levels
Y = aX3 + bX2 + cX + d
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
a = coefficient 1
b = coefficient 2
c = coefficient 3
d = Y-intercept

Calibration Range
For Quantitation with nonlinear fits, the Quantitation routine module will provide concentrations
for unknowns that are bound by the lower/upper limits of the amounts for calibration curves.

Note: Ideally, the equation generated should include the origin (for example, the Y-
intercept = 0, detector has zero response when the compound is not present). The user
has the option to force the fit through zero.

Correlation Coefficient
The correlation coefficient measures how well a polynomial fit matches the data. As the
coefficient approaches one, the curve is a better representation of the data.
0 ==> No fit
1 ==> Perfect fit

Weighting Factor
A weighting can be applied to each point in a calibration curve. The choice of weighting factor
determines the importance of a data point within a given data range. For instance, a weight of 1/
Amount places more emphasis on points with a smaller amount.

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Table 10-1 Weighting Factors

Weight Description
None equal weights for all points
1/X² 1/amount²
1/X 1/amount
X amount
X² amount²
1/Y 1/Response
Y Response
Y² Response²

Scaling Factors
The Quantitation module includes the ability to scale the X-axis of the calibration curves. For a
list of available scale factors, refer to Table 10-2.
Table 10-2 Scale Factors
Scale Factor
None
1/Amount
ln(Amount)
1/ln(Amount)
Sqrt(Amount)
Amount²
1/ResponseFactor
1/ResponseFactor²
ln(ResponseFactor)
1/ln(ResponseFactor)
Sqrt(ResponseFactor)
ResponseFactor²
Log(Amount)
1/Log(Amount)
Log(ResponseFactor)
1/Log(ResponseFactor)

Calibration Table
The calibration table contains all of the necessary information to perform Quantitation. The
following information is required to create the table:
• The retention time for each named peak
• Amounts for each peak

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• Response for each peak

Each row of the table corresponds to a given compound. For a description of each column, refer
to Table 10-3.

Note: The user can bypass calibration and perform peak identification by supplying the
retention time for a named peak.

Table 10-3 Calibration Table Columns

Column Description
Peak Name Name of the peak.
RT Retention Time of Peak
Width Width of identification window. Visible only if absolute windows are used.
Amount Amount for a level.
Area Area of the peak.
Height Height of the peak.
Multiplication Factor Factor used to convert the units of the amount.
Dilution Factor Factor used for serial dilution.
Used Determines if the point is used in the curve fit.
ISTD Check box denoting if the compound is an ISTD
Associated ISTD Name of the ISTD associated with ESTD - blank if the peak is an ISTD
ISTD Amount Amount of the Associated ISTD - blank if the peak is an ISTD
ISTD Area Area of the Associated ISTD - blank if the peak is an ISTD
Response Accuracy The ratio of calculated response and measured response multiplied by
100.
ISTD Ratio
Sample Name Name of the sample.
Sample ID ID of the sample.
Date Date the sample was acquired.
User Name Name of the user.
Filename Name and location of the file.

External Standard Calculation

For ESTD calculations, the calibration curve is generated by examining a single analyte from a
solution or serial dilution. The calibration standards and unknown are analyzed under the same
conditions. Because the response is sensitive to changes in concentration, care must be taken to
ensure that the injection volume cannot vary.
The amount is calculated by solving the equation from its calibration curve using the response of
the unknown. Figure 10-8 shows a single-level calibration using the height as the response.

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Figure 10-8 The Calibration Curve for a Linear Response (Height)

The equation for curve and the response of the unknown is required for calculation.
If an unknown sample has a peak area of 19.5 units, the amount would be calculated as follows:
For a linear response,

Where:
a is the slope with units of Response/Amount.
The example equation is

Rearranging and solving for the unknown gives

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Internal Standard Calculation

An ISTD sample is prepared by adding a standard to the solution. The internal standard and the
analyte should have similar chemical properties and retention time. An ISTD calculation
eliminates the error from differing injection volumes because the ratio of the responses is used.
An ideal ISTD calculation uses the same amount of internal standard for each level of a multi-
level calibration. The Quantitation module allows the user to use different internal amounts for
each level if needed. Figure 10-9 shows the calibration curve for a multi-level ISTD calibration
using the peak area as the response.

Figure 10-9 Multi-Level ISTD Calibration Curve

The equation of the calibration curve, the amount of internal standard in the unknown sample,
and response ratio are necessary for the calculation.

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For a linear response ratio,

Where:
a is the ratio:

b is the y – intercept.
Rearranging the equation leads to:

And multiplying by the amount of internal standard

Automated Calibration Table Generation through

the Run Manager

Overview
The Run Manager allows the user to automatically update calibration tables. Three pieces of
information are required for automation: an analysis method file, the standard amounts (ESTD/
ISTD), and the type of sample. Figure 10-10 shows the run table for generating an automated
two level ISTD calibration.

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Figure 10-10Run Table to Generate a Two Level ISTD Calibration Table

Automatic Quantitation allows for a maximum of five calibration standards. The amounts should
be listed in order of retention time, where Amount 1 has the shortest retention time and amount 5
has the longest retention time. There are two types of samples: standard and unknown.
• If unknown is selected, the analysis will calculate the unknown amount from the
calibration table of the chosen analysis method file. For internal standard
calculations, the internal standard concentration must be entered into the calibration
table.
• If standard is chosen, the calibration table will be updated according to the analysis
method file. It is important the user note the following:
• The analysis method file will be updated with each run; the calibration table
generated for run 4 will contain data from run 2, but the calibration table for run
2 will not contain any data from run 4.
• Each sample file generated will contain a copy of the calibration table
generated for that run. Hence, the only file with the complete calibration table
is the analysis method file.
The analysis method contains information about how the calibration table will be generated. The
adding standards frame contained in the options tab of the Analysis Method Settings dialog
(Figure 10-10) allows the user to choose how the standards will be added to the table.

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User Manager
11
Overview
Eksigent® instrument software comes equipped with system administration functions that enable
a system administrator to configure user and group privileges to maximize security and efficiency
of the system. A Windows network or local administrator can use the User Manager to assign
user and group privileges to various features within the software. Proper user configuration
effectively turns the software into a closed system where user authentication is required. In this
environment, user actions can be clearly defined and carefully monitored.

User Authentication
By default, the user authentication features are disabled when the software is first installed. This
is an open system configuration where every user who has access to the computer will have full
access to the software.
The first step to using user authentication is to enable it. Once user authentication has been
enabled, all users will be required to logon in order to access the software.
The software automatically queries both the domain controller and the local computer for a list of
available users. These user accounts are defined on the primary domain controller or on the local
computer, but the privileges that these users will have is defined on the software. Any Windows
user can access the software using the same accounts, assuming the right privileges have been
granted to the user.
To enable user authentication, access User Authentication on the System menu. If this feature
is accessed for the first time, or if you are positive that User Authentication is disabled, a user
logon prompt will appear. Before you can start the user authentication functions, you must
establish your role as a system administrator or a user with the User Administration right, for
more information, refer to Configure the User Manager on page 130.

Figure 11-1 User Logon Dialog

You will then need to supply credentials to establish that you have Windows administration
privileges on the local computer.
Select Log on, and type in your administrator username followed by your password.

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If a valid system administrator username and password combination is supplied for the domain/
computer, the User Authentication dialog opens, refer to Figure 11-2.

Figure 11-2 User Authentication Window for Administrators

Select the Require User Authentication check box and click OK to start user authentication.
Restart the software to make the user authentication active.
To cancel logon at any time, click Cancel on the User Logon dialog.
If User Authentication is selected the User Logon dialog will appear when anyone starts the
software. To successfully logon, enter your user name and password.
If the user is a system administrator, or if the user has Start/Exit software rights, the software will
start as usual. If not, a warning dialog opens, refer to Figure 11-3:

Figure 11-3 User does not have Software Start/Exit Rights

Configure the User Manager

User Manager Dialog

The User Manager dialog (Figure 11-4) is where the system administrator controls and maintains
user actions. The specific system functions that are controlled by the User Manager include:
• Adding and removing Windows users and groups to the software
• Granting system privileges to Windows users and groups
• Define electronic signature roles
• Define electronic signature reasons
To start the User Manager from the main acquisition window, select User Manager from the
System menu. The action that occurs is dependent on whether User Authentication has been
enabled and the privileges you have when you log on.
• If User Authentication has been enabled, and you are logged on as a system
administrator or a user with User Administration privileges on software startup, you
will be able to launch the User Manager.

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• If User Authentication has been enabled, and you are not logged on as a system
administrator or a user with User Administration privileges on software startup, this
feature will be grayed-out on the main menu.
• If User Authentication is not enabled, you will be asked to establish system
administration credentials before you can access the User Manager dialog. In this
case, the User Logon window opens, refer to Figure 11-1.

Figure 11-4 User Manager Window

Add and Remove Users and Groups

The list of users and groups that have been permitted to use the application program appears in
the Current Members region of the User Manager dialog.
The User Manager dialog supports both local users and network users and groups. To view the
local users that are permitted to use the application program, select the computer name in the
Show members for the menu. The list of added users will appear in the Current Members for
<computer name> region. Similarly, to view the network users and groups that are added, select
the domain name in the menu. The list of added network users and groups will then appear in the
same area. If you do not see any users appear in either scenario, it means no users have been
added. A single-head icon represents a user, and a double-head icon represents a group. If you
are not using a network domain, the only available item in the Show members for the menu will
be the computer name. In this environment, only local users can be added to the software.

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User Manager

To add and remove local or network users, make sure that the respective computer or domain is
being displayed in the User Manager, and click Add/Remove to open the Add Members dialog,
refer to Figure 11-5.

Figure 11-5 Add Members Dialog

The Available Members region on the left shows all available users or groups that exist on the
domain/computer who have not been added to use the software. The Added Members region on
the right shows all users or groups that have already been added. To add a member, select the
member to be added and click the right arrow. This member will then appear in the Added
Members region. Likewise to remove a member, select the member to remove in the Added
Members region and click the left arrow. This member name will then go back in the Available
Members region. When you are satisfied with the membership arrangement, click OK to confirm
the changes and return to the User Manager dialog. The members displayed will be the same as
those that you specified in the Added Members pane.
Click Cancel at any time in the Add Members dialog to exit without making any changes.

Manage Electronic Signature Roles

Electronic signature roles can be assigned to each user who has been added to the software.
The names of the roles will appear in the Electronic Signature Roles region in the User Manage
dialog, refer to Figure 11-4. By default, five levels of electronic signature roles are used, and the
names of the roles are predefined for each level in the software. The roles are arranged so that
the role with the highest level of authority is placed at the top, and the role with the lowest level of
authority is placed at the bottom.

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To change the number of levels used and/or the names of the roles, click Modify in the Electronic
Signature Roles region. This will display the Electronic Signature Roles dialog, refer to Figure 11-
6.

Figure 11-6 Electronic Signature Roles Dialog

To change the name of any of the roles, type the new role name into the text box for that role.
To change the number of active roles, choose a number between 1 and 5 in the Number of
Levels menu. When reducing the number of roles, the highest signatures roles will be de-
activated first.
For example, choosing 3, will gray out the top two levels of electronic roles indicating that these
two roles are not active, and only the bottom three roles can be assigned to your users. In this
case, if any users had previously been assigned to Operations Manager or QA Manager, their
role will now default to Lab Manager, the highest role available at this point.
Click OK to confirm your modifications, or click Cancel to exit the Electronic Signature Roles
dialog without making the changes.

Manage Electronic Signature Reasons

The electronic signature reasons are defined in the Electronic Signature Reasons region of the
User Manager dialog, refer to Figure 11-4. By default, five electronic signature reasons are pre-
defined when the software is first installed. You can add, modify, or delete any electronic
signature reason at any time.
To add a new electronic signature reason, click Add in the Electronic Signature Reasons region
of the User Manager dialog to present the Adding Electronic Signature Reasons, refer to
Figure 11-7.

Figure 11-7 Add Electronic Signature Reasons

Type a new reason into the text box and click OK. This new reason will then appear in the
Electronic Signature Reasons region. To cancel adding the reason, click Cancel.
To modify an existing reason, select the reason to be modified in the Electronic Signature
Reasons region and click Edit. The Adding Electronic Signature dialog will open, refer to
Figure 11-7.

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User Manager

The reason selected will appear with this dialog. Edit the reason, and click OK to confirm the
changes. Click Cancel to exit without making any changes.
To delete an existing reason, select the reason to be deleted in the Electronic Signature Reasons
region and click Delete. Click Yes to proceed with deleting the reason, or No to cancel.

Managing User Permissions

Once a user or group has been added to the software, the system administrator can assign the
proper system privileges to this user or group. To do so, select the user name and click
Permissions in the User Manager, or double-click on the user name.
The system administrator will always have full access to the software, and therefore their
permissions do not need to be set. For any other user, the General tab of the Member
Permissions dialog opens, refer to Figure 11-8.

Figure 11-8 Member Permissions Window - General Tab

The Member Permissions dialog includes five tabs: General, Run Manager, Data, Diagnostics,
and Other. Each tab contains permission settings that regulate user actions in the portion of the
software specified in the tab title. When managing these user permissions, please keep in mind
that User permissions only take effect when User Authentication is enabled. When User
Authentication is disabled, all users will have full access to every feature of the software and
assigning user per-missions in this environment has no effect. All system administrators will
always have full access to the software, regardless of the permissions granted.

General Tab
The General tab of the Member Permissions dialog contains several permissions that deal with
general usage of the software. By default, all members automatically have permission to the
Start/Exit Software when they are added to the system while all other permissions under the
General tab are not granted. To give a member a particular permission under this tab, check the
check box of that right.
Start/Exit Software grants a user the right to log in to the software when it is launched. A user can
also exit the software in the main program under File, Exit. A user cannot log in to the software
without this right.

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The UV Detector Toolbox right allows a user to launch the UV Detector Toolbox from the menu
option View > UV Detector Toolbox in the Acquisition dialog (this menu option is grayed-out if a
user does not have this right). For more information, refer to UV Detector Toolbox on page 23.
The Peak Park Toolbox right allows a user to launch the PeakPark Toolbox from the menu option
View > PeakPark Toolbox in the Acquisition window (this menu option is grayed-out if a user
does not have this right). For more information, refer to Peak Park Toolbox on page 22.
The System Logs right allows a user to view any of the available system logs from the menu
option
View > System Logs in the Acquisition dialog (this menu option is grayed-out if a user does not
have this right). For more information, refer to System Logs on page 25.
The Analysis Settings right allows a user to access the Analysis Settings dialog from the menu
option Analysis > Settings in the Acquisition window and Analysis Methods in the Run
Manager dialog (these controls are grayed-out if a user does not have this right). For more
information, refer to Chapter 8.
The Notification Options right allows a user to access the Notification Options dialog from the
menu option System > Notification Options in the main program (this menu option is grayed-
out if a user does not have this right). For more information, refer to Notification Options on
page 33.
The Appearance right allows a user to access the Appearance Settings dialog from the menu
option System > Appearance Settings in the Acquisition dialog (this menu option is grayed-
out if a user does not have this right). For more information, refer to Appearance Settings Dialog
on page 33.
The Mobile Phases right allows a user to access the Mobile Phases dialog from the menu option
System > Mobile Phases in the Acquisition dialog (this menu option is grayed-out if a user dos
not have this right). For more information, refer to Mobile Phases Dialog on page 35.
The Direct Control right allows a user to access the Direct Control dialog from the menu option
System > Direct Control in the Acquisition dialog (this menu option is grayed-out if a user
does not have this right). For more information, refer to Direct Control on page 37.
The Updates / Web Access right allows a user to check for software updates from the Eksigent
web site from the menu option Help > Check for Updates in the Acquisition dialog (this menu
option is grayed-out if a user does not have this right).
If you want to quickly select or deselect all permissions on this tab click on Check All or
Uncheck All.

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User Manager

The Runmanager Tab

The Runmanager tab (Figure 11-9) of the Member Permissions dialog contains permissions that
deal with using the Run Manager. This tab contains a slider on the left side that will determine a
user access level for the Run Manager. The access levels which range from least access to most
access are: None, Low, Medium, High, and Full. By default, all members have access level None
in the Run Manager when they are added to the system.

Figure 11-9 Runmanager Tab

The Run Manager tab in Figure 11-9 shows a user with an access level of Full. This user has full
access permissions in the Run Manager. To set the permission level of a user set the slider to the
appropriate level.
For a summary of the basic intent for each access level, refer to Table 11-1.
Table 11-1 Run Manager Permissions for Each Access Level
None Low Medium High Full
Launch Run Manager    
Start/Stop Runs   
Modify Run Table  
Save Changes to Run Table 

None: Users cannot launch the Run Manager. The Run Manager button in the main program is
grayed-out.
Low : Low permission users can launch the Run Manager by clicking Run Manager in the main
program. The user can also exit the Run Manager. Under the File menu, the user can open,
export, and print pre-defined run tables.
Low permission users can also copy Run Table contents to an external medium such as Excel,
they can switch to the Acquisition dialog, they can view the contents of the Run Table by using
the scroll bars and resizing the column and they can access the Help menu.
Medium : Medium includes all actions available under Low, and the user can start and stop runs
by clicking Start or Stop.

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 User Manager

Medium permission users can also select or deselect the Flush/Equilibrate When Idle selection
box.
High : High includes all of the actions available under Medium and the user can import content
into the Run Table from the File menu. The user has access to all items under the Edit menu to
modify the Run Table and has full direct access to modify the Run Table.
In addition, the High permissions user can use the tray graphic in the Current Tray frame to
modify the Run Table.
Full: Full permissions include all actions available under high as well as saving new or modified
Run Tables by using Save or Save As on the File menu.
The access permissions controls for some features of the Run Manager are not located in the
Run Manager tab of the Member Permissions dialog. These features include items in the Device
menu and buttons in the Method Definitions dialog. The right to access the Analysis Methods
button is controlled on the General tab, as outlined previously in this section. The access to the
remaining controls is defined on the Other tab, for more information refer to Other Tab on
page 140.

Data Tab
The Data tab of the Member Permissions Window (Figure 11-10) contains permissions that
deal with access of data in the main program and the application of electronic signatures. Much
like the Run Manager tab, this tab also uses a slider to determine a user level for data access.
The access levels, from least access to most access, are: None, Low, Medium Low, Medium,
Medium High, High, and Full. By default, all members have data access level None when they
are added to the system.

Figure 11-10Member Permissions Window - Data Tab

The figure shows a user with a data access level of None. To set the data permission level of a
user set the slider to the appropriate level.
Table 11-2 outlines the privileges granted to each data access level.
Table 11-2 Run Manager Permissions for Each Access Level
None Low Medium Medium Medium High Full
Low High
Open Data      

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User Manager

Table 11-2 Run Manager Permissions for Each Access Level (Continued)
None Low Medium Medium Medium High Full
Low High
Toggle Auto-Print     
Save Data     
Toggle Auto-Save   
Apply E-Signatures  
Revoke E-
Signatures 

All controls for data access are found under the File menu in the Acquisition dialog. The
electronic signatures are applied in the Electronic Signatures dialog.
Open Data enables the Open command under the File menu in the Acquisition dialog.
Toggle Auto-Print enables the Auto-Print command under the File menu in the main Acquisition
dialog.
Save Data enables the items Save As and Output Options in the File menu of the Acquisition
dialog.
Toggle Auto-Save enables the Autosave command in the File menu of the Acquisition dialog.
Apply E-Signatures allows a user to apply electronic signatures in the Electronic Signatures
dialog.
Revoke E-Signatures allows a user to revoke electronic signatures in the Electronic Signatures
dialog.
The Electronic Signature role of the user can also be set in the Data tab. The E-Signature Role
menu is only enabled when the user has a Data level of Apply E-Signatures or Revoke E-
Signatures. By default all users have the lowest level of E-Signature role when they are added to
the system. Select a role appropriate for the user by using the menu. For more information, refer
to Chapter 12.

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 User Manager

Diagnostics Tab
The Diagnostics tab of the Member Permissions dialog (Figure 11-11) contains permissions that
deal with using features in the Hardware Diagnostics dialog, refer to Hardware Diagnostics on
page 27. Much like the General tab, permissions are granted by checking the appropriate check
box. By default, all members have no permissions in the Hardware Diagnostics dialog when they
are added to the system.

Figure 11-11Member Permissions Window - Diagnostics Tab

Initialize Transducers enables the Re-Initialize Transducers check box. Leak Check enables the
Check For Leaks/Blockage check box.
Flow Stability Check enables the Check Flow Stability check box.
Flow Meter Calibration enables the Calibrate Flowmeter button.
Auto Tune enables the Auto Tune Controllers button and the Pump Time Response slider.
Reset Usage Statistics enables all CLR buttons in the Usage Information region.
Optical Diagnostics enables the Optical Diagnostics tab.
If you want to quickly select or deselect all permissions on this tab click Check All or Uncheck
All.

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User Manager

Other Tab
The Other tab of the Member Permissions dialog (Figure 11-12) contains the remaining
permissions. Permissions are granted by checking the appropriate check box. By default, no
permissions on the Other tab are granted when members are added to the system.

Figure 11-12Member Permissions Window - Other Tab

The User Administration permission grants a non-system administrator the right to access User
Authentication and the User Manager dialog. This permission is useful when you want to grant
administrative privileges to a user for the software, but not administrative privileges for the
Windows operating system. A user with this right is able to control user membership and manage
user permissions and should be used judiciously.
Modify/Save Instrument Configuration enables the LC Device Settings and LC Wait for Contact
Closure commands on the Devices menu of the Run Manager.
Modify/Save Instrument Methods enables the LC Methods button on the Run Manager.
Modify/Save Autosampler Configuration enables the items Autosampler Type, Autosampler
Device Settings, and Skip Missing Vials on the Devices menu of the Run Manager.
Modify/Save Autosampler Methods enables the Autosampler Methods on the Run Manager.
Click OK to confirm all permission changes for a user, or click Cancel to exit without saving.

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Electronic Signatures
12
Role of the Electronic Signatures Dialog
The Electronic Signatures dialog is used to view, apply, and revoke electronic signatures from
data files. There are several items included in any particular electronic signature including the
user-name and signature role of the signer, the date and reason of the signature, any additional
comments about the signature that the user may have, and the revoke date if the signature is
revoked.
To display the Electronic Signatures Dialog (Figure 12-1) select System > Electronic
Signatures in the Acquisition dialog.

Figure 12-1 Electronic Signatures Dialog

Components of the Electronic Signatures Dialog

The Electronic Signatures dialog is composed of three regions: the Explorer region on the left,
the Data Files region on the top right, and the Signatures region on the bottom right. The regions
can be sized at will.

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Electronic Signatures

Explorer
To locate the data files you want to view, use the Explorer region. When folders are expanded,
only data files and other folders, if any, will be displayed.
To view the data files in any particular folder, click on the folder in the explorer region. If any data
files exist in that folder, the files will be displayed in the Data Files region. A data file with a blank
notepad icon indicates that the file contains no signatures, while a data file with a pencil-notepad
icon indicates that the file contains at least one signature.

Data Files
The Data Files region contains three columns: File Name, Creation Date, and Last Modified. Like
the column titles suggest, the File Name column contains the name of the data file, the Creation
Date contains the date that the data file was created, and the Last Modified column contains the
date that the data file was last modified. Data file can be sorted in the Data Files region by any of
these three parameters. To sort, press on the column heading of the parameter to sort by. The
size of the columns can also be adjusted to suit your needs.
To view the signatures for any particular data file, click on any data file with the Pencil-Notepad
icon in the Data Files region, and all the signatures for that file will appear in the Signatures
region. Signature items are displayed with a paper-pencil icon. If the icon has a red X marked
through it, the signature has been revoked.

Signatures
The Signatures region contains six columns which are the aspects of an electronic signature
saved to file.
Signer is the Windows user name of the user signing the document.
Date is the date when the document was signed.
Role is the signature role of the user.
Reason shows the reason for the signature.
Revoke Date is the date a signature was revoked.
For signatures that are not revoked, the revoke date field will indicate active instead of a date.
The signatures can be sorted in the Signatures region by any of these parameters. To do so, click
on the column heading of the parameter. The size of the columns can also be adjusted to suit
your needs.

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 Electronic Signatures

To view a signature in detail, select the signature in the Signatures region and click View. The
signature will be displayed in a separate dialog (Figure 12-2). This is useful if a signature
contains long comments.

Figure 12-2 Individual Electronic Signature

To exit the Electronic Signatures dialog click X in the top right corner.

Signing Data Files

To apply electronic signatures to any data file, you must be either a system administrator or a
user with the Apply E-Signatures right. For more information, refer to Chapter 11.
It will be necessary to logon and establish that you have proper document signing rights before
you can proceed. You will only be asked to establish your credentials once within the one session
of using the Electronic Signatures dialog. If this dialog is exited and then entered, user
credentials will have to be established again.
To sign data files, first select the file(s) that you want to sign in the Data Files region.
To sign one data file, select the file in the Data Files region and then click Add Signature or
double-click on the Data File. To select multiple files, drag the mouse across all required files,
hold down Shift and select a range of files, or hold down Ctrl to select each file individually, then
click Add Signature. The User Logon dialog will open, refer to Figure 12-1.

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Electronic Signatures

At this point, you must logon as a system administrator or a user with the Apply E-Signatures
rights. If you logged on successfully, the Sign Document dialog will open.

Figure 12-3 Sign Document Dialog

In the Your Information region, verify that your username and your Electronic Signature role are
accurate. For more information, refer to Manage Electronic Signature Roles on page 132.
A list of filenames that appear in the box titled You are signing these files will be presented.
These should include all the files that you selected to sign in the Data Files region of the
Electronic Signature dialog.
When you apply the signature, all these documents will be stamped with that signature.
The Signature Reason menu contains a list of available signature reasons. You must choose a
reason before signing a document. These reasons are defined in Manage Electronic Signature
Reasons on page 133.
Any comments you may want to supply with the signature can be typed into the Optional
Comments box.
When you are ready to sign the document, click Sign. If you did not select a signature reason,
you will be prompted to do so. The Signature Reason list will then automatically expand. Click
Cancel at any time to cancel signing the document.
If signing the document was successful, the Sign Document dialog will close and the Electronic
Signature dialog will open. You can verify that the signature was applied by clicking on the signed
data file. The signature that you just applied will appear in the Signatures region.

Revoke Signatures on Data Files

To revoke electronic signatures to any data file, you must be either a system administrator or a
user with the Revoke E-Signatures right.
To revoke an electronic signature, select the signature to be revoked in the Signatures region,
and click Revoke.

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 Electronic Signatures

If you have already established your credentials, as detailed in the last section, you will not need
to logon at this point. If you did not, the logon prompt (Figure 12-1) will open. Supply a valid user
account that is either a system administrator or a user with the Revoke E-Signatures right. If your
user account is neither of these, you will not be allowed to revoke a signature.
When revoking signatures, keep in mind that once a signature is revoked, it cannot be activated.
Signatures can only be revoked one at a time; there are no controls to revoke multiple signatures
simultaneously. Also users can only revoke their own signatures. No user can ever revoke any
other user signatures.

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Index

automatic peak detection algorithm, described

81
Numerics automatically flush 36
2-D methods, creating and editing 75 automatically purge 36
AutoNumber Spot Positions 43
A Autosampler Aspirate 43
Autosampler Device Settings 41, 43
A/D channel, Appearance Settings 35
Autosampler Dispense (µL) 43
absorbance, Appearance Settings 35
autosampler methods
Acquisition Window
defined 49
components 14
Run Table 43
menus 16
Autosampler Tray 43
Open command 18
Autosampler Vial 43
overview 13
Autosave
Run Manager 42
File menu 16
acquisition, progress of 44
format 20
Add Integration Event 16
using 19
adding users and groups 131
Additional Tasks Setup 9 B
Advanced Options, 2-D Method Editor 78
Advanced tab Back Skim event 98
Acquisition Window 32 Backward Horizontal Baseline 100
Alert messages, using 27 C
Alerts log 25
Amount Ratio 118 calculation methods 86
Analysis methods calibrate the LC hardware 27
defined 49 calibration
Run Manager 49 curves, storage of 118
Analysis methods, Run Manager 81 curves, types 119
analysis module, overview 81 described 118
Analysis Settings 38, 52 range 122
Analysis Settings Editor 55 terms 118
ANDI files 20 values, location 7
annotations Calibration Disk button 11
peak table 52 calibration functions 28
Sample Report 52 calibration table
Appearance Settings 34 Quantitation tab 82
Appendable Peak Table Format 20 requirements for creating 123
attributes, data 33 Calibration Values tab 28
Auto Scale All Plots 61, 63 capacity factor, defined 86
Auto Tune Controllers 28 Channel 1 log 26
Auto-Complete Command, Run Manager 46 Check For Leaks/Blockage 28
Auto-Diagnose region 27 chromatograms
Automated Calibration Table Generation 127 analyzing 38
automated diagnostic routines, performing 27 integration timed events 91
Automatic background, turning on or off 24 LC Method Editor 74

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Index

overlaying 63 De-Salt Wash Manual Control, 2-D Method Ed-

Color and Grid Line options 62 itor 79
Column Flow Rate Reference Method 23 detection threshold asymmetry, overview 92
column heaters 69 detection threshold, overview 92
column pressure 14, 23, 32, 33, 34 Detector tab 73
column sorting 47 Detector Wavelength Range 73
columns, Run Table 47 Device I/O tab, signal polarity 30
COM port devices
communication 12 Run Manager 42, 65
commands Diagnostics tab 139
Auto-Complete, Run Manager 46 Direct Control dialog box 37
Import 41 directory, location of software 8
Open 18 displaying
Save As 18 Electronic Signatures window 141
configuring multiple plots 56
drivers 11 Driver Configuration Utility dialog box 11
HPLC system 11 drivers, configuring 11
operating fluids 35 Dual beam operation 74
Plot window 51
system 11 E
User Manager 130 Edit menu 41
conserved flow 70 editing
contour plot region 15 LC methods 67
Copy Plot Selection 58 electronic signatures
correlation coefficient, described 122 defined 38
creating displaying Electronic Signatures window
2-D methods 75 141
LC methods 67 reasons 130
cubic fit 122 roles 130
cubic spline fit, applying 24 system administrator rights 144
current mobile phase flow rates 14 Electronic Signatures window
Current Tray 48 components 141
custom formula 54 use 141
customize e-mail
peak tables 16 notification options 33
Status area 14 settings 33
enabling user authentication 129
D events
data acquisition, LC Method Editor 73 conflicting 108
data files Force Peak Start 104
locating 142 Force Peak Stop 104
peak analysis 55 Force Result 106
revoking signatures 144 Front Skim 96
sample reports 52 incompatible events 108
signing 143 LC methods 71
viewing signatures 142 Manual Baseline 98
Data Set Origin 20 Merge Peak 105
Data Set Owner 20 Minimum Area 93
data, setting attributes 33 Minimum Peak Height 93

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 Index

Minimum Peak Width 92

Negative Peaks 94 H
Reference Peak 107 hardware configuration options, setting 29
Reset Baseline 102 HTML report 21
Reset Baseline at Valley 103
Shoulder Detection 93 I
Split Peak 105 icons, installing 9
Valley To Valley 95 ignore external triggers 23
events Manual Peak 106 Import command 41
Explorer, electronic signatures 141 incompatible events 108
Exponential Modified Gaussian (EMG) Calcu- independent flow 70
lation Method 89 Inject Ahead 41
Exponential skim 98 Input A/D Range 32
Export Settings Button 30 Insert New Table Entry 83
Extend Run Icon 15 installing, icons 9
External Standard Calculation, described 124 Instrument Configuration dialog box 11
Instrument Configuration window 29
F instrument usage statistics 27
File menu Integration Off 94
Acquisition Window 18 integration timed events, chromatograms 91
Run Manager 41 internal flowmeter pressures 14
filter usage 28 Internal Standard Calculation, described 126
Find Peaks 52, 59
Find Peaks button 52 J
fits, types of 121 Japanese Pharmacopoeia (JP) Calculation
Flow Calibration tab 27 Method 89
Flow Data, Appearance options 34
Flow Metering and Control region 28 L
Flow Mode, LC Method Editor 70 lamp, direct control 37
Flow Profile 72 LC Channel 44
Flow Stabilization Limits 32 LC Column Temp 44
Flow Table tab 72 LC Flow Rate 44
Flowmeter Calibration dialog box 28 LC Injection Vol 44
Flowmeter Serial 28 LC methods
Flowrate field 22 creating 67
Flowrate reference option 22 data acquisition 73
Force Peak Start 104 defined 49
Force Peak Stop 104 editing 67
Force Result 106 events 71
Forward Horizontal Baseline 99 Flow Mode 70
Front Skim 96 Mode 74
Run Manager 49
G Summary tab 67
Gaussian skim 98 LC Wait for Contact Closure 41
General tab, member permissions 134 LC. Inj Type 44
German Pharmacopoeia (DAB) Calculation linear fit 121
Method 88 log files 25
Lowest Point Horizontal Baseline 101

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Index

Overlay Selection 61
M overlaying, chromatograms 63
Main Plot Region, modifying the plot scale 15 Ownership Tags 20
Make All Plots Identical 61, 63
Managing Electronic Signature Roles 132 P
Managing User Permissions 134 Park Now button 22
Manual Baseline 98 Pause button 15
manual flush settings 36 PDF
Manual Peak 106 printing 21
manual purge settings 36 report 21
Math on/Between Sets 64 peak analysis 55
math operations, performing 64 peak asymmetry 87
menus peak detection events, defined 91
Acquisition Window 16 Peak Detection tab, overview 82
Edit 41 peak detection, disabling 94
File 18, 41, 57 peak identification 81
Peak Viewer 57 described 113
Plots 61 Options tab 84
Run Manager 39 peak integration events, defined 91
Merge Peak 105 peak integration parameters, setting 38
metered injection mode 76 peak integration, disabling 94
method editors 49 peak label options 62
Method Steps tab, 2-D Method Editor 76 Peak Park Toolbox, overview 22
Minimum Area 93 Peak Preview
Minimum Peak Height 93 File menu 57
Minimum Peak Width 92 function 20
mobile phases 36, 70, 71 overview 20
Mode, LC Method Editor 74 Peak Preview function 20
Monitor Folder 57 peak results
monitoring peak trends 54 calculation methods 87
moving multiple cells 46 displaying 85
Multi-Level Calibration 120 peak shapes, defined 87
Multiplication Factor 119 peak table
annotations 52
N customizing 16
Negative Peaks 94 overview 52
nonlinear fits 121 peak trends, monitoring 54
notification events 33 Peak Viewer utility
notification frequency 33 described 13
Notification Options 17 menus 57
overview 51
O peak-park for a fixed duration 23
Open command 18 Peaks menu 59
Options tab, peak identification 84 peaks, monitoring peak trends 54
Other tab 140 PID region, Calibration Values tab 29
Output D/A Range 32 plot axes, Appearance options 35
Output Folder field 19 Plot window, configuring 51
output options 19 plots
overlaid data, removing 56 areas 56

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 Index

attributes 63 Automated Calibration Table Generation

Plots menu 61 127
Pre/Post Run Options, 2-D Method Editor 79 described 13
pressure, Appearance Settings 34 devices 42, 65
printing Import command 41
PDF 21 overview 39
preview function 21 sample tray status 48
Profile Editor, LC Method Editor 71 Sequential option 50
programmable events, LC Method Editor 71 Run Manager tab 136
Prompt to save 19 Run Replicates 43
properties, Plots menu 61 Run Sequence 50
pump manual control 37 Run Table
pump power 14, 33 columns 47
Pump Response Time 28 editing 43
pumps, direct control 37 files 41
LC Channel 44
Q navigation 45
quadratic fit 122
quantitation S
automatic 128 salt content, Method Steps tab 76
defined 113 salt elution channel, Advanced Options 78
Quantitation tab, overview 82 salt elution, manual control 78
Quick Launch icon 8 sample injection modes 69
Sample Queue log 26
R Sample report 52
rapid injection mode 76 sample status 48
reference acquisition 24 scaling factors, described 123
Reference Peak 107 security, setting 129
Reference/Background options 24 selected 2-D method 75
Re-Initialize Transducers 28 selecting
removing multiple cells 46
overlaid data 56 vials 48
Users and Groups 131 Seq. # 43
Report Comments 60 Sequential option, Run Manager 50
Report window 21 settings
reports data attributes 33
HTML 21 email 33
PDF 21 Shoulder Detection 93
Sample Reports 52 Signal Input Polarity 31
Reset Baseline 102 Signal Output Polarity 31
Reset Baseline at Valley 103 signatures, viewing 143
Response Factor 118 signing data files 143
Response Ratio 119 Single beam operation 74
Reverse Phase Method, 2-D Method Editor 77 Single Level Calibration 119
revoking signatures 144 Skip Missing Vials 41
Run Conditions tab, overview 68 Smoothing Toolbox 17
Run Interval 43 spectrometer
Run Manager Detection region 68
Analysis Method 81 Detector tab 73

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Index

Split Peak 105 user permissions, managing 134

Spotter Device Settings 41 UV Detector Toolbox, overview 23
Spotter Methods button 49
Spotter Methods, Run Manager 49 V
Spotter plate # 44 Validate Installation option 10
Spotter Time 44 Valley To Valley 95
Spotter Time/Drop (ms) 44 valve, direct control 37
statistics, generating 54 vials, selecting 48
Status area, customizing 14 View menu 22
status, sample 48
Stop button 15 W
Summary tab weighting factor, described 122
2-D methods 75 Wizard Completion dialog box 10
LC methods 67
Sync. options 24 Z
Sync. with Gradient Start option 24 zoom window 15
Sync. with Injection start option 24
synchronization, 2-D Method Editor 77
System Configuration log 26
System Logs submenu 25
System menu 27
System Shut Down 30
System tab 29

T
Tangent skim 98
Tile 56
total flow rate 14, 23, 37
Total Flowmeter Usage 28
Total Sample Injections 28
Trend tab 54

U
United States Pharmacopoeia (USP) Calcula-
tion Method 88
unknown chemical compounds, determining
83
usage counters, resetting 35
usage information 28
user
authentication 38, 129
permission 38
user authentication 129
User Authentication Window 130
User Logon dialog box 130
User Manager
configuring 130
overview 129
User Manager dialog box 130

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