LCquan 2.8 User Guide Version A

LCquan 2.8 User Guide Version A
Xcalibur
LCquan
User Guide
Software Version 2.8
XCALI-97546 Revision A
April 2013
© 2013 Thermo Fisher Scientific Inc. All rights reserved.
Foundation, LCquan, Q Exactive, and Web Access Suite are trademarks, and Accela, Exactive, LCQ, LTQ,
Surveyor, Thermo Scientific, TSQ Quantum, DCMSLink, and Xcalibur are registered trademarks of Thermo
Fisher Scientific Inc. in the United States.
The following are registered trademarks in the United States and other countries:
Adobe and Flash are registered trademarks of Adobe Systems Incorporated. Excel, Microsoft, Vista, and
Windows are registered trademarks of Microsoft Corporation. Oracle is a registered trademark of Oracle
Corporation and/or its affiliates.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, April 2013
Software version: (Thermo) Foundation 2.0 SP1, Xcalibur 2.2 SP1, LC Devices 2.7 or later, Exactive Series 2.2
SP1, DCMSLink 2.13, TSQ Series 2.3 SP3, (Microsoft) Windows 7 Professional SP1 (32-bit or 64-bit) and Office
2010
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Quantitative Analysis with the LCquan Application . . . . . . . . . . . . . . . . . . . . . . 1
Overview of the LCquan Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Introduction to the Instrument Setup Window . . . . . . . . . . . . . . . . . . . . . . . . . . 2
LCquan Application Folder Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
LCquan Applications Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Acquiring and Processing Data With the LCquan Application . . . . . . . . . . . 10
LCquan Application for Web Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 2
Preparing to Perform Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Creating a New Study and Workbook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Create a New Workbook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Saving a Workbook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
File Tracking Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Workbook Summary Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Introduction to the Instrument Setup Window . . . . . . . . . . . . . . . . . . . . . . . . . 27
Creating Instrument Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Importing an Existing Instrument Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Introduction to the Acquisition Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Using the Setup Sequence View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Acquisition Sequence Header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Acquisition Sequence History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Acquisition Sequence Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Specify the Injection Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Using the Run Sequence Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Change Instruments Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
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Using the Status View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Using the Status View Control Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Acquisition – Status – Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . 86
Acquisition – Status – Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Acquisition – Status – Run Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Acquisition – Status – Acquisition Queue . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Acquisition – Status – Acquisition History . . . . . . . . . . . . . . . . . . . . . . . . . 104
Processing Data While Continuing to Acquire Data . . . . . . . . . . . . . . . . . . 107
Verifying Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Save Settings Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Emergency Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Shutting Down the LCquan Application While Acquiring . . . . . . . . . . . . . . . 112
Remote Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Chapter 3
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LCquan User Guide
Exploring the Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117
Introduction to the Explore Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Creating Explore Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Defining Chromatographic Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Defining Peak Integration Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Acquisition Sequence History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Exploring the Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Navigation Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Opening a Raw File and Displaying the Chromatogram . . . . . . . . . . . . . . . 145
Generating a Peak List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Identifying Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Exporting the Active Raw File to Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . 151
Data Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Toolbar for Selectable Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Chromatogram List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Error Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Filter List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
General Parameters Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Instrument Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Mass List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Peak List View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Sample Info View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Status Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Status Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Tune Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Multi Peak Plot View for Review Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Thermo Scientific
Contents
Chapter 4
Thermo Scientific
Creating a Processing Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183
Creating a Processing Method with the New Method Wizard . . . . . . . . . . . . . 184
Start the Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Create or Import a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Import a Processing Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Specify Calibration Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Select a Raw File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Complete the Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Importing Information for a Q Exactive Mass Spectrometer Quantitation
Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Specifying Method Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Chromatogram Definition Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Retention Time Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Peak Integration Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Peak Identification Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Ion Ratio Confirmation Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Summing Ions Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Chromatogram Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Specifying Component ID Parameters and Integrating the Peaks . . . . . . . . 208
Defining Peak Integration Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
IRC Detection Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Identification Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
Ion Ratio Confirmation of Analytes Example . . . . . . . . . . . . . . . . . . . . . . . 241
Specifying Method Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
Component Type Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Target Compound Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Component List Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Calibration Shortcut Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Correction for Isotope Contribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Specifying Calibration Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Specifying Internal Standards and Target Compounds . . . . . . . . . . . . . . . . 254
Reviewing the Integrated Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Saving the Processing Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Importing a Processing Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Exporting Components and Levels to an Acquisition Sequence . . . . . . . . . . . . 259
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Contents
Data Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Toolbar for Selectable Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Calibration Curve View for Survey or Review All Results Only . . . . . . . . . . 263
Chromatogram View for Create Method Only . . . . . . . . . . . . . . . . . . . . . . 266
Chromatogram View for Survey or Review All Results Only . . . . . . . . . . . . 270
Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
IRC Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Chromatogram List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Error Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Filter List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
General Parameters Plot View for Survey or Review All Results Only . . . . . 284
Instrument Method List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Mass List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
Peak List View for Survey or Review All Results Only . . . . . . . . . . . . . . . . . 289
Sample Info View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Status Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
Status Report View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Tune Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296
Multi Peak Plot View for Survey or Review All Results Only. . . . . . . . . . . . 297
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LCquan User Guide
Chapter 5
Creating a Processing Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .301
Defining a Processing Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
Using the New Processing Sequence Wizard . . . . . . . . . . . . . . . . . . . . . . . . 304
Copying an Acquisition Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
Importing a Processing Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
Copying the Last Acquired Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Editing a Processing Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Using the Create Sequence (edit) View . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Using the Create Sequence (create) View. . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Resolving Discrepancies in Level Names . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Exporting a Processing Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Chapter 6
Processing the Raw Files and Reviewing the Analytical Results. . . . . . . . . . .331
Processing the Raw Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
Reviewing the Calibration Curve and QCs . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
Opening the Survey View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Reviewing the Calibration Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
Modifying Calibration Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
Excluding a Calibration Standard from the Calibration Curve . . . . . . . . . . 350
Modifying the Peak Detection and Integration Settings. . . . . . . . . . . . . . . . 353
Specifying Additional Peak Detection Criteria. . . . . . . . . . . . . . . . . . . . . . . 354
Manually Integrating Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
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Reviewing All Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Opening the Review All Results View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Reviewing the Unknowns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374
Reviewing Peak Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375
Adding Comments to the Chromatogram Display . . . . . . . . . . . . . . . . . . . 382
Creating and Reviewing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
Review Reports Warning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
Report Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
Exporting Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
Locking the Workbook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405
Saving the Workbook and Exiting the LCquan Application . . . . . . . . . . . . . . 408
Appendix A Quantitative Analysis Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .409
About Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Considering the Variables of Quantitative Analysis by LC/MS/MS . . . . . . . . . 410
Using LC for Analyte Separation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410
Using MS/MS for Analyte Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Quantitative Analysis Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412
Using External Standards for Quantitative Analysis . . . . . . . . . . . . . . . . . . . 414
Using Internal Standards for Quantitative Analysis . . . . . . . . . . . . . . . . . . . 414
Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Standards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Unknowns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
QCs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417
Blanks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417
Appendix B LCquan Application Flow Diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .419
LCquan Application Flow Diagram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420
LCquan Application for Web Access Flow Diagram . . . . . . . . . . . . . . . . . . . . 421
LCquan Application Acquisition Flow Diagram . . . . . . . . . . . . . . . . . . . . . . . 422
LCquan Application Quantitate Flow Diagram. . . . . . . . . . . . . . . . . . . . . . . . 423
Appendix C LCquan Application Menu and Toolbar Reference. . . . . . . . . . . . . . . . . . . . . . . .425
Using the Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
Actions Menu for Acquisition Window Only . . . . . . . . . . . . . . . . . . . . . . . . . 426
Apps Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427
Change Menu for Acquisition Window Only . . . . . . . . . . . . . . . . . . . . . . . . . 427
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432
Options Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Zoom Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438
Icon Bars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .445
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Preface
The LCquan™ application is part of the Thermo Xcalibur™ mass spectrometry data system.
This user guide describes how to use LCquan to perform quantitative analysis of compounds.
The LCquan application is a secure data quantitation package. It provides all the tools you
need to perform quantitation tasks, including importing sequence information from external
systems, acquiring data, developing processing methods, reviewing and processing data,
generating reports, and exporting results to external systems.
Note
• This version of the application only supports the Microsoft™ Windows™ 7 operating
system.
• The LCquan for Web Access application supports data processing, but it does not
support data acquisition.
Contents
• Related Documentation
• Special Notices
• Contacting Us
 To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
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Related Documentation
In addition to this guide, the following LCquan manuals are available on the LCquan
software CD as PDF files:
• LCquan Administrator Guide describes how to configure the software for compliance and
security.
• LCquan Tutorial describes step-by-step procedures to perform quantitative analysis with
sample data.
 To view the product manuals
Go to Start > All Programs > Thermo Xcalibur > Manuals > LCquan.
 To open Help
From the LCquan window, choose Help > LCquan Help.
To find a particular topic, use the Help Contents, Index, or Search panes.
For more information, visit www.thermo.com.
Special Notices
This guide includes the following types of special notices.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
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Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
 To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
 To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
 To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
 To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[email protected]
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Introduction
The LCquan application is a complete quantitative analysis software package. This chapter
provides an overview of the application as a quantitative analysis tool and briefly describes its
use with Thermo Scientific™ Web Access Suite™ for application virtualization.
Contents
• Quantitative Analysis with the LCquan Application
• LCquan Application for Web Access
Quantitative Analysis with the LCquan Application
Use the LCquan application to acquire data specifically for an analyte of interest, to quantitate
the results, and to produce reports. For more information about quantitative analysis
concepts, see Appendix A, “Quantitative Analysis Overview.”
This section contains the following topics:
• Overview of the LCquan Application
• LCquan Application Folder Structure
• LCquan Applications Menu
• Acquiring and Processing Data With the LCquan Application
Overview of the LCquan Application
The LCquan application is divided into four main windows: Instrument Setup, Acquisition,
Explore, and Quantitate. By using these windows, you can develop instrument methods,
acquire data, explore data, and process data files.
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Introduction to the Instrument Setup Window
Introduction to the Instrument Setup Window
Use the Instrument Setup window to create the following:
• Startup methods to prepare the LC/MS system for data acquisition
• Instrument methods with the appropriate settings for data acquisition
• Shutdown methods to return the LC/MS system to the appropriate idle conditions
The Instrument Setup window contains an Instrument Setup view for each configured
instrument in your LC/MS system.
To access instrument specific parameters, menus, or Help, do the following:
• To open the Instrument Setup view for a specific instrument, click the instrument’s icon
on the navigation pane. The green triangle in the lower-right corner of the icon indicates
the active view.
• To open a menu with additional commands for the instrument, choose
Instrument Name on the menu bar of the Instrument Setup view. The menu commands
for some autosampler and LC pump instruments include direct controls. You can also
access these direct controls from the mass spectrometer’s Tune window.
• To access the Help for an instrument, choose Help > Instrument Name Help (see
Figure 1).
Note The instrument Help is independent of the LCquan Help.
Figure 1.
Instrument Setup window
Instrument menu
Instrument Help
Navigation pane
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Introduction to the Instrument Setup Window
Acquisition Window
In the LCquan Acquisition window, you can set up a sequence of samples for acquisition
(Figure 2). The sequence can contain unknown samples, calibration standard samples, quality
control samples, and blank samples. After you have defined a sequence, you can specify
acquisition options and processing action options for the sequence and start running it. The
Acquisition window also contains a real-time display so that you can watch updates of the
acquisition status and the data being acquired.
The Acquisition window contains the Setup Sequence view, the Run Sequence dialog box,
and the Status view.
Note The Acquisition window is not available in the LCquan application for the Web
Access environment.
Figure 2.
Acquisition window
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Introduction to the Instrument Setup Window
Explore Window
In the Explore window, you can display a multi-peak chromatogram for a single sample and
experiment with peak detection and integration parameters to see how they affect the
chromatogram (Figure 3). Use the Explore window to determine the optimum parameters
used in the processing method. The LCquan application can also generate a peak list that you
use to generate the quan components in the processing method. Click Explore to open the
Create Explore Methods view of the Explore window.
Figure 3.
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Introduction to the Instrument Setup Window
Quantitate Window
In the Quantitate window, the LCquan application steps you through a procedure for batch
processing raw files during quantitative analysis (Figure 4). Because the application window
incorporates an integrated calibration curve, peak integration, and results view, you can
interactively review and rework standards, QCs, and unknowns in one window. You can also
enter the Quantitate window to process the acquired data as you acquire it.
Figure 4.
Quantitate window
The LCquan application uses a processing method to automatically determine the
concentration (or amount) of the sample being analyzed. The processing method measures
the response of the detection system to the compounds in your sample by integrating the area
under each peak.
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Introduction to the Instrument Setup Window
After measuring several known standards, the LCquan application constructs a calibration
curve that it uses to accomplish the quantitative analysis of unknown samples. It provides a
number of options for fitting the calibration data to generate the calibration curve. You can
have it fit the calibration data to the following curve types:
• Linear
• Quadratic
• Linear log-log
• Quadratic log-log
• Average response factor (RF)
• Point-to-point
• Cubic spline
• Locally weighted
You can also have the LCquan application weight the calibration data with the following
weighting functions when performing the least squares fit to the calibration data:
• Equal
• 1/X
• 1/X2
• 1/Y
• 1/Y2
• 1/S2, where S2 = X2 + Y2
In addition, you can have it ignore the origin, use the origin as a data point, or force the
calibration curve to include the origin.
The Quantitate window contains these views: Create Method, Create Sequence, Survey,
Review All Results, and Review Reports.
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Introduction to the Instrument Setup Window
LCquan Application Folder Structure
When you start a new quantitative analysis project, the LCquan application creates a
hierarchical folder structure for the project on the hard drive.
The top-most level in the file structure is the study folder. This folder is used to organize
one or more workbook folders. Each workbook folder holds all the information used by the
LCquan application for an individual quantitative analysis project. The workbook folder
contains the LCquan file (.lqn), the instrument method files (.meth), and the audit log files.
In addition, the workbook folder contains these folder names: Exports, Imports, Rawfiles, and
Temp.
The Exports folder stores copies of all files that are exported from the LCquan application,
such as report files. The Imports folder stores a copy of legacy files that you import into the
workbook, such as instrument method files or sequence files. The Rawfiles folder contains
acquired data files (.raw), and any imported raw files. The Temp folder contains backup and
temporary files that it uses.
When you create a new project, the LCquan application requires you to name the study folder
and the workbook folder. You can have as many different workbooks in the same study folder
as you want, but each workbook must have a unique name. This is convenient for organizing
your quantitative analysis projects. For example, you can use one study folder to organize all
the separate quantitative analysis projects that you are doing for a particular client. You cannot
rename the folders that the LCquan application creates in the workbook folder.
The LCquan application manages all the files associated with the project. You do not have to
remember what individual files are named or where they reside on your hard drive. All
necessary files are contained within the workbook. In addition, it uses a file tracking feature to
maintain a secure file system. Check with your administrator if you have problems with the
security configuration.
IMPORTANT Always use the LCquan application to open and modify the workbook and
its associated files. To maintain secure file operations, it tracks the files in the workbook to
ensure that none has been modified by an external process. If you modify a file in the
workbook by using another software application (including Xcalibur), it prevents you
from reopening the workbook.
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Introduction to the Instrument Setup Window
LCquan Applications Menu
To provide quick access to external applications, you can add them to the Apps menu
(Figure 5). Table 1 lists the App Selection dialog box parameters.
 To add an application to the Apps menu
1. Choose Apps > Add Apps from any view.
The App Selection dialog box opens.
2. Click Add to open the Add App dialog box.
3. Click Browse to open the Locate Programs to be Added dialog box and find the program.
4. Select the program to add to the menu and click Open.
5. Click OK in the Add App dialog box.
6. Click Close in the App Selection dialog box.
Figure 5.
Apps menu
Step 2
Step 3
Result
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Introduction to the Instrument Setup Window
Table 1. App Selection dialog box parameters
Thermo Scientific
Parameter
Description
Add
Adds an application to the Apps menu. Select the executable file
(.exe) of the application that you want to add to the menu.
Remove
Removes the selected application from the menu list.
Move Up
Moves the selected application up the menu list. When the top is
reached, the button is disabled.
Move Down
Moves the selected application down the menu list. When the
bottom is reached, the button is disabled.
Menu Text
Lists the text that appears in the Apps menu list.
Program
Lists the full path to the program to be run. When you click Add,
the Program field automatically fills. No validation is made on
user-specified data.
Arguments
Lists arguments that are to be passed to the application when it is
started. No validation is made to the argument list.
Initial Directory
Defines the starting directory. You can manually enter a path or
use Browse to select a location. No validation is made to the initial
directory.
Browse
Browses for an initial directory. When you select an application
with Browse, the Initial Directory field automatically fills.
Close
Closes the dialog box and accepts the changes.
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Introduction to the Instrument Setup Window
Acquiring and Processing Data With the LCquan Application
With the LCquan application, quantitative analysis usually involves the following processes.
The order of some of these processes is not rigid. For example, before you acquire data, you
can create the processing method and processing sequence and use these to define the
acquisition sequence.
1. Developing an instrument method (not available for the Web Access environment):
The LCquan application uses an instrument method to store the specific set of parameters
that operate the autosampler, LC pump or MS pump, mass spectrometer, divert valve, or
syringe pump during analysis. For more information, see Chapter 2, “Preparing to
Perform Quantitative Analysis.”
2. Building an acquisition sequence of samples (not available for the Web Access
environment):
An acquisition sequence defines each sample as a standard, unknown, QC, or blank, and
identifies its position on an autosampler tray (if appropriate). For more information, see
Chapter 2, “Preparing to Perform Quantitative Analysis.”
3. Acquiring data (not available for the Web Access environment):
With the LCquan application you can run one sample or a series of samples from the
current acquisition sequence. For more information, see Chapter 2, “Preparing to
Perform Quantitative Analysis.”
4. Exploring your data:
The Explore window is a “sandbox” where you can open a raw file and play with peak
detection and integration parameters that you use in the Quantitate window. For more
information, see Chapter 3, “Exploring the Data.”
5. Creating a processing method:
The LCquan application uses a processing method to identify, detect, and integrate
components in a chromatogram, generate calibration curves, quantify unknowns, and
produce reports. For more information, see Chapter 4, “Creating a Processing Method.”
6. Building a processing sequence:
A processing sequence consists of a list of sample data files and includes information
about sample type and calibration or QC level. For more information, see Chapter 5,
“Creating a Processing Sequence.”
7. Processing the raw files and reviewing the calibration and quantitative analysis results:
After the LCquan application processes the raw file, you can evaluate and rework the
calibration standards by modifying the peak detection and integration settings. You can
also manually integrate peaks. For more information, see Chapter 6, “Processing the Raw
Files and Reviewing the Analytical Results.”
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LCquan Application for Web Access
8. Creating reports:
The LCquan application provides both standard and custom-printed reports. Standard
reports contain preselected methods and results summaries. Custom reports contain
methods and results summaries that you select from a list of options. For more
information, see Chapter 6, “Processing the Raw Files and Reviewing the Analytical
Results.”
LCquan Application for Web Access
The LCquan application supports the Thermo Scientific Web Access Server, which is hosted
on a Web page, allowing full, secure high-performance access to Watson using a web browser.
Web Access is used for application virtualization to manage the LCquan application
configuration and maintenance. The LCquan virtual application runs on centralized servers;
only keystrokes and mouse clicks travel over the network from the user’s computer, and only
screen images travel over the network to the user’s computer. Validate the application only on
the server.
The application supports the Web Access environment for data processing. The LCquan
application for Web Access includes only the Explore and Quantitate windows of the
application. You can perform certain actions within the application, such as data acquisition,
only on a local, validated computer and not the server.
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Preparing to Perform Quantitative Analysis
This chapter describes procedures for starting the LCquan application and creating a new
study and workbook in preparation for analyzing pre-existing data. This chapter also describes
the Instrument Setup window and the Acquisition window and outlines procedures to create
instrument methods and acquire data; however, these steps are not required to perform
quantitative analysis.
Contents
• Creating a New Study and Workbook
• Introduction to the Instrument Setup Window
• Introduction to the Acquisition Window
• Using the Setup Sequence View
• Using the Run Sequence Dialog Box
• Using the Status View
• Emergency Shutdown
Creating a New Study and Workbook
When you start the LCquan application, you can open an existing study and workbook or
you can create a new study and workbook set. You can also open a workbook in review mode
where you can analyze existing data and create methods, but you cannot acquire data or save
any changes you make to the workbook.
This section includes instructions for using an LCquan workbook.
• Create a New Workbook
• Saving a Workbook
• File Tracking Results
• Workbook Summary Information
To start your quantitative analysis, create a new study or workbook and import raw data.
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Creating a New Study and Workbook
Create a New Workbook
To get started, create a new workbook in an existing study or create both a new study and a
new workbook.
Start the Wizard
Start the New Study or Workbook Wizard.
 To open the New Study or Workbook Wizard
1. Choose Start > All Programs > Thermo Xcalibur > Thermo LCquan to open the
LCquan application (Figure 6).
From the LCquan startup dialog box, you can open the last used workbook, open an
existing workbook, or create a new workbook (see Table 2).
Figure 6.
LCquan Open Workbook
Open in Review Mode check box
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Creating a New Study and Workbook
2. Ensure that the Open in Review Mode check box is cleared.
You cannot create a new workbook in read-only mode.
3. Click Create a New Workbook.
The Welcome page of the New Study or Workbook Wizard opens (Figure 7).
Figure 7.
Welcome page of the New Study or Workbook Wizard
4. Click Next.
Table 2. New Study or Workbook Wizard page parameters
Thermo Scientific
Parameter
Description
Last used workbook
The name of the most recently opened workbook.
Open Last Used
Workbook
Opens the most recently opened/viewed workbook.
Open Existing
Workbook
Opens a dialog box where you can select any workbook.
Create a New
Workbook
Opens the New Study or Workbook Wizard that walks you
through the steps to create a new LCquan workbook.
Most recently used
Workbooks
Displays up to eight of the most recently opened workbooks.
Summary Info
Displays created/modified/saved by information about the
highlighted workbook. Hold the cursor over the workbook
name—without clicking—to see the summary information.
Open in Review Mode
Opens a workbook in read-only mode.
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Creating a New Study and Workbook
Name the New Study or Workbook
Name the new study or workbook (see Table 3).
 To specify a name for the new study or workbook
1. Type the new study name (Figure 8).
2. Type the new workbook name.
3. (Optional) Select the Change Study Root Folder check box.
Figure 8.
Create new study and workbook page
4. Click Next.
Note You cannot overwrite existing data in the LCquan application. When you
specify a new study and workbook set with the same name as an existing set, it
displays an error message. In this case, enter another name for your study or
workbook.
• To change the root folder, go to Specify the Root Folder.
• To keep the current root folder, go to Import Raw Files.
Table 3. Options for study and workbook name page
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Parameter
Description
Study Name
The LCquan application creates a new folder with this name
in the root folder.
Workbook Name
The LCquan application creates a new workbook with this
name in the Study folder.
Change Study Root
Folder
Select to change the project root folder. The default root
folder is C:\Xcalibur\QuanRoot. Changing the root folder
requires authorization from your administrator.
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Creating a New Study and Workbook
Specify the Root Folder
Specify a root folder for the study. The default root folder is C:\Xcalibur\QuanRoot
(Figure 9).
 To specify the root folder for the study
1. Type the new study root folder name or click Browse to find the folder.
Figure 9.
Study root folder page
2. Click Next.
Import Raw Files
Import raw files into the workbook.
 To import raw files into the new workbook
1. Select the Import Raw Files check box (Figure 10).
2. Click Browse to open the Select Raw File dialog box.
Figure 10. Import raw files option page
3. Browse to the location of your raw files.
For example: C:\Xcalibur\QuanRoot\examples\data
4. Select your raw files (see Table 4).
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Creating a New Study and Workbook
To highlight a group of raw files, click the first file name, press SHIFT, and click the last
file name (Figure 11).
Figure 11. Select Rawfile dialog box
5. To return to the wizard, click Open.
The wizard displays the selected raw files (Figure 12).
Figure 12. Import raw files page
6. Click Next.
Table 4. Import Rawfiles page parameters
Parameter
Description/Condition
Import Rawfiles
Activates the File Location list.
File Location (Displays the location of the raw files listed in the File name list.)
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File name
Lists the raw files in the selected file location.
Modified
Lists the dates the raw files were modified.
Browse
Click Browse to find or change the files.
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Creating a New Study and Workbook
Import Data
Import existing instrument methods, acquisition sequences, or processing methods. To
import processing information for the Q Exactive™ mass spectrometer from an exported
inclusion list, see “Importing Information for a Q Exactive Mass Spectrometer Quantitation
Method” on page 188.
 To import methods or sequences
1. Select the Import Instrument Method, Acquisition Sequence and Processing
Parameters check box (Figure 13).
2. Select either the Import from Existing Workbook or the Import Legacy Files option
(see Table 5).
Figure 13. Import data page
3. Click Next.
Depending on the options you chose, do one of the following:
• When you are not importing files, the final page of the wizard opens. Go to
Complete the Wizard.
• To import files from an existing workbook, go to Import Files From Workbook.
• To import legacy files, go to Import Legacy Files.
Table 5. Import data page parameters
Parameter
Description
Import Instrument
Method, Acquisition
Sequence and
Processing Parameters
Enables the import options.
Import from existing
workbook
Imports the instrument method, acquisition sequence, or
processing methods for a particular workbook.
Import legacy files
Imports existing instrument methods, acquisition sequences,
or processing methods that reside in different workbooks.
–or–
Imports methods and sequences not created by the LCquan
application.
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Creating a New Study and Workbook
Import Files From Workbook
Import existing instrument methods, acquisition sequences, or processing methods from
existing workbooks.
 To import files from an existing workbook
1. Click Browse to find the workbook whose files you want to copy (Figure 14).
Figure 14. Existing workbook path page
2. Click Next and go to Specify the Processing Sequence.
Import Legacy Files
Import existing instrument methods, acquisition sequences, or processing methods from
legacy files.
 To import legacy files
1. Click Browse to display the Import Instrument Method File dialog box (Figure 15) and
find the instrument method file (see Table 6).
Figure 15. Import legacy files page
2. Click Browse to display the Load Sequence File dialog box and find the sequence file.
3. Click Browse to open the Import Quantitation Method dialog box and find the
processing method file.
4. Click Next.
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Preparing to Perform Quantitative Analysis
Creating a New Study and Workbook
Table 6. Import legacy files page parameters
Parameter
Description
Instrument Method
Specifies the instrument method to import.
Acquisition/Processing
Sequence
Specifies the sequence to be both the acquisition sequence and
the processing sequence.
Note When you do not specify a processing method or the
processing method is unavailable, the LCquan application
does not make the processing sequence the same as the
sequence specified with this wizard.
Processing Method
Specifies the processing method to import.
Specify the Processing Sequence
Specify the processing sequence path.
 To specify a processing sequence path
1. Click Browse and find a folder in which to store processing sequences (Figure 16).
Figure 16. Set the processing sequence path page
2. Click Next.
Complete the Wizard
To complete the New Study or Workbook Wizard, click Finish.
The LCquan application creates the new study and workbook folders and imports the raw
files into the raw files folder.
Saving a Workbook
After you create a new workbook or study, save the workbook to the current study folder or to
a new study or workbook name.
To save the new workbook to your current location, choose File > Save from the main menu.
You can also use this wizard to save the new workbook with a new workbook name.
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Creating a New Study and Workbook
Start the Wizard
Use the Save As Wizard to save the workbook to a new location.
 To save the workbook to a new location
1. Verify that you have read and write privileges for the location where you intend to save
the workbook.
2. From the main menu, choose File > Save As.
The Save As Wizard opens (Figure 17).
Figure 17. Create new study and workbook page
3. Type the study and workbook names for this workbook (see Table 7).
4. Click Next.
Depending on the options you chose, do one of the following:
• When you are changing the root folder, go to Change the Root Folder.
• When you are keeping the current root folder, go to “Complete the Wizard” on
page 24.
Table 7. New study or workbook page parameters
Parameter
Description
Study Name
Creates a new study folder with this name in the root folder
(for example, C:\Xcalibur\QuanRoot).
Workbook Name
Creates a new workbook with this name in the study folder.
Change Study Root
Folder
Changes the root folder for the study. The default root folder
is C:\Xcalibur\QuanRoot\.
Changing the root folder requires authorization from your
administrator.
Open in New Window Opens a new window using the new workbook or study. The
original window remains open.
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Creating a New Study and Workbook
Change the Root Folder
Save the study to a new root folder. The default root folder is C:\Xcalibur\QuanRoot\.
 To specify a new root folder for the study
1. Type the new study root folder name or click Browse to find the folder (Figure 18).
Figure 18. Root folder path page
2. Click Next.
Copy the Files
Select the files you want to copy from the current workbook to the new workbook.
 To copy the files
1. Select the files you want to copy (Figure 19) to the new workbook name (see Table 8).
Figure 19. Copy files page
2. Click Next.
Table 8. Copy files page parameters (Sheet 1 of 2)
Option
Description
Copy Files from
Import Folder
Duplicates the files in the Import folder of the original
workbook.
Note These files are generally archival copies of imported
files.
Copy Files from Export Duplicates the files in the Export folder of the original
Folder
workbook. Copies of reports and exported files are stored
here.
Note These files are generally archival copies of exported
files.
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Creating a New Study and Workbook
Table 8. Copy files page parameters (Sheet 2 of 2)
Option
Description
Copy Files from
Rawfiles Folder
Duplicates the raw files found in the Rawfiles folder of the
original workbook.
Note The raw files are generally files acquired by the
original workbook or raw files that were copied when the
original workbook was created.
Copy Instrument
Method Files
Duplicates up to three instrument method files found in the
original workbook folder: the Startup Method, the
instrument method used for acquisition, and the Shutdown
Method files.
Clear Acquisition
History
Clears the Acquisition Sequence History information from
the workbook. The Acquisition Sequence History is intended
to show how the workbook acquired data. The original
workbook contains this information.
Start New Audit Trail
Creates a new Audit Trail. An Audit Trail entry states that this
workbook was created from another workbook and includes
the original workbook file path.
Note If this check box is cleared, the application copies the
Audit Trail first and makes the creation entry.
Complete the Wizard
To complete the Save As Wizard, click Finish. After you create a new workbook, the
application opens the Instrument Setup window. When you have not created instrument
methods for the configured devices, the application creates default methods.
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Creating a New Study and Workbook
File Tracking Results
For validation purposes, the application keeps track of whether files in a workbook have been
deleted or modified since the last application session with that workbook. If you attempt to
open an existing workbook and a validation-error message about a file-tracking failure
appears, click OK in the message dialog box. The File Tracking Results dialog box opens
(Figure 20). It lists the files in your workbook and flags the files that have been deleted or
modified (see Table 9).
Figure 20. File Tracking Results dialog box
Table 9. File Tracking Results dialog box parameters
Parameter
Description
Highlighting—in the grid
Thermo Scientific
Red highlighting
Signifies that the file has been modified.
Yellow highlighting
Signifies that the file is missing.
Filter
Sets the grid to display only the files that have been deleted or
modified. The button changes to Un-Filter after you click it; click
again to restore the full list of files.
Allow
Opens the workbook if all currently required files are available.
(This item can be configured by the administrator in the
Authorization Manager application.)
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Creating a New Study and Workbook
Workbook Summary Information
Use this dialog box to find information about the current workbook and to enter information
about the current workbook (see Table 10).
To open the Workbook Summary Info dialog box (Figure 21), choose File > Summary Info
from any window.
Figure 21. Workbook Summary Info dialog box
Table 10. Workbook Summary Info dialog box parameters
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Parameter
Description
Header
Displays the workbook creation date and time, the last modified
date and time, the user name of the last person to save the
workbook, and the number of times the workbook has been saved.
Comment
Type or edit information about the active workbook.
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Introduction to the Instrument Setup Window
Introduction to the Instrument Setup Window
Use the Instrument Setup window (Figure 22) to define a set of experimental parameters for
each configured instrument. These parameters include the operating settings for the
instrument (collectively referred to as the instrument method) and any optional instrument
settings to be used before or after the application runs a sequence of samples (startup method
and shutdown method, respectively). The parameters that are displayed in the Instrument
Setup window depend on the instrument that you select in the pane on the left side of the
window. While the application displays different parameters for the different instruments you
are working with, it creates only one instrument method to control the entire system.
Note The Instrument Setup window is not available in the LCquan application for Web
Access.
Figure 22. Instrument Setup window
Instrument setups are specific to each instrument. Refer to your instrument Help for setup
instructions for your instrument.
Each configured device of the LC/MS instrument appears as an icon on the navigation pane
of the Instrument Setup window.
• To open the Device view, click the Device icon.
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Introduction to the Instrument Setup Window
• To open the Help for the device, choose Device Help. This Device Help is independent
of the application Help.
• To open the Help topic for the current page of the Device view, choose Help > Current
View Help or press F1, or if available for the page, click Help. (see Figure 23).
Figure 23. Help for instrument devices
This section contains the following topics:
• Creating Instrument Methods
• Importing an Existing Instrument Method
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Creating Instrument Methods
Creating Instrument Methods
You must configure the instrument before you can define an instrument method. To
configure an instrument, close the LCquan application and Xcalibur data system and choose
Start > All Programs > Thermo Foundation > Instrument Configuration.
 To create an instrument method for the workbook
1. On the navigation pane, click Instruments.
The Instrument Setup window opens.
2. Click Instrument Method if it is not already selected.
3. For each instrument of your LC/MS system, do the following:
a. Open the Instrument Setup view for the instrument by clicking its icon in the
navigation pane (see Figure 24).
The application displays one or more pages of instrument parameters.
b. Make the appropriate entries and selections for each parameter.
Figure 24. Instrument Setup window
Green triangle
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Creating Instrument Methods
 To create a startup method for the workbook
Note The application runs the startup method before it runs the first sample in an
acquisition sequence. No raw file is acquired by this method, and no autosampler
injection takes place.
Use a startup method to equilibrate the LC column. For example, use a startup
method to set the mobile phase conditions to the initial gradient conditions in the
chromatographic method, and if applicable, set the column oven temperature.
1. Open the Instrument Setup window.
2. Click Startup Method.
3. For each instrument that is affected by this method, do the following:
a. Open the Instrument Setup view for the instrument by clicking its icon in the
navigation pane.
The application displays one or more pages of instrument parameters.
b. Make the appropriate entries and selections for each parameter.
 To create a shutdown method for the workbook
Note The application runs the shutdown method after it runs the last sample in an
acquisition sequence. No raw file is acquired by this method, and no autosampler
injection takes place.
Use a shutdown method to set the system to the appropriate idle conditions. For
example, use a shutdown method to turn off the solvent flow from the LC pump and
return the temperature controlled zones to ambient temperature.
1. Open the Instrument Setup window.
2. Click Shutdown Method.
3. For each instrument that is affected by this method do the following:
a. Open the Instrument Setup view for the instrument by clicking its icon in the
navigation pane.
The application displays one or more pages of instrument parameters.
b. Make the appropriate entries and selections for each parameter.
When you create or modify an instrument method, the application automatically saves it
when you leave the Instrument Setup window. The file name is based on the workbook name,
for example, 3 month time point.meth (see Figure 25).
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Importing an Existing Instrument Method
Figure 25. Directory structure for an LCquan study
After you save a method in the workbook, it remains part of the workbook even if the
instrument configuration is changed.
Importing an Existing Instrument Method
Instead of creating a new method, you can import an existing instrument method into your
current workbook. You can use the method as is or you can edit it.
Import an instrument method in one of the following ways:
 To use the New Study or Workbook Wizard
When creating a new workbook, use the New Study or Workbook Wizard to import
instrument methods, acquisition sequences, and processing parameters.
You can import this data from an existing workbook, or import an instrument method
from an individual legacy file (.meth).
See “Creating a New Study and Workbook” on page 13.
 To use the Import Instrument Method File dialog box
Choose File > Import Instrument Method to open the Import Instrument Method File
dialog box.
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Introduction to the Acquisition Window
Introduction to the Acquisition Window
Use the Acquisition window to define an acquisition sequence, run individual samples and
sequences, and monitor real-time data acquisition.
This section describes the features of the following views:
• Using the Setup Sequence View
• Using the Run Sequence Dialog Box
• Using the Status View
Use the navigation pane on the left side of the window to select the view or function.
Using the Setup Sequence View
Use the Acquisition – Setup Sequence view (Figure 26) to modify an acquisition sequence
containing Unknown samples, calibration Standard samples, quality control (QC) samples,
and Blank samples.
Figure 26. Acquisition – Setup Sequence dialog box
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The Acquisition – Setup Sequence view includes the following:
• Acquisition Sequence Header
• Acquisition Sequence History
• Acquisition Sequence Grid
A sequence is a defined set of experiment parameters that define operating settings for a single
sample or list of samples. The acquisition sequence is a list of samples and defined settings
that the application uses to acquire data. The acquisition sequence can contain Unknown
samples, calibration Standard samples, quality control (QC) samples, and Blank samples.
Each sample can be defined by some or all of the following settings:
• Sample type
• File name
• Sample identification
• QC or Standard level
• Internal standard correction amount
• Dilution factor
• Vial position
• Injection volume
• Sample volume
• Sample weight
• Sample name
• Additional user-defined parameters (such as Study, Client, Laboratory)
Each row of the sequence corresponds to one sample injection. You must have an acquisition
sequence to acquire data and a processing sequence to process data. The acquisition sequence
and the processing sequence can be the same. Each sequence has a limit of 5000 samples.
From the Sequence Setup view, you can do the following:
• Create a new acquisition sequence.
• Create a new processing sequence.
• Import, view, and modify an existing acquisition sequence.
• Import, view, and modify an existing processing sequence.
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Using the Setup Sequence View
 To open the Setup Sequence view
When the left navigation pane is displayed:
a. Click Acquisition.
b. Click the Setup icon.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Setup.
Acquisition Sequence Header
The Sequence Header area (Figure 27) displays information about the current sequence,
including user label names (see Table 11), and function buttons for navigating the sequence
grid. Your changes are reflected in the sequence header and in the user-defined columns on
the grid. For an example of user-defined columns and values, see “User-Defined
Columns/Values Examples” on page 53.
Figure 27. Sequence header page
 To modify the sequence user labels
1. To enter comments, type them in the Comment box.
2. Change a User Label name or value:
a. Right-click anywhere on the sequence to display the shortcut menu.
b. Choose User Labels and Values to open the Change Sequence User Labels dialog
box (Figure 28).
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Figure 28. Change Sequence User Labels dialog box
c. Type your label name changes, and select values for those labels.
d. To return to the Sequence view, click OK.
Table 11. Parameters in the Change Sequence User Labels dialog box
Parameter
Description
User Label 1 to 5
Displays information pertinent to the selected sample row in the sequence. Use these boxes
to convey information about this sample to others or as a reminder to yourself.
•
•
•
•
•
User Value 1 to 5
The User Label 1 default name is Study.
The User Label 2 default name is Client.
The User Label 3 default name is Laboratory.
The User Label 4 default name is Company Name.
The User Label 5 default name is Phone.
Displays the value in the header of the acquisition sequence. Use this user-defined box to
convey information about a sample to others or as a reminder to yourself.
The application automatically substitutes certain selected values in the box:
•
•
•
•
•
Thermo Scientific
$Operator substitutes the name of the operator.
$Study substitutes the name of the Study.
$Workbook substitutes the name of the Workbook.
$Workstation substitutes the name of the Workstation.
$Do Not Change prevents the LCquan application from substituting anything in the
box.
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Using the Setup Sequence View
 To view or edit the sequence with the function buttons
Select a row in the sequence grid:
• To move up or move down a row in the sequence, click Prev Row or Next Row.
As you move through the rows, the sequence header information for each sample is
displayed.
• To remove all empty rows in the sequence grid, click Compress.
• To remove all samples from the sequence, click Clear All.
Table 12 describes each of the function buttons.
Table 12. Sequence grid function buttons
Buttons
Description
Highlights the sequence row that precedes the currently highlighted row.
Highlights the sequence row that follows the currently highlighted row.
Deletes all samples from the sequence.
Deletes all empty sequence rows.
Acquisition Sequence History
The Acquisition Sequence History pane displays the history of all sequences (and samples)
acquired by the current workbook along with other relevant information, such as the operator,
start and end times, status, and comment. You can modify the Acquisition Sequence History
pane (see Table 13).
 To populate a sequence from the history to the sequence grid
1. Select a sequence or combination of sequences in the Acquisition Sequence History pane
(Figure 29).
2. Drag the sequence to the Acquisition Sequence grid.
The LCquan application confirms that you want to replace the sequence.
3. Click OK.
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Figure 29. Acquisition Sequence History pane
Table 13. Acquisition Sequence History pane parameters (Sheet 1 of 2)
Parameter
Description
Info
Operator
Displays the login ID of the person who is logged onto the system
and who is acquiring the sequence.
Start Time
Displays the time when the first sample (or startup method)
began.
End Time
Displays the time when the last sample (or shutdown method)
completed. When the application is closed before acquisition is
complete but the acquisition is allowed to complete in the
background, the end time is displayed as “Unknown.”
Comment
Displays a comment about the sequence, as entered in the
Run Sequence dialog box. For more information, see “Run
Sequence dialog box parameters” on page 78.
Status
Displays the sequence status (one of the following):
• Waiting: Created but not yet submitted.
• Submitted: Submitted but not yet validated (data file has not
yet been accepted for acquisition) and not yet running.
• Queued: Submitted and validated.
• In Progress: Currently being acquired.
• Stopped: Stopped either at the request of the operator or
because of an error in acquisition.
• Complete: Successfully completed.
• Rejected: Failed validation; rejected and did not run.
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Table 13. Acquisition Sequence History pane parameters (Sheet 2 of 2)
Parameter
Description
Components
Displays the acquisition component names and their associated level amounts.
Samples
Displays all the sequence row information set at the time of the sample acquisition.
Shortcut Menu
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Show Sequence Items
Collapses the Acquisition Sequence History tree so that only the
first-level items (sequences) are shown.
Show
Info/Level/Sample
Items
Displays second-level items for each sequence in the Acquisition
Sequence History tree. These are Info, Levels, and Samples.
Show
Info/Level/Sample
Details
Displays third-level items for each sequence in the Acquisition
Sequence History tree. These are Info details, Level details, and
Sample details.
Show Info Details
Expands the Acquisition Sequence History tree to show details for
each Info item and collapse all other branches.
Show Level Details
Expands the Acquisition Sequence History tree to show details for
each Level item and collapse all other branches.
Show Sample Details
Expands the Acquisition Sequence History tree to show details for
each Sample item and collapse all other branches.
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Acquisition Sequence Grid
This section describes the functions you can perform from the Acquisition Sequence grid.
• Creating an Acquisition Sequence
• Importing or Copying a Sequence
• Printing or Exporting the Acquisition Sequence
• Modifying a Sequence
• Using the Acquisition Sequence Grid Shortcut Menu
• Editing Column Values from the Sequence Grid
This section includes examples of user-defined columns and definitions of all the Acquisition
Sequence grid columns.
• User-Defined Columns/Values Examples
• Acquisition Sequence Grid Column Parameter Definitions
Creating an Acquisition Sequence
Use the New Acquisition Sequence Wizard to create a new acquisition sequence and
optionally a new workbook or new study folder for the sequence.
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Start the Wizard
Use the New Acquisition Sequence Wizard to create a new acquisition sequence.
 To open the New Acquisition Sequence Wizard
1. Do one of the following:
• When you have a sequence open:
Right-click the acquisition sequence and choose New Acquisition Sequence Wizard
from the shortcut menu (Figure 30).
• When you do not have a sequence open:
In the left navigation pane, click Acquisition.
Figure 30. Welcome page of the New Acquisition Sequence Wizard
2. Click Next.
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Create a Workbook
When you do not want to create a new workbook, click Next on this wizard page and go to
the instructions to “Import an Acquisition Sequence” on page 42.
 To create a new workbook
1. Select the Create a New Workbook check box (Figure 31).
Figure 31. Create a new workbook page
2. Click Next.
Study and Workbook Names
Name the new study or workbook.
 To specify a name for the new study or workbook
1. Type or browse to the new study name (Figure 32).
2. Type or browse to the new workbook name (see Table 14).
3. (Optional) Create a new root folder or open a new LCquan application session in a new
window.
Figure 32. Create new study and workbook page
4. Click Next.
Table 14. Study and Workbook Names parameters
Parameter
Description
Study Name
The LCquan application creates a new folder with this name in the root folder.
Workbook Name
The LCquan application creates a new folder with this name in the Study folder.
Change Project Root
Folder
Select to change the Project root folder. The default root folder is
C:\Xcalibur\QuanRoot\.
Changing the root folder requires authorization from your administrator.
Open in New Window Opens a new LCquan window using the new workbook or study. The original LCquan
window remains open.
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Specify a Root Folder
Specify a root folder for the study. The default root folder is C:\Xcalibur\QuanRoot. When
you are keeping the current root folder, go to Import an Acquisition Sequence.
 To specify the root folder for the study
1. Type the new study root folder name or click Browse to find the folder (Figure 33).
The default root folder is C:\Xcalibur\QuanRoot\.
Figure 33. Root folder path page
2. Click Next.
• To import an acquisition sequence, go to Import an Acquisition Sequence.
• When you are not importing an acquisition sequence, go to Sample Sequence Name.
Import an Acquisition Sequence
When you are not importing an acquisition sequence, ensure that the Base Acquisition on a
Previously Saved File check box is cleared, click Next, and go to Sample Sequence Name.
 To import an acquisition sequence
1. Select the Base Acquisition on a Previously Saved File check box.
Note Ensure the Create a New Workbook check box is cleared on the first page of the
wizard.
2. In the Acquisition Sequence box (Figure 34), enter the sequence name or click Browse to
find the sequence.
Figure 34. Acquisition sequence page
3. Click Next and go to Complete the Wizard on page 52.
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Sample Sequence Name
Specify the base file name and starting sequence number that are used to generate names for
the raw files during a sequence run. The derived names are a concatenation of a base name
and a three-digit incremental number for each sample. For example, if the Base file name is
APN_ and 1 is the starting number, the application creates the new sequence with the first file
name, APN_001.
 To specify the sample sequence names
1. Type the Base file name (Figure 35).
2. Type a starting suffix number.
Figure 35. Sample sequence name page
3. Click Next.
Specify Sample Information
The application generates sample IDs that uniquely identify the unknown samples in the
sequence. The derived names are a concatenation of a sample ID and an incremental number
for each sample.
 To generate sample IDs for the sequence
1. Type the number of unknown samples to include in the new sequence (Figure 36).
Table 15 lists the parameters for the sample information page.
2. Type the number of replicate samples to include in the new sequence.
3. Type an alphanumeric prefix to the sample ID for each sample in the new sequence.
Figure 36. Sample information page
4. Click Next.
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Table 15. Sample information page parameters
Parameter
Description/Condition
Number of Samples
Specifies the number of unknown samples to run. The
total number of unknowns is the number of samples times the
number of injections.
Injections per Sample
Specifies the number of injections to be performed for each
unknown.
Base Sample ID
Sample ID numbering starts at 001.
For example, when you enter AB12, the numbers of the first
five samples are as follows:
•
•
•
•
•
AB12001
AB12002
AB12003
AB12004
AB12005
Specify the Injection Information
The injection information includes the tray type in use; the vial position for each injection,
including whether replicate injections are to be made from the same vial or from different
vials; and the injection volume.
 To specify tray and vial information
1. Click the arrow to display the list of vial tray type options and select one of the vial tray
types (Figure 37).
2. Type the first vial position in the new sequence (see Table 16 on page 46).
Note The vial position notation depends on the autosampler and the tray type in use.
If you are unfamiliar with the vial position notation for your autosampler, use the
alphanumeric and special character entry in the Initial Vial Position box as an
example or check the autosampler documentation.
Figure 37 and Figure 38 show the default Initial Vial Position entries for an Accela
Autosampler with the vial or 96-well microplate tray type in use.
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3. Specify the vial positions for multiple injections of the same sample (Injections per
Sample) and the same calibration level (Number per Level) as follows:
• To specify that multiple injections of samples or calibration levels are to be made
from the same vial, select the Re-Use Vial Positions check box.
• To specify that multiple injections of a sample or a calibration level are to be made
from the different vials, clear the Re-Use Vial Positions check box.
4. Specify the injection volume as follows:
• To use the injection volume that you specified for the autosampler in the instrument
method, select the Injection Volume Obtained from Autosampler Method check
box (Figure 37).
The Injection Volume box becomes unavailable and the Inj Vol column of the
acquisition sequence lists From AS. You cannot modify the injection volume in the
sequence table.
Figure 37. Default initial vial position for an Accela Autosampler
with standard vial trays in use
Tray:Vial
where:
Tray = A–E
Vial = 1–40
• To specify a different injection volume from that in the instrument method, clear the
Injection Volume Obtained from Autosampler Method check box. Then, type an
appropriate volume in the Injection Volume box.
The LCquan application validates the entry against the maximum injection volume
range for the configured autosampler. The application does not use the sample loop
size that is specified in the autosampler configuration to validate this entry, nor does
it use the injection mode that is specified in the instrument method (Figure 38).
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Figure 38. Default initial vial position for an Accela Autosampler
with the 96-well microplate tray type in use
Plate:RowColumn
where:
Plate = A, B, or C
Row = A–H
Column = 1–12
5. Click Next.
Table 16. Tray and vial information page parameters (Sheet 1 of 2)
Parameter
Description
Tray Type
Lists the autosampler tray types. Select the tray type to be
used in the current session. If the currently configured
autosampler does not support multiple trays, a message
confirming this is displayed.
Initial Vial Position
Specifies the first vial position in the new sequence. The vial
position notation depends on the autosampler tray type in
use.
Re-Use Vial Positions
To specify that multiple injections of samples or calibration
levels are to be made from the same vial, select the Re-Use
Vial Positions check box.
To specify that multiple injections of a sample or a calibration
level are to be made from the different vials, clear the Re-Use
Vial Positions check box.
Injection Volume
Obtained from
Autosampler Method
When you select this check box, the application uses the
injection volume specified in the autosampler section of the
instrument method and the Injection Volume box becomes
unavailable. The Inj Vol column of the acquisition sequence
contains the following uneditable entry: From AS.
When you clear this check box, the Injection Volume box
becomes available for you to enter an appropriate injection
volume.
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Table 16. Tray and vial information page parameters (Sheet 2 of 2)
Parameter
Description
Injection Volume
Type an appropriate injection volume for your
chromatographic method.
The ToolTip lists the maximum injection range for the
autosampler. The application does not limit the injection
volume based on the sample loop volume specified in the
instrument configuration or the injection mode specified in
the instrument method.
If applicable, make sure that the injection volume is
compatible with the injection mode specified in the
instrument method and in the autosampler configuration
(sample loop size).
You can edit the user-specified injection volume in the Inj Vol
column of the acquisition sequence.
Initial Vial Position
Specifies the first vial position in the new sequence. The vial
position notation depends on the autosampler tray type in
use.
Specify Calibration Standards
Add calibration standards to the acquisition sequence (see Table 17).
 To add calibration standards
1. Select the Add Standards check box (Figure 39).
Figure 39. Standards information page
2. Select either the Based on Existing Cal Levels from Method or Based on Automatically
Generated Cal Levels option.
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3. If you selected the Based on Automatically Generated Cal Levels option, specify the
number of calibration levels and the calibration level base name.
4. Specify the Number of Injections per Level.
5. (Optional) Select the Add Blanks check box.
6. (Optional) Select the Fill in Sample ID for Standards check box.
When your sequence contains Standard samples, the order used is as follows:
• Optional Blank samples
• First half of the calibration Standard samples
• Optional Blank samples
• Unknown samples
• Optional Blank samples
• Second half of the calibration Standard samples
• Optional Blank samples
7. Click Next.
Table 17. Add Standards page parameters (Sheet 1 of 2)
Parameter
Description
Add Standards
Adds calibration standards to your acquisition sequence.
Based on Existing Cal
Levels from Method
Uses the calibration levels from an existing processing
method.
Based on Automatically Generate names for the calibration levels. The derived names
Generated Cal Levels
consist of a base name concatenated with an incremental
number for each level.
For example, if the base name is Cal and the number of levels
is 5, the calibration levels are named Cal01, Cal02, Cal03,
Cal04, and Cal05.
• Number of Cal Levels
• Cal Level Base Name
Number of Injections
per Level
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Specifies the number of replicate calibration Standard samples
that are to be run at each defined calibration level. The
application groups replicate calibration samples in the new
sequence.
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Table 17. Add Standards page parameters (Sheet 2 of 2)
Parameter
Description
Add Blanks
Adds blank samples s to your sequence. The application places
one blank before and one blank after each series of calibration
standard samples in the new sequence.
Fill in Sample ID for
Standards
Automatically fills in the calibration sample ID in the new
sequence. This information is defined in the processing
method for each calibration standard level.
Add Quality Controls
Add quality control samples to the sequence (see Table 18).
 To add quality controls
1. Select the Add QCs check box (Figure 40).
Figure 40. Add Quality Controls page
2. Select either the Based on Existing QC Levels from Method or Based on
Automatically Generated QC Levels option.
3. (Optional) Select the Add Blanks option.
4. (Optional) Select the Fill in Sample ID for QCs option.
When your sequence contains QC samples, the order used is:
• Optional Blank samples
• First half of the calibration Standard samples
• Optional Blank samples
• QC samples
• Optional Blank samples
• Unknown samples
• Optional Blank samples
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• Second half of the calibration Standard samples
• Optional Blank samples
5. Click Next.
Table 18. Add Quality Controls page parameters
Parameter
Description
Add QCs
Adds quality control samples (QCs) to your acquisition sequence.
Based on Existing QC
Levels from Method
Select this option to use QC levels from an existing processing
method.
Based on Automatically Generates names for the QC levels. The derived names are a
Generated QC Levels concatenate of a base name and an incremental number for each
level.
For example, if the base name is QC and the number of levels is 3,
QC levels are named QC1, QC2, and QC3.
• Number of QC Levels
• QC Level Base Name
Add Blanks
Adds quality control (QC) blanks to your sequence. The LCquan
application places one blank after each series of quality control
samples in the new sequence.
Fill in Sample ID for
QCs
The LCquan application automatically fills in the quality control
(QC) sample ID in the new sequence. This information is defined
in the processing method for each quality control level.
Specify Components Names
Name the components used in the sequence (see Table 19).
 To name the components
1. Select the Use Processing Method Component Names check box (Figure 41).
Figure 41. Processing method component names page
2. Type the number of component names you want to generate.
3. Type component base name.
4. Click Next.
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Table 19. Component names parameters
Parameter
Description
Use Processing Method Use the component names from an existing processing method.
Component Names
Number of
Components
The number of component names you want to generate. The
derived names are a concatenate of a base name and an
incremental number for each component.
For example, if the base name is Component_ and the number of
components is 3, the component names are Component_1,
Component_2, and Component_3.
Component Base
Name
Specifies the component base name.
Specify User Labels
Specify heading labels and displayed values for each user-defined column (see Table 20).
 To specify labels and values
1. Type a label for the column heading in the acquisition sequence header and type a value
for the column or select a macro from the list (Figure 42).
When you select a macro name, the application displays the actual text that corresponds
to the macro name in the Sequence Header. For example, when you select $Workbook,
the application displays the name of the current workbook in the field in the Sequence
Header.)
The values you enter here create the user-defined column headings in your sequence and
specify a static value or macro for each sample in the sequence. These names and values
are displayed at the top of the Acquisition – Setup Sequence view. See “User-Defined
Columns/Values Examples” on page 53.
Figure 42. User labels and values page
2. Click Next.
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Table 20. User labels and values parameters
Parameter
Description
User Label 1 to 5
Displays information pertinent to the active sample row in the
sequence. Use these boxes to convey information about this
sample to others or as a reminder to yourself.
•
•
•
•
•
User Value 1 to 5
The User Label 1 default name is Study.
The User Label 2 default name is Client.
The User Label 3 default name is Laboratory.
The User Label 4 default name is Company Name.
The User Label 5 default name is Phone.
Displays the value in the header of the acquisition sequence. Use
this user-defined box to convey information about a sample to
others or as a reminder to yourself.
The application automatically substitutes certain selected values in
the box:
•
•
•
•
•
$Operator substitutes the name of the operator.
$Study substitutes the name of the Study.
$Workbook substitutes the name of the Workbook.
$Workstation substitutes the name of the Workstation.
$Do Not Change prevents the application from substituting
anything in the box.
Complete the Wizard
To complete the New Acquisition Sequence Wizard, click Finish.
The LCquan application creates a new acquisition sequence and displays it in the Acquisition
– Setup Sequence view. See “Using the Setup Sequence View” on page 32.
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User-Defined Columns/Values Examples
• Example 1
• Example 2
Example 1
This example shows a set of custom columns and values for Client One at the San Jose Lab as
they would appear on the Setup Sequence view.
These are the user labels and values you specified on the Change Sequence User Labels dialog
box or the equivalent page on a wizard.
The user labels and values are displayed in the setup sequence header area.
The user labels and values are reflected in the user-defined columns in the sequence grid.
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Example 2
This example shows a set of custom columns and values for a New Client at the West Palm
Beach Lab as they would appear on the Setup Sequence view.
These are the user labels and values you specified on the Change Sequence User Labels dialog
box or the equivalent page on a wizard.
The user labels and values are displayed on the setup sequence header area.
The user labels and values are reflected in the user-defined columns in the sequence grid.
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Importing or Copying a Sequence
When an imported acquisition sequence is also used as the processing sequence, the level
names must match those defined in the processing method:
• When the calibration or quality control level names in the sequence are different from
those in the processing method, the LCquan application displays the Standard Level
Names Association dialog box of the QC Level Names Association dialog box. Use these
dialog boxes to associate the level names in the sequence with the level names in the
processing method.
• When the imported sequence contains calibration or QC levels but the processing
method does not, the LCquan application displays a warning box to inform you and then
displays the Sample Type Assignment dialog box. Change the sample type of these
samples to Unknown in the processing sequence or discard the samples that have these
levels in the processing sequence.
There are several ways to import or copy an acquisition sequence:
 To drag and drop sequences from the Acquisition Sequence History pane
The acquisition sequence history lists all acquisition sequences in the workbook that were
submitted to the acquisition queue.
1. Select one or more of these sequences and drag them into the sequence grid.
2. Hold down the CTRL key to select multiple sequences.
The application confirms that you want to replace the current sequence. You cannot copy
an individual sample; you can copy only an entire sequence.
 To use the shortcut menu
• Choose Import Acquisition Sequence > From File and use the dialog box to find a
sequence file.
–or–
• Choose Import Acquisition Sequence > Copy from Processing Sequence.
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 To copy the processing sequence in the current workbook
From the window File menu or the shortcut menu, choose Import Acquisition
Sequence > Copy From Processing Sequence.
The application asks if you want to modify the user labels and values of the imported
sequence. Keep the current user-defined labels and values or create new ones for the
sequence.
• If you click No, the application overwrites your acquisition sequence with the
imported processing sequence without keeping your user-defined columns and
values.
• If you click Yes, the Change Sequence User Labels dialog box opens.
See “Parameters in the Change Sequence User Labels dialog box” on page 35.
When you complete the Change Sequence User Labels dialog box, the application
overwrites your acquisition sequence with the imported processing sequence.
 To import an acquisition sequence from a file
From the window File menu, choose Import Acquisition Sequence > From File.
Printing or Exporting the Acquisition Sequence
Print the acquisition sequence grid or export the sequence information to an .sld file.
 To print the acquisition sequence
Choose File > Print Sequence Info.
The Print dialog box opens where you select the format of the printing output.
 To export the acquisition sequence
1. Choose File > Export Acquisition Sequence.
The LCquan acquisition sequence dialog box opens.
2. Type a name for the sequence file. Do not enter a path or an extension.
The extension defaults to .sld, and the LCquan application creates a copy of the file in the
Exports folder for the workbook.
Modifying a Sequence
Use keyboard keys and the acquisition sequence grid shortcut menu to modify the sequence.
See “Using the Acquisition Sequence Grid Shortcut Menu” on page 58.
 To select rows and cells by using the arrow keys
1. Click the grid to make it active.
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2. Use your keyboard up and down arrow keys to highlight a row.
Use the right and left arrow keys to highlight a cell.
Highlighted rows are not selected. You must click the number of the row to select the row.
 To insert rows in the grid
1. Select the row in the sequence below where you want the new row (sample) to be located.
2. Right-click the sequence and choose Insert Rows.
An empty row is added above the selected (or highlighted) row.
 To duplicate rows in the grid
1. Select the rows in the sequence that you want to duplicate.
2. Right-click the sequence and choose Duplicate Selected Samples.
The selected rows are copied and added to the end of the sequence.
 To move rows
1. Select the row in the sequence below where you want the row (sample) to be moved.
2. Right-click the sequence and choose Insert Rows.
An empty row is added above the selected (or highlighted) row.
3. Select the row you want to move.
4. While holding the mouse button down on the selected rows (in the row number column),
drag your cursor to the location in the grid above the empty row you added.
5. Release the mouse button.
6. The selected row overwrites the empty row.
When you move a row, it leaves an empty row behind.
7. Click Compress to remove all empty rows.
 To delete rows
1. Select the entire row or rows that you want to delete:
• To select a series of rows, position the cursor over the starting row number and drag
the cursor over the rows.
• Use the CTRL key to select non contiguous rows.
2. Press DELETE, or right-click the sequence and choose Delete Rows from the shortcut
menu.
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Using the Acquisition Sequence Grid Shortcut Menu
You can perform many functions from the shortcut menu (Figure 43). Some of these
commands are also found on the window menus, and others are unique to the shortcut menu.
Figure 43. Acquisition Sequence Grid shortcut menu
• Fill Down fills sequential rows with duplicate or sequential values.
• Sort reorders the rows in the sequence.
• Columns customizes column arrangement.
• User Labels and Values changes user labels and values.
• Standard and QC Levels changes or imports calibration and QC levels.
• Get Injection Volume from AS uses an autosampler injection volume.
• Insert Rows inserts rows in the grid.
• Delete Rows deletes rows from the grid.
• Duplicate Selected Samples duplicates rows in the grid.
• Import Acquisition Sequence imports an acquisition sequence.
• New Acquisition Sequence Wizard creates a new acquisition sequence.
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Fill Down
Use the Fill Down command to fill sequential rows with duplicate or sequential values (see
Table 21).
 To fill sequential rows
1. Choose Fill Down to open the dialog box (Figure 44).
2. Select the columns whose data you want to duplicate.
3. Specify the rows that you want to fill.
For example: Fill From Row 1
To Row 10
4. Specify the number of the row you want to duplicate.
For example: Using Row 1
5. Click OK.
The LCquan application duplicates or appropriately sequences column entries.
Figure 44. Fill Down dialog box
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Table 21. Fill Down dialog box parameters
Parameter
Description
Select Columns
See “Acquisition Sequence Grid Column Parameter Definitions”
on page 70 for descriptions of all column names and values.
Row Controls
Fill From Row
Specifies the first row to receive new data.
To Row
Specifies the last row to receive new data.
Using Row
Specifies which row the initial data comes from.
Create Samples in
Selected Empty Rows
During Fill Down
Specifies that a new sample be created in an empty row during a
fill down that includes the row in its fill down range. When not
selected, specifies that the empty row is ignored during a fill down
that includes the row in its fill down range.
Buttons
Selects all the check boxes in the Select Columns area.
Clears all the check boxes in the Select Columns area.
Sort
Use the Sort command to reorder the rows in the sequence (see Table 22).
 To reorder a sequence
1. Choose Sort to open the Sort Sequence dialog box (Figure 45).
Figure 45. Sort Sequence dialog box
2. Select the columns on which to sort and reorder the sequence.
3. Select to sort in ascending (1-to-n) or descending (n-to-1) order. The default is ascending.
Note To prevent any sorting from occurring, select <none> in all three sort order
fields.
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Table 22. Sort Sequence dialog box parameters
Parameter
Description
Sorting Options
The following sorting options are applicable to all three sort orders.
Thermo Scientific
File Name
Sorts the list so the file names are in alphabetical order.
Level Name
Sorts the list so the calibration standard and QC level names are in
alphabetical order.
Sample ID
Sorts the list so the sample IDs are in alphabetical or numerical
order.
Sample Type
Sample types are not sorted alphabetically. In ascending order, the
types are: Standards, QCs, Blanks, and Unknowns.
First Order
Specifies the first order of sorting for the sequence. For the
LCquan application, the default first order of sorting is by sample
type.
Second Order
Specifies the second order of sorting for the sequence.
Third Order
Specifies the third order of sorting for the sequence.
Sort in Descending
Order
The LCquan application sorts the list in descending (n-to1) order.
Clear this option to have the LCquan application sort the list in
ascending order.
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Columns
Use the Columns command to customize the column arrangement (see Table 23).
 To customize column arrangement
1. Choose Columns to open the Column Arrangement dialog box opens (Figure 46).
Figure 46. Column Arrangement dialog box
2. To hide currently displayed columns, select the check box before the column and click
Remove.
This does not delete the column; it simply hides it from display on the sequence grid. All
hidden columns are displayed in the Available Columns list.
3. To display currently hidden columns, select the check box before the column and
click Add.
The column is added to the Displayed Columns list and is displayed on the sequence
grid.
4. To change a column position:
a. Select the check box before the column name in the Displayed Columns list.
b. To move the column left in the grid, click Move Up.
c. To move the column right in the grid, click Move Down.
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5. To change the display precision:
a. In the Places column of the Displayed Columns list, select the value you want to
change.
b. Type a new value for the number of decimal places to display in the column.
Note When the Values column is unavailable, your LCquan administrator has
specified decimal rounding for exported Microsoft Excel™ reports. In this case,
the number of decimal places is fixed and cannot be edited.
6. To change a column width:
a. In the Width column of the Displayed Columns list, select the value you want to
change.
b. Type the new value.
Tip To resize a column width, drag the column boundary in the heading row of
the sequence grid.
7. To change an item name:
a. In the Item column of the Displayed Columns list, select the item name you want to
change.
b. Type the new name.
8. To reset column values, click Factory Defaults.
There is no “undo” for this function.
Table 23. Column Arrangement dialog box parameters
Thermo Scientific
Parameter
Description
Available Columns
Lists parameters that are not currently selected for display.
Displayed Columns
Lists currently selected parameters that appear in the data grids.
Add / Remove
Displays / Hides selected columns.
Move Up /
Move Down
Move Up moves columns left in the grid.
Move Down moves columns right in the grid.
Factory Defaults
Resets original column values as described in “Grid parameters”
on page 394 in Chapter 6, “Processing the Raw Files and
Reviewing the Analytical Results.”
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User Labels and Values
Use the User Labels and Values command to change user labels and values. For details about
the parameters, see “Parameters in the Change Sequence User Labels dialog box” on page 35.
For an example of how the user labels and values are displayed in the sequence grid, see
“User-Defined Columns/Values Examples” on page 53.
 To change user labels and values
1. Choose User Labels and Values to open the Change Sequence User Labels dialog box
opens.
2. Type your label name changes.
3. Select variable values or type static values.
4. Click OK.
All rows in the sequence reflect the changes.
Standard and QC Levels
Use the Standard and QC Levels command to change or import calibration and QC levels
(see Table 24 on page 66).
 To change or import calibration and QC levels
1. Choose Standard and QC Levels.
The Acquisition Levels dialog box opens (Figure 47 on page 66). Use this dialog box to
modify calibration levels and QC levels specified for the Standard and QC samples in the
acquisition sequence. You can also import component names and calibration levels from a
processing method into the acquisition sequence (step 7).
2. Edit the component list:
• To add a component, enter the name into the empty row at the end of the
component list.
• To delete a component, click the row number and press DELETE.
• To rename a component, select the component name and enter a new name.
3. Edit the calibration levels list for the selected component:
• To add a calibration level, enter the name into the empty row at the end of the Cal
Level list.
• To delete a calibration level, click the row number and press DELETE.
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• To rename a calibration level, select the level name and enter a new name.
Note When the Cal Level list is empty and the sequence contains some samples
with Standard or QC sample type, the Sample Type Assignment dialog box opens
when you click OK in this dialog box. You can change the sample type of these
samples to Unknown in the processing sequence or discard the samples that have
these levels in the processing sequence.
• To enter a calibration amount, enter the appropriate level in the Amount box.
4. Edit the QC levels for the selected component:
• To add a QC level, enter the name into the empty row at the end of the QC Level
list.
• To delete a QC level, click the row number and press DELETE.
• To rename a QC level, select the level name and enter a new name.
• To edit a QC amount, enter the appropriate level in the Amount box.
5. To display the shortcut menu, right-click the Acquisition Levels dialog box.
From the shortcut menu, you can
• Copy current component levels to all target components
• Load default levels for current component
• Import processing components
6. To replace the current levels with the defaults stored in the registry, click Load Default
Levels.
7. To import component names and calibration levels from the processing method, click
Import Processing Components, or right-click and choose Import Processing
Components from the shortcut menu.
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Figure 47. Acquisition Levels dialog box
Table 24. Acquisition Levels dialog box parameters (Sheet 1 of 2)
Parameter
Description
Components
Component 1–n
Lists the components in the sequence.
Levels – Cal Level
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Cal Level
Displays calibration levels for the selected component. The
LCquan application can accommodate up to 50 calibration levels.
Amount
Displays the amounts of the target compound used for each
calibration level.
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Table 24. Acquisition Levels dialog box parameters (Sheet 2 of 2)
Parameter
Description
Levels – QC Level
QC Level
Displays the QC (quality control) levels for the selected
component. Use QC samples containing known amounts of a
component to help ensure the accuracy of an analysis. The
LCquan application measures the quantity of the QC component
in the same manner as for unknown components. The measured
quantity is then compared with a user-defined expected quantity
and a user-defined percent test.
Value: up to 15 QC levels
Amount
Displays the amounts of the target compound used for each QC
(quality control) level.
%Test
Displays a value for the acceptable difference (as a percentage)
between the known amount and calculated (measured) amount of
each QC level.
Shortcut Menu
Copy Current
Copies the current Calibration Levels and QC Levels tables to all
Component Levels to other target components.
All Target Components
Load Default Levels for Loads the default level tables for the current component.
Current Component
Import Processing
Components
Imports the component names and levels tables from the
processing method. Functions exactly the same as the Import
Processing Components button.
Buttons
Thermo Scientific
Import Processing
Components
Imports the component names and levels tables from the
processing method. Functions exactly the same as the Import
Processing Components menu command.
Load Default Levels
Loads the default level tables for the current component, replacing
the current levels with the defaults stored in the registry. The
defaults are set on the calibration page, as described in “Specifying
Method Calibration” on page 242 and in Chapter 4, “Creating a
Processing Method.”
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Get Injection Volume from AS
Use the Get Injection Volume from AS command to use the default injection volume for the
autosampler in the instrument method.
 To use an autosampler injection volume
Select Get Injection Volume from AS.
This sets the currently selected row to get an injection volume from the instrument
method at run time (instead of from the Inj Vol column of the sequence list), using the
default injection volume that you set for the autosampler. The Inj Vol column value
displays “From AS” in place of a numeric value.
Insert Rows
Use the Insert Rows command to insert rows in the grid.
 To insert rows in the grid
1. Select the rows in the sequence below where you want the new rows (samples) to be
located.
2. Right-click the sequence and choose Insert Rows.
Empty rows are added above the selected (or highlighted) rows. The LCquan application
adds as many empty rows as the number of selected rows.
Delete Rows
Use the Delete Rows command to delete rows from the grid.
 To delete rows from the grid
1. Select the row in the sequence that you want to delete.
2. Right-click the sequence and choose Delete Rows.
Duplicate Selected Samples
Use the Duplicate Selected Samples command to duplicate rows in the grid.
 To duplicate rows in the grid
1. Select the rows in the sequence that you want to duplicate.
2. Right-click the sequence and choose Duplicate Selected Samples.
The selected rows are copied and added to the end of the sequence.
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Import Acquisition Sequence
Use the Import Acquisition Sequence command to import a sequence from a file or the
processing sequence.
 To import an acquisition sequence
• From the shortcut menu, choose Import Acquisition Sequence > From File and use the
dialog box to find a sequence file.
–or–
• From the shortcut menu, choose Import Acquisition Sequence > Copy from
Processing Sequence.
The LCquan application asks if you want to modify the user labels and values of the
imported sequence. Keep the current user-defined labels and values or create new ones for
the imported sequence.
–
If you click No, the LCquan application overwrites your acquisition sequence with
the imported processing sequence without keeping your user-defined columns and
values.
–
If you click Yes, the Change Sequence User Labels dialog box opens.
See “Creating an Acquisition Sequence” on page 39.
When you complete the Change Sequence User Labels dialog box, the LCquan
application overwrites your acquisition sequence with the imported processing sequence.
New Acquisition Sequence Wizard
Use the New Acquisition Sequence Wizard command to open the wizard and define a new
sequence.
 To create a new acquisition sequence
Choose New Acquisition Sequence Wizard.
See “Creating an Acquisition Sequence” on page 39.
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Acquisition Sequence Grid Column Parameter Definitions
Table 25 defines the available columns for the acquisition sequence grid.
Table 25. Acquisition sequence grid column parameters (Sheet 1 of 3)
Parameter
Description
Sample Type
Displays the type of sample described by the sequence row. The
sample type defines how the LCquan application processes the
sample data. Each sample must be classified as one of the
following sample types:
•
•
•
•
FileName
Unknown
Blank
QC (quality control)
Standard
Displays the name of the raw file that contains the sample data.
The file name is a combination of the base file name prefix
assigned to the sequence and a sequential sequence number.
When the default sequence starting number 1 was not changed,
the suffix number is the same as the row number of the sequence:
001, 002, and so on.
When the default sequence starting number was changed to
another number, the first sample has the starting number and
subsequent rows in the sequence are incremented by 001. For
example, if the starting number was 100, the file name for the first
sample would have a suffix of 100, the second sample would have
a suffix of 101, and so on.
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Table 25. Acquisition sequence grid column parameters (Sheet 2 of 3)
Parameter
Description
Sample ID
Displays the sample ID for each data file. The sample ID is an
alphanumeric string of characters that identifies a sample.
Level
Indicates the level defined for a calibration sample or quality
control sample.
ISTD Corr Amt
Specifies an updated amount of internal standard for the
corresponding sample. The default value is 0.0.
For each component defined as an internal standard, a bulk
adjustment factor can be applied to the base response of each
internal standard defined in the processing method. When no
adjustment is required, verify that a value of 0.000 is entered in
the ISTD Corr Amt box. When an adjustment is required, enter
the actual value of all internal standard amounts or concentrations
in the sample into the ISTD Corr Amt box for the sample row or
rows requiring adjustment.
The new value entered must use the same units as specified in the
processing method. Do not enter the units of measurement into
the box. For example, for 20 ng, type 20.
Dil Factor
Displays the dilution factor used to prepare the sample. The valid
range is 0.000 to 10 000.000. The LCquan application interprets
a value of 0.000 as no dilution.
When you have specified a processing method for the current
sequence, the LCquan application automatically enters the Dil
Factor value from the processing method settings.
Vial Pos
Displays the sample’s position in the autosampler. This value can
be numeric, alphanumeric, and can use symbols.
Inj Vol
Displays the injection volume in microliters of sample to be
injected.
When you are using an autosampler, you can set the default
injection volume in the Autosampler dialog box in the Instrument
Setup window. The minimum and maximum injection volumes
that you can use depend upon the Autosampler you select. The
usable range is dependent upon the injection mode and might be
smaller than the range displayed in the status bar. For more details,
consult your Autosampler manual.
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Table 25. Acquisition sequence grid column parameters (Sheet 3 of 3)
Parameter
Description
Sample Vol
Displays the volume of a component that has been placed in the
sample. The unit for this volume is specified in the Xcalibur
Processing Setup window and is included only in the LCquan
application reports. The LCquan application does not convert
units.
When you have specified a processing method for your sequence,
the LCquan application automatically enters the sample volume of
the Calibration samples, QC samples, or both from the processing
method settings.
Sample Wt
Displays the amount of a component that has been placed in the
sample. The unit for this sample weight is specified in the
Xcalibur Processing Setup window and is included only in the
LCquan application reports. The LCquan application does not
convert units.
When you have specified a processing method for your sequence,
the LCquan application automatically enters the sample weights
of the calibration samples, QC samples, or both from the
processing method settings.
Sample Name
Displays the sample name that you specified when you created the
sequence.
Comment
Displays the comment entered for this sample.
Barcode
Displays the barcode for this sample.
Fill Down cannot be used on Barcode column values.
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Barcode Status
Displays the status of the barcode reading.
User Columns
1–5
(User-defined) Displays information pertinent to the active
sample row in the acquisition sequence. Use these columns to
convey sample information to others or as a reminder to yourself.
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Using the Setup Sequence View
Editing Column Values from the Sequence Grid
There are several ways to change column values from the sequence grid:
 To change a sample type
1. Click the cell in the Sample Type column (Figure 48).
Figure 48. Sample Type column
2. Select from the list of sample type options.
 To change a file name
1. Click the cell in the File Name column.
2. To open a dialog box where you can select a new file, click the arrow.
3. Navigate to the new file, select it, and click Open.
 To change a calibration level
1. Click the cell in the Level column (Figure 49).
Figure 49. Level column
2. Select from the list of calibration levels.
 To change an ISTD correlation amount
1. Click the cell in the ISTD Corr Amt column.
2. Highlight the text and type over it.
 To change the dilution factor
1. Click the cell in the Dil Factor column.
2. Highlight the text and type over it.
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 To change the vial position
1. Click the cell in the Vial Pos column.
2. Highlight the text and type over it.
 To change the injection volume
1. Click the cell in the Inj Vol column.
2. Highlight the text and type over it.
3. When you are using an autosampler, set the default injection volume in the Autosampler
dialog box in the Instrument Setup window.
 To change the sample volume
1. Click the cell in the Sample Vol column.
2. Highlight the text and type over it.
 To change the sample weight
1. Click the cell in the Sample Wt column.
2. Highlight the text and type over it.
 To change the sample name
1. Click the cell in the Sample Name column.
2. Highlight the text and type over it.
 To change user-defined column values
1. Right-click the grid and choose User Labels and Values.
The Change Sequence User Labels dialog box opens.
2. Edit the values and click OK.
For details about the parameters, see “Parameters in the Change Sequence User Labels
dialog box” on page 35. For an example of how the user labels and values are displayed in
the sequence grid, see “User-Defined Columns/Values Examples” on page 53.
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Tray Selection
Use the Tray Selection dialog box to select the autosampler tray type to be used in the current
session. If the currently configured autosampler does not support multiple trays, a message
confirming this is displayed.
The selected tray is used to validate sequence vial positions.
 To open this dialog box
Choose Change > Tray Name.
The Tray Selection dialog box lists autosampler tray types available for use in the current
session.
Using the Run Sequence Dialog Box
Use the Run Sequence dialog box to select acquisition options and processing actions for the
acquisition sequence (see Table 26 on page 78). You can run one sample or a sequence of
samples.
After you have created your acquisition sequence, click the Acquire icon in the navigation
pane to open the Run Sequence dialog box. Use this dialog box to run one sample or a
sequence of samples and select acquisition options and processing action options for the
acquisition sequence.
 To open the Run Sequence dialog box
When the left navigation pane is displayed:
a. Click Acquisition.
b. Click the Acquire icon.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Acquire.
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 To run a series of samples in the current acquisition sequence
1. In the Run Rows box, enter the range of row numbers of the samples that you want to
run (Figure 50).
Figure 50. Run Sequence dialog box
2. To add a comment to the acquisition sequence, enter your text in the Comment box.
The comment will appear for this run in the Acquisition Sequence History.
3. Specify the instruments that you want to run your samples:
a. Click Change Instruments to open the Change Instruments In Use dialog box.
b. To specify the instruments that you want to use and the start instrument for the
current acquisition sequence, click the In Use and Start Instrument columns. Yes
appears in the column to indicate that the instrument is selected.
c. Click OK to save changes and close the dialog box.
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4. Specify whether or not to start the acquisition when the instruments are ready:
• When you want the LCquan application to start the data acquisition automatically
and perform an autosampler injection as soon as all instruments are ready, select the
Start When Ready check box.
• When you want the LCquan application to pause the acquisition sequence after all
the devices are ready, clear the Start When Ready check box. You must manually
start the acquisition by using the control buttons in the Status view of the Acquisition
window.
5. Specify the processing actions:
• When you want the LCquan application to automatically process the data after it is
acquired, select the Process after Acquisition check box.
Note For the LCquan application to automatically process the data after it is
acquired, a processing method must already be defined and the acquisition
component names must match the processing component names.
When you want to have the LCquan application automatically print Sample Reports
and Summary Reports after the data is processed, select the Generate Selected
Reports check box.
• When you do not want the LCquan application to automatically process the data
after it is acquired, clear the Process after Acquisition check box.
6. Specify any optional startup or shutdown instrument methods:
• When you want the startup method to run before the sequence starts, select the Use
Startup Method check box.
• When you want the shutdown method to run after the sequence is completed, select
the Use Shutdown Method check box.
7. Specify any optional pre-acquisition or post-acquisition programs:
a. In the Pre-Acquisition box, specify the program to run prior to running the sequence.
Use the Browse button to find the program.
b. In the Post-Acquisition box, specify the program to run after the sequence is
completed. Use the Browse button to find the program.
8. To synchronously run the pre- or post-acquisition programs:
a. Select the Pre-Acquisition check box.
b. Select the Post-Acquisition check box.
By default, these programs run asynchronously (in parallel) with data collection.
9. Specify the status of the system after data acquisition by selecting one of the After
Sequence Set System options: On, Standby, or Off. “On” is the default setting.
10. Click OK to save the settings and close the dialog box.
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When you acquire data, the LCquan application requires that you save the workbook.
The LCquan application places the selected samples at the end of the acquisition queue
and opens the Status view of the Acquisition window.
Table 26. Run Sequence dialog box parameters (Sheet 1 of 4)
Parameter
Description
General Controls
User
Displays the name of the operator who ran the acquisition
sequence. This box is non editable.
Run Rows
The list of rows must be consecutive. For example, you can run
samples 1 through 10 by using the Run Sequence dialog box only
one time. However, to run samples 1 through 3 and samples 5
through 10, you must use the Run Sequence dialog box twice.
The first time, select samples 1 through 3; the second time, select
samples 5 through 10.
Comment
(Optional) A comment that identifies the sequence. The
comment appears in the Acquisition Sequence History.
Instrument
Displays all the instruments that have been configured for
operation as LCquan application devices. Shows “In Use” status in
the Change Instruments In Use dialog box, in a read-only list.
Start Instrument
This read-only list can have either one “Yes” in one of the
instrument rows or all blanks in all instrument rows (no “Yes”
entries).
Start When Ready
Automatically begins (the LCquan application performs an
autosampler injection) acquisition when all devices are ready.
When you clear this check box, the sequence waits until all devices
are ready and pauses so you can check device statuses. To continue
the acquisition, click Start in the Status view of the Acquisition
window. See “Using the Status View” on page 83.
This ability to pause is useful if any external equipment is in use
that cannot return status to the LCquan application. This feature
applies only to the first sequence row.
Change Instruments
Opens the Change Instruments In Use dialog box where you can
change the status of instruments in use or select a different start
instrument. See “Change Instruments Dialog Box” on page 81.
Processing Actions
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Process After
Acquisition
Specifies that the LCquan application runs the processing
sequence at the end of data acquisition.
Generate Selected
Reports
Specifies that the LCquan application creates reports
automatically after data acquisition and processing completion.
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Table 26. Run Sequence dialog box parameters (Sheet 2 of 4)
Parameter
Description
Instrument Method
Use Startup Method
Specifies that the LCquan application runs the (optional) startup
method before the sequence starts. No raw file is acquired by this
method, and no autosampler injection takes place. This feature is
not available for all devices.
Use Shutdown Method Specifies that the LCquan application runs the (optional)
shutdown method after the sequence has completed. No
autosampler injection takes place. This feature is not available for
all devices.
Programs
Pre-Acquisition/
Browse
Displays the current Pre-Acquisition program (.exe or .bat
program) that runs before data acquisition for every sequence row.
Post-Acquisition/
Browse
Displays the current Post-Acquisition program (.exe or .bat) that
runs after data acquisition for every sequence row.
Run Synchronously
Pre-Acquisition
Specifies that the Pre-Acquisition program displayed in the
Pre-Acquisition box runs synchronously (in series). The
Run Manager waits until the Pre-Acquisition program can be run
prior to data acquisition. For example, when you want to switch
the divert valve before a run, you can select a synchronous
Pre-Acquisition program.
By default, the program runs asynchronously (in parallel) with
data collection. For example, you can use the XConvert.exe
program to perform file conversions from one data type to another
data type during processing.
Post-Acquisition
Specifies that the Post-Acquisition program displayed in the
Post-Acquisition box runs synchronously (in series) with data
collection. The Run Manager waits until the Post-Acquisition
program can be run after data acquisition. For example, when you
want to convert data from one data type to another data type
while you are acquiring data, you can select a synchronous
Post-Acquisition program.
By default, the program runs asynchronously (in parallel) with
data collection. For example, you can perform operations that do
not involve taking data.
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Table 26. Run Sequence dialog box parameters (Sheet 3 of 4)
Parameter
Description
[Optional Macro
Arguments]
You can use macro arguments when entering the run arguments.
Supported macro arguments and their replacements:
• %R : Provides the current raw file.
• %I : Provides the instrument method name.
• %S : Provides the sequence name.
• %V : Provides the vial (or well) number in the Position
column of the sequence.
• %% : Provides a single % character in the run line.
After Sequence Set System
On
Keeps the system in the On state when the current sequence is
completed. When On is selected, you can run another sequence
without waiting. All power and flows are maintained at
operational levels. Default: On
Note This option has the same effect as choosing
Actions > Devices On.
Standby
Keeps the system in the Standby state when the current sequence
is completed. When you select Standby, you can run another
sequence with only a short delay between runs.
Some devices do not have a Standby feature. For devices with this
feature, a power-saving or consumable-saving mode is entered,
and the devices can be switched back on in approximately
15 minutes or less. Depending the instrument, this state turns gas
and liquid flows to Off, but maintains heaters and other
subsystems in an On state so that there is no warm-up time
required when you change from Standby to On.
Note This option has the same effect as choosing
Actions > Devices Standby.
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Table 26. Run Sequence dialog box parameters (Sheet 4 of 4)
Parameter
Description
Off
Keeps the system in the Off state when the current sequence is
completed. The Off state indicates that all power to the
instrument, which can be controlled by the LCquan application,
is turned Off. This includes power to all heaters and most
subassemblies, but in some cases not all subassemblies.
Some devices do not have an Off feature. For devices that do have
this feature, a power-saving or consumable-saving mode is entered
and you can switch the devices back on in an undetermined time.
When several sequences are queued, the power setting of the last
submitted sequence is used.
Note This option has the same effect as choosing
Actions > Devices Off.
CAUTION The Off state does not guarantee that all voltages are
turned off nor does it indicate that all heated components are at
room temperature. To perform maintenance on an instrument,
refer to the hardware manual for your instrument.
Change Instruments Dialog Box
Use the Change Instruments In Use dialog box to change the status of instruments in use or
select a different start instrument (see Table 27).
 To select the instruments used to run the current acquisition sequence
1. From the Run Sequence dialog box, click Change Instruments.
The Change Instruments In Use dialog box opens (Figure 51).
Figure 51. Change Instrument In Use dialog box
2. Click the In Use or Start Instrument fields to activate the instrument with Yes for On.
3. Click OK to save changes and close the dialog box.
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Table 27. Change Instruments In Use dialog box parameters
Parameter
Description
Instrument list
Displays all the instruments that have been configured for operation as LCquan application
devices.
In Use list
The rows in this list display a Yes or a blank space to indicate whether or not the instrument
displayed in the same row is In Use (Yes) or Not In Use (a blank space). When you configure
an instrument using the Instrument Configuration window, the default status of the
instrument is In Use, Yes. When you do not want to use an instrument for the current
sequence, click the In Use Yes entry to change it to a blank space. Instruments with a blank
space in the In Use row are not available for the current sequence.
For example, if a sample is to be manually injected by syringe into a mass spectrometer or
MS detector, the In Use entries for all instruments, except the mass spectrometer or MS
detector, must show blank spaces.
All instruments to be used for the sequence that you are about to submit for processing must
display In Use Yes.
Note The Automatic Devices On command in the Actions menu applies only to In Use
devices.
Start Instrument list
Note This list has either one Yes in one of the instrument rows or all blanks for all
instrument rows (no Yes entries).
 To add an instrument to the instruments list
1. Close all running Thermo Scientific applications.
2. From the Windows taskbar, choose Start > All Programs > Thermo Foundation >
Instrument Configuration to open the Instrument Configuration window.
3. Select and configure the instrument you want to add.
4. From the Run Sequence dialog box, click Change Instruments.
The newly configured instrument appears on the Instrument list.
 To specify the Start Instrument
1. From the Run Sequence dialog box, click Change Instruments.
2. Click the Start Instrument list in the row of the instrument you want to be the “start”
instrument.
The blank space changes to display a Yes.
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The autosampler is usually selected to be the start instrument because this is the
instrument that controls when a run starts. In this case, all instruments to be used for the
sequence submission, including the autosampler, display In Use Yes. This means they are
waiting for a contact closure event to start operation. When this status has been achieved
by all devices used in the run, the start instrument initiates the run.
Using the Status View
The Status view of the Acquisition window (Figure 52) provides a real-time display of the data
acquisition. Use the Status view to monitor data acquisition and display chromatograms and
mass spectra in real time (Table 28 on page 85).
Figure 52. Status view of the Acquisition window
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The following topics provide information about the Status view of the Acquisition window:
• Using the Status View Control Buttons
• Acquisition – Status – Chromatogram Pane
• Acquisition – Status – Spectrum Pane
• Acquisition – Status – Run Status
• Acquisition – Status – Acquisition Queue
• Acquisition – Status – Acquisition History
• Processing Data While Continuing to Acquire Data
The Status view of the Acquisition window contains the following:
• A set of control buttons
• The Run Manager status that provides a summary of the acquisition progress. It lists the
sequence and sample information and the readback status of each configured instrument.
• The Instrument status that provides the complete readback status of each configured
instrument.
• The Acquisition queue that displays all the sequences that have been submitted for
acquisition, including those for other workbooks.
The sequences and their individual sequence rows are organized in a tree view. Each row
of the tree view contains a check box to indicate when it is selected or not selected.
• The Acquisition Sequence history that lists all acquisition sequences in the workbook that
were submitted to the acquisition queue. It provides information about each sequence,
including the operator, the start and end times, comments, and the status of the sequence,
and the calibration and QC level data. While the LCquan application is acquiring data,
the history is dynamically updated with samples that have been fully acquired. To display
the history, click the Acquisition History tab.
• The Chromatogram pane, where you can monitor chromatograms for each of the defined
components, plus up to ten user-defined chromatograms in real time (up to five are
visible at one time). It can also display data from an existing raw file.
• The Spectrum pane, where you can monitor the mass spectrum in real time or view the
mass spectrum of a selected raw file.
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The Acquisition icon in the lower right of your window that lets you control an
acquisition while it is running. This icon is visible only while an acquisition is running.
To display the shortcut menu, right-click the blue-vial icon.
Table 28. Acquisition Status view buttons
Command
Description
Acquisition Status
View
Switches to the Status view of the Acquisition window.
Process Using Current
Acquisition List
Switches to the processing view with the current acquired
sample list.
Stop Current Sample
and Pause
Stops acquiring the current sample and pauses the acquisition.
Stop Current Sequence Stops acquiring the current sequence and pauses the
and Pause
acquisition.
 To open the Status view
When the left navigation pane is displayed:
a. Click Acquisition.
b. Click the Status icon.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Status.
Using the Status View Control Buttons
The control buttons on the Status view of the Acquisition window let you control the
acquisition process (Figure 53).
Figure 53. Status view control buttons
 To start, stop, or pause an acquisition
• To start an acquisition or restart an acquisition that has been paused, click
.
• To pause an acquisition after the current sample has been completely acquired, click
To restart the acquisition, click
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• To stop an acquisition, click
and choose one of the following:
• Stop acquisition for the current sample and pause
• Stop acquisition for the current sequence and pause
• Stop acquisition for all sequences
• To pause the Chromatogram and Spectrum displays, click
To restart the displays, click
.
again.
• To display the Spectrum pane below the Chromatogram pane, click
To hide the Spectrum pane, click
.
again.
Acquisition – Status – Chromatogram Pane
The Chromatogram pane is the upper right pane on the Status view of the Acquisition
window. While the LCquan application is acquiring data, you can display an existing
chromatogram in the Chromatogram pane using the current set of filters and settings. The
LCquan application continues to acquire data while displaying a raw file, but the screen is in
pause mode.
 To navigate the Chromatogram pane
Do one of the following:
• Use the display buttons in the toolbar to zoom in or out along the axes.
• Drag your cursor in the Chromatogram pane to define a region and zoom in. When
you zoom in, the trace does not expand if the data extends out of the pane.
 To display a raw file
Do one of the following:
• Right-click the Chromatogram pane and choose Display Raw File from the shortcut
menu, and select an appropriate raw file from the Select Raw File dialog box.
• Drag a raw file from Windows Explorer to the Chromatogram pane.
• Drag an older sample from the acquisition sequence history to the Chromatogram
pane.
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Realtime Display Settings
Use the Realtime Display Settings dialog box (Figure 54) to specify the properties of the
chromatograms that the LCquan application displays. This dialog box consists of two areas:
the Options area and the User-defined traces area.
Use the settings in the Options area to specify the types and number of chromatograms to
display, the time range information for the chromatograms, and whether or not to display the
spectrum trace in the Spectrum pane (see Table 29 on page 89). (Many of these options also
appear in a shortcut menu that you access by right-clicking the Acquisition – Status view
Chromatogram pane.)
Figure 54. Realtime Display Settings dialog box
 To open the Realtime Display Settings dialog box
Right-click in the Chromatogram pane and choose Realtime Display Settings.
Use this dialog box to specify the properties of the real-time chromatograms that the
LCquan application displays in the Chromatogram and Spectrum panes of the
Acquisition window (Table 29 on page 89).
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 To specify the Chromatogram pane display options
1. To filter the chromatograms according to the mass range and scan filters associated with
each component, select the Show Traces Defined by Components check box.
2. To display user-defined real-time chromatograms:
a. Specify the traces in the Trace Properties box.
b. Select the Show User Defined Traces check box.
3. To limit the number of displayed chromatograms, enter the number of chromatograms to
display in the Max Number of Visible Chromatograms box.
4. To display the mass spectrum in the Spectrum pane:
a. Select the Show Spectrum Trace check box.
The Auto Update Spectrum to Last Scan check box becomes active.
b. To automatically update during each refresh to show the spectrum from the last scan,
select the Auto Update Spectrum to Last Scan check box.
5. To display the mass spectrum for a particular chromatogram and scan, click the displayed
chromatogram.
The LCquan application displays a marker on the chromatogram to show which scan was
selected.
6. To display the same time range for all chromatograms, select the Link Chromatogram
Time Ranges check box.
7. To display a specific time range for all chromatograms:
a. Select the Use User-Defined Time Range check box.
The Link Chromatogram Time Ranges option is automatically selected.
b. To specify the beginning and ending retention times, enter values for Min RT and
Max RT.
 To specify and display properties of user-defined chromatogram traces
1. To add a chromatogram trace, click the box next to a blank line.
You can enter up to 10 chromatograms.
2. In the Trace Properties area, define the trace:
a. Type a title for the chromatogram trace.
b. Select mass range chromatograms or total ion current [TIC] chromatograms as the
Trace type.
c. Specify the scan filter to be applied to the acquired data.
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d. Specify the mass or mass range of a mass range chromatogram.
e. Type the number of smoothing points that the smoothing algorithm applies to the
data.
3. To select traces for display, select the check box before the trace entries.
4. Use the Up and Down buttons to change the position of a selected trace.
5. When you have finished your display settings, click OK.
The Chromatogram pane in the Status view of the Acquisition window reserves a display
area for each trace you chose to display.
Table 29. Realtime Display Settings dialog box parameters (Sheet 1 of 3)
Parameter
Description
Options
Show Traces Defined
by Components
Displays real-time chromatograms corresponding to the
components you defined in the processing method.
Show User Defined
Traces
Displays real-time chromatograms defined when using the settings
in the Trace Properties box in the lower portion of this view.
Max Number of
Visible
Chromatograms
The number of chromatograms to display.
Range: 1 to 5
Show Spectrum Trace
Displays the mass spectrum in the Spectrum pane. The
application filters the spectrum in the same manner as the
chromatogram.
Auto Update Spectrum Displays the mass spectrum of the latest scan, and the current
to Last Scan
spectrum updates during each refresh to show the spectrum from
the last scan in the selected chromatogram.
Note Auto Update Spectrum to Last Scan becomes active only
when you select Show Spectrum Trace.
Link Chromatogram
Time Ranges
Displays the same time range for all chromatograms. Any change
in the time range displayed on any chromatogram is reflected in
all chromatograms.
When not selected, the time ranges for each chromatogram are
independent.
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Table 29. Realtime Display Settings dialog box parameters (Sheet 2 of 3)
Parameter
Description
Use User Defined Time Displays chromatograms with a time range between the times
Range
specified by Min RT and Max RT, and enforces the link time
range feature.
When not selected, the time base limits come from the raw file
being acquired.
Note Use User Defined Time Range becomes active only when
you select Link Chromatogram Time Range.
Min RT
The beginning time of the chromatogram traces.
Note The Minimum Retention Time box becomes active only
when you select Use User Defined Time Range.
Max RT
The ending time of the chromatogram traces.
Note The Maximum component Retention Time box becomes
active only when you select Use User Defined Time Range.
User Defined Traces
Trace Table
Displays the properties of the user-defined chromatogram traces.
Trace Properties
Title
The title for the chromatogram trace.
Maximum length: 60 characters
Default: User Trace [trace number]
Trace Type
Mass range chromatograms or total ion current [TIC]
chromatograms.
Scan Filter
The scan filter to be applied to the acquired data.
The application creates scan filters from the instrument settings
that you specified in the Instrument Setup view. For more
information about filter formats, refer to Xcalibur Help.
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Table 29. Realtime Display Settings dialog box parameters (Sheet 3 of 3)
Parameter
Description
Range(s)
The mass or mass range of a mass range chromatogram. You can
enter multiple mass ranges separated by commas. Up to 50 mass
ranges are summed to form a chromatogram. For a single mass,
the chromatogram is generated from that mass +/- the mass
tolerance. For a mass range, the chromatogram includes all masses
between the exact masses entered.
Format: Low Mass – High Mass
Units: mass/charge [z]
Example, for the ranges m through n, and x through y, enter m–n,
x–y.
Note The Range(s) box is inactive when you select trace type
TIC.
Smoothing Points
The number of smoothing points that the smoothing algorithm
applies to the data. By reducing the level of noise through
smoothing, you improve the graphical appearance of data.
Format: integers
Range: 1 to 15, odd numbers only
Note To disable filtering, set the parameter to 1.
Move Trace Up
Moves the selected trace up by one position in the Trace table.
Move Trace Down
Moves the selected trace down by one position in the Trace table.
Chromatogram Pane Shortcut Menu
Right-click the Chromatogram pane to display the shortcut menu (Figure 55). See Table 30
for information about the shortcut commands.
Figure 55. Chromatogram pane shortcut menu
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Table 30. Chromatogram pane shortcut menu commands
Command
Description
Show Component
Traces
Displays real-time chromatograms corresponding to the
components you defined in the processing method.
Show User Traces
Displays real-time chromatograms that you defined by using the
settings in the Realtime Display Settings dialog box. For more
information, see “Realtime Display Settings” on page 87.
Show Spectrum Trace
Displays the mass spectrum in the Spectrum pane.
Filter Spectrum
Applies a scan filter to the acquired data. The application creates
scan filters from the instrument settings that you specified in the
Instrument Setup window.
Link Trace Time Bases
Displays the same time range for all chromatograms.
Use User Defined Time Displays chromatograms with a time range between the times
Range
specified in the Min RT and Max RT boxes in the Realtime
Display Settings dialog box. For more information, see “Realtime
Display Settings” on page 87.
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Settings
Displays the Realtime Display Settings dialog box where you can
specify the properties of the real-time chromatograms that the
application displays in the Chromatogram and Spectrum panes of
the Acquisition window.
Display Raw File
Displays the Select Raw File dialog box where you can open a
previously acquired raw file to view its chromatograms and mass
spectra.
Reset Scaling
Resets the x-axis and y-axis ranges in the Chromatogram pane or
the Spectrum pane to their default values.
Copy to Clipboard
Copies a chromatogram or mass spectrum to the Clipboard. You
can then paste it from the Clipboard into a document.
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Acquisition – Status – Spectrum Pane
The Spectrum pane displays the data for the currently selected scan in the currently selected
chromatogram. Use the Show Spectrum Trace command on the shortcut menu to display the
Spectrum pane.
 To select a scan
Click a chromatogram.
A red vertical line appears on the selected scan in the Chromatogram pane, and the
spectrum that corresponds to that scan appears in the Spectrum pane (Figure 56).
Figure 56. Chromatogram pane (top) and Spectrum pane (bottom)
 To apply a scan filter to the data based on the selected chromatogram
1. Right-click the Spectrum pane and choose Filter Spectrum from the shortcut menu.
2. To remove the filter and show every scan, select this command again.
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 To navigate the Spectrum pane
Do one of the following:
• Use the display buttons in the toolbar or the items in the Zoom menu to zoom in or
out along the axes.
• Drag your cursor in the Chromatogram pane to define a region and zoom in. When
you zoom in, the trace does not expand if the data extends out of the pane.
 To use the Spectrum pane shortcut menu
Right-click the Spectrum pane to display the shortcut menu (Figure 57). See Table 31 for
information about the shortcut commands.
Figure 57. Spectrum pane shortcut menu
Table 31. Spectrum pane shortcut menu commands
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Command
Description
Filter Spectrum
Applies a scan filter to the acquired data. The application
creates scan filters from the instrument settings that you
specified in the Instrument Setup window.
Display Options
Displays the Spectrum Display Options dialog box where you
can modify the appearance of the spectrum in the Spectrum
pane. For more information, see “Spectrum Display Options
dialog box parameters” on page 95.
Reset Scaling
Resets the x axis and y axis ranges in the Chromatogram pane
or the Spectrum pane to their default values.
Copy to Clipboard
Copies a chromatogram or mass spectrum to the Clipboard.
You can then paste it from the Clipboard into a document.
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 To customize the spectrum display
1. Right-click the Spectrum pane and choose Display Options from the shortcut menu.
The Spectrum Display Options dialog box opens (Figure 58).
Figure 58. Spectrum Display Options dialog box
2. Specify the labeling, plotting, and axis display styles you want in the Spectrum pane (see
Table 32).
Table 32. Spectrum Display Options dialog box parameters (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
Label With
Specifies the data attributes to show in the data plots.
Mass
Labels the mass value above the spectral line.
Relative to
Specifies the mass offset value. The displayed value is actually
the defined / chosen mass offset subtracted from the actual
mass.
Decimals
Specifies the number of decimal places for the mass label.
Label Styles
Specifies the labeling styles displayed with the data.
Offset
Moves the label a defined distance from the data.
Rotated
Rotates the labels above the peaks to rotate degrees.
Boxed
Displays boxes around the labels above the peaks.
Size
Define the distance the label is offset from the data.
Label Threshold (%)
Set a threshold so that peaks above this level can show labels.
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Table 32. Spectrum Display Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Plotting
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Automatic
Lets the application determine the best spectrum display. The
graphic style chosen is based upon the data acquisition
method used for the active spectrum.
Point to Point
Displays the active chromatogram or spectrum using
point-to-point peak profile.
Stick
Displays the active chromatogram using vertical lines.
Axis Offset
Offsets the displayed plot from the x axis, y axis, or both.
X
Displays the y axis slightly above the x axis so you can see
baseline details.
Y
Displays the x axis slightly to the right of the y axis so you can
see plot details at low x axis values.
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Acquisition – Status – Run Status
The Run Status page in the Status view of the Acquisition window provides an overall
summary of application status (Figure 59). The application updates the information as
conditions change. Table 33 lists the parameters for the Run Status tab.
Figure 59. Acquisition – Run Status Tab view
 To open the Run Status tab
When the left navigation pane is displayed:
a. Click Acquisition.
b. Click the Status icon.
c. Click the Run Status tab.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Status.
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c. Click the Run Status tab (Figure 60).
Figure 60. Run Status tab
 To display an instrument’s status
Click the instrument name in the list of instruments.
The status displays below the Run Manager status in the lower left area of the page.
Table 33. Run Status page parameters (Sheet 1 of 2)
Parameter
Description
Run Manager
<Run Manager Status> “Acquiring” or “Acquiring in another Workbook” (displays the
latter if the currently acquiring sample is being acquired by
another client).
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Sequence
Displays which sequence is currently being acquired.
Sample Name
Displays a unique alphanumeric name assigned to each sample. In
the LCquan application the assigned name can be up to 50
characters long.
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Table 33. Run Status page parameters (Sheet 2 of 2)
Parameter
Description
Working On
Displays a sequence spreadsheet row that describes the
characteristics of a single sample. The LCquan application
numbers all sequence rows with a row number. You can select
multiple row numbers to define a sample sequence. Rows
(samples) are created, modified, and deleted using the Setup
Sequence view. For more information, see “Acquisition Sequence
Header” on page 34.
Position
Also called the vial number, displays the vial position of the
current sample in the autosampler tray. This readback value is
displayed only if your LC provides this information under direct
control of the LCquan application. This value is not displayed if
your LC is under contact closure control of the LCquan
application.
Raw File
Displays a data file with the raw extension, created by the mass
spectrometer when a sample is run, that contains raw analysis
data.
Instrument Method
Displays a defined set of experiment parameters that define
operating settings for the autosampler, liquid chromatograph (LC)
pump, mass spectrometer, divert valve, and syringe pump.
Instrument methods are defined by using the Instrument Setup
window. Instrument methods are saved as the file type .meth.
Instruments
The readback status of each LCquan-configured instrument appears on the Run Status
page.
Shortcut Menu
Each instrument’s shortcut menu contains the following commands:
Thermo Scientific
Turn Device On
Puts an instrument in the On state.
Turn Device into
Standby
Puts an instrument in the Standby state.
Turn Device Off
Puts an instrument in the Off state.
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Acquisition – Status – Acquisition Queue
The Acquisition Queue page in the Status view of the Acquisition window displays all the
sequences that are queued, including those from other workbooks (Figure 61). The
acquisition queue proceeds from the top sequence to the bottom sequence and from the top
sequence row to the bottom sequence row for each sequence. The LCquan application places
a large X to the left of each completed sequence row as samples are acquired. Each sequence is
labeled with the client doing the acquisition.
Sequences are stored in the All Sequences folder, and sequence rows are stored in the Sequence
folder specified by their paths, for example, C:\methods\Test.sld. The sequences and sequence
rows are organized in a tree view that displays the folders as an indented outline.
Table 34 on page 102 lists the parameters for the Sample Information dialog box.
 To open the Status – Acquisition Queue page
When the left navigation pane is displayed:
d. Click Acquisition.
e. Click the Status icon.
f.
Click the Acquisition Queue tab.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Status.
c. Click the Acquisition Queue tab.
Figure 61. Acquisition Queue tab
When the LCquan application is acquiring a sample, the background of its test tube is green.
After the sample is acquired, the LCquan application changes the background to blue and
places a large X in a circle in the selection box to the left of each numbered sequence row.
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 To expand or collapse a folder
• Click the “+” icon to expand a folder.
• Click the “-” icon to collapse a folder.
 To remove a list or sequence row from the queue
1. Click the sequence or sequence row to select it. The application places a small check mark
in the box to the left of the sequence or sequence row.
2. To delete the selected sequence or sequence row, press the DELETE key.
 To view specific information about an individual sample
1. Right-click the row in the queue.
2. Choose Properties from the shortcut menu.
 To remove a sequence or sequence row that has not been acquired
Select the sequence and press DELETE.
You cannot delete a sequence that another workbook or application submitted.
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 To view sample-specific information for a selected sequence row
1. Right-click a sample in the acquisition queue.
2. Choose Sample Info from the shortcut menu to open the Sample Information dialog box
(Figure 62).
Figure 62. Sample Information dialog box
Table 34. Sample Information dialog box parameters (Sheet 1 of 3)
Parameter
Description
Sample Type
Displays the type of sample described by the acquisition sequence
row. The sample type defines how the LCquan application
processes the sample data. Each sample must be classified as one of
these sample types:
•
•
•
•
Sample Name
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Unknown
Blank
QC (quality control)
Standard
When this box is in a sequence or Result grid row: Displays the
sample name that you specified when you created the sequence.
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Table 34. Sample Information dialog box parameters (Sheet 2 of 3)
Parameter
Description
File Name
When this box is in an acquisition sequence: Displays the name of
the raw file that contains the sample data. The File Name is a
combination of the Base File Name prefix assigned to the sequence
and a sequential sequence number.
When the default sequence starting number 1 is not changed, the
suffix number is the same as the row number of the sequence: 001,
002, and so on.
When the default sequence starting number is changed to another
number, the first sample has the starting number and subsequent
rows in the sequence are incremented by 001. For example, if the
starting number is 100, the File Name for the first sample has a
suffix of 100, the second sample has a suffix of 101, and so on.
Sample ID
Displays the sample ID for the data file. The sample ID is an
alphanumeric string of characters that uniquely identifies a
sample.
Path
Displays the path to the raw files that the LCquan application
creates for the sample data. The LCquan application creates these
files with extension raw. A path contains the drive and one or
more folders. A typical path is:
C:\Xcalibur\data
Instrument File
Specify the path and file name of the instrument method to be
used to analyze the samples in the active sequence. A path contains
the drive and one or more folders. A typical path for instrument
method file ABC is:
C:\Xcalibur\methods\ABC
Position
Displays the sample’s position number in the autosampler.
Inj Volume
Displays the injection volume in microliters of sample to be
injected.
When you are using an autosampler, you can set the default
injection volume in the Autosampler dialog box in the Instrument
Setup window. The minimum and maximum injection volumes
that you can use depends upon the Autosampler you select. The
usable range depends on the injection mode and can be smaller
than the range displayed in the status bar. For more details,
consult your Autosampler manual.
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Table 34. Sample Information dialog box parameters (Sheet 3 of 3)
Parameter
Description
Level
Displays the calibration level whenever the acquisition sequence
row corresponds to a calibration sample or a quality control (QC)
sample for which a level is defined.
Sample Weight
Displays the amount of a component that has been placed in the
sample.
Sample Volume
Displays the volume of a component that has been placed in the
sample.
ISTD Corr Amt
Specifies an updated amount of internal standard for the
corresponding sample. The default value is 0.0.
Dil Factor
Displays the dilution factor that was used to prepare the sample.
The valid range is 0.000 to 10 000.000. The application interprets
a value of 0.000 as no dilution.
User Label 1 to 5
Displays information pertinent to the active sample row in the
sequence. Use these boxes to convey information about this
sample to others or as a reminder to yourself.
•
•
•
•
•
Comment
The User Label 1 default name is Study.
The User Label 2 default name is Client.
The User Label 3 default name is Laboratory.
The User Label 4 default name is Company Name.
The User Label 5 default name is Phone.
Displays comments about the sample selected from the acquisition
sequence.
Note By default, the dialog box is pinned in place (you see the pin icon in the upper left
corner of the dialog box), meaning the dialog box stays open when you select a new
sample. The content of the dialog box fields is updated for the new sample.
Acquisition – Status – Acquisition History
The Acquisition History page in the Status view of the Acquisition window displays a history
of all sequences (and samples) that have been acquired by the current workbook, along with
other relevant information, such as the operator, start and end times, status, and comment.
Table 35 lists the parameters for the Acquisition History tab.
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 To open the Status – Acquisition History page
When the left navigation pane is displayed:
a. Click Acquisition.
b. Click the Status icon.
c. Click the Acquisition History tab.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Acquisition Section.
b. Choose View > Step Selector > Acquisition Status.
c. Click the Acquisition History tab (Figure 63).
Figure 63. Acquisition History tab
Table 35. Acquisition History page parameters (Sheet 1 of 2)
Parameter
Description
Info
Thermo Scientific
Operator
Displays the login ID of the person who is logged onto the system
and who is acquiring the sequence.
Start Time
Displays the time when the first sample (or startup method)
began.
End Time
Displays the time when the last sample (or shutdown method)
completed. When the LCquan application is closed before
acquisition is complete but the acquisition is allowed to complete
in the background, the end time is displayed as Unknown.
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Table 35. Acquisition History page parameters (Sheet 2 of 2)
Parameter
Description
Comment
Displays a comment about the sequence as entered in the Run
Sequence dialog box. For more information, see “Run Sequence
dialog box parameters” on page 78.
Status
Displays the sequence status:
• Waiting (created but not yet submitted)
• Submitted (submitted but not yet validated and not yet
running—that is, the data file has not yet been accepted for
acquisition)
• Queued (submitted and validated)
• In Progress (currently being acquired)
• Stopped (stopped either at the request of the operator or
because of an error in acquisition)
• Complete (successfully completed)
• Rejected (failed validation; rejected and did not run)
Components
Displays the acquisition component names and their associated level amounts.
Samples
Displays all the sequence row information set when acquisition for that sample was made.
Shortcut Menu
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Show Sequence Items
Collapses the Acquisition Sequence History tree, so only the
first-level items (sequences) are shown.
Show
Info/Level/Sample
Items
Displays second-level items for each sequence in the Acquisition
Sequence History tree. These are Info, Levels, and Samples.
Show
Info/Level/Sample
Details
Displays third-level items for each sequence in the Acquisition
Sequence History tree. These are Info details, Level details, and
Sample details.
Show Info Details
Expands the Acquisition Sequence History tree to show details for
each Info item and collapse all other branches.
Show Level Details
Expands the Acquisition Sequence History tree to show details for
each level item and collapse all other branches.
Show Sample Details
Expands the Acquisition Sequence History tree to show details for
each sample item and collapse all other branches.
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Processing Data While Continuing to Acquire Data
While acquiring data, you can enter the Quantitate window to process the data you have
already acquired. You must first complete the procedures for defining a processing method
and a processing sequence. For more information, see Chapter 4, “Creating a Processing
Method,” and Chapter 5, “Creating a Processing Sequence.”
You can use the defined processing sequence, or you can replace the defined processing
sequence with a shortened sequence that is based on the data already acquired.
 To update the processing sequence with the most recent list of acquired samples
1. To enter the Quantitate window, click Quantitate in the navigation pane.
2. Choose Options > Acquisition Sequence Info to open the Acquisition Sequence dialog
box (Figure 64).
Figure 64. Acquisition Sequence dialog box
3. To update the sequence, select the Auto Update the Processing Sequence When
Acquiring check box.
If you are currently acquiring data when you select this option, a message box prompts
you to update the current processing sequence with the most recent list of samples
acquired. If you do not respond to the message box after five seconds, the LCquan
application automatically updates the sequence.
For more information about defining a processing sequence, see Chapter 5, “Creating a
Processing Sequence.”
Table 36 lists the parameters for the Acquisition Sequence dialog box.
Table 36. Acquisition Sequence dialog box parameters
Thermo Scientific
Parameter
Description
Auto Update the
Processing Sequence
When Acquiring
Select to automatically add sample information to the processing
sequence as samples are run.
Maximum Number of
Rows Allowed in the
Acquisition Sequence
Type a value between 1 and 5000 for the maximum number of
rows in the acquisition sequence.
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Use the Switching to Processing during Acquisition features to determine what processing
sequence you want the LCquan application to use when you switch to the Quantitate window
from the Acquisition window during an acquisition (see Table 37).
 To switch to processing during acquisition
1. During data acquisition, click Quantitate.
The Switching to Processing during Acquisition dialog box opens (Figure 65).
Figure 65. Switching to Processing During Acquisition dialog box
2. Select the Update Sequence with Data Acquired or Keep Current Processing Sequence
option.
Table 37. Switching to Processing During Acquisition dialog box parameters
Parameter
Description
Update Sequence with
Data Acquired
Specifies that the LCquan application automatically updates the
processing sequence with sample information from the acquisition
sequence as new sample data is acquired. The LCquan application
requantitates your data as new samples are completed.
If you clear this option, click
in the toolbar to force the
processing sequence to update using all the samples acquired at
that moment.
Keep Current
Processing Sequence
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Specifies that the LCquan application does not modify the
currently defined processing sequence when you switch to the
Quantitate window from the Acquisition window during data
acquisition. If no processing method or processing sequence is
available yet, the LCquan application displays the appropriate
view within the Quantitate window to be completed first.
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Verifying Disk Space
Verifying Disk Space
The Disk Space dialog box (Figure 66) provides information about the active storage disk (see
Table 38).
To open the Disk Space dialog box, choose Actions > Check Disk Space.
Figure 66. Disk Space dialog box
Table 38. Disk Space dialog box parameters
Parameter
Description
Current Directory
This area at the top of the dialog box displays the path to the current directory. For
example, the path can be C:\Xcalibur\System\Programs.
Free Disk Space
This area above the pie chart displays the currently available (free) disk space on the
current drive. The current drive is displayed as Current Directory. The free disk
space is also given as a percentage of the total disk space. For example, if your drive
has a total disk space of 5090 MB and you have 1860 MB free, the LCquan
application displays the percentage free as:
[1860/5090] × 100 = 36.5%
Total Storage Area
This area below the pie chart displays the total disk space on the current drive. The
current drive is displayed as Current Directory.
Graphical Display of Storage
Status
The pie chart displays the unavailable (occupied) disk space in red and the available
(free) disk space in green.
Directory
Click Directory to open the Select Directory dialog box (Figure 67) where you can
change the default path (see Table 39).
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Save Settings Options
Figure 67. Select Directory dialog box
Table 39. Select Directory dialog box parameters
Parameter
Description
Directory Selected
Displays the current directory.
Drives
Opens the Map Network Drive dialog box where you can change
the drive location. You can gain access to additional drives by
connecting to a network.
Disk Space/No Chart
Displays or hides a pie chart that displays the unavailable
(occupied) disk space in red and the available (free) disk space in
green.
Network
Opens the Map Network Drive dialog box where you can connect
to a shared network drive or folder and assign a drive letter to the
connection.
Save Settings Options
This dialog box warns you that you changed components or views without saving the latest
setting changes.
Select Discard Any Changes if you do not want the latest changes saved in the settings when
you change components or views.
Default: The latest changes are saved in the settings when you change components or views.
Note After the default is set up, select the Don’t Tell Me About This Again check box.
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Emergency Shutdown
Emergency Shutdown
From the Emergency Shutdown dialog box, specify what you want the LCquan application to
do before it puts all instruments into their Stop condition (see Table 40).
 To define the emergency shutdown procedures
1. In the toolbar, click the shutdown icon
(Figure 68).
to open the Emergency Shutdown dialog box
Figure 68. Emergency Shutdown dialog box
2. Select one of the following:
• To pause the current acquisition, select the Pause the Acquisition option.
You can restart the acquisition sequence later.
• To quit the current acquisition and delete the sequence from the acquisition queue,
select the Delete the Current Acquisition Sequence and Pause option.
3. To quit the acquisition and delete all queued acquisition sequences, select the Delete All
Queued Sequences option.
Table 40. Emergency Shutdown dialog box parameters
Thermo Scientific
Parameter
Description
Pause the Acquisition
Pauses the current acquisition and date/time stamps the current
raw file. When you restart the acquisition, you must rerun this raw
file from the beginning.
Delete the Current
Acquisition Sequence
and Pause
Pauses the current acquisition and deletes the current sequence.
Use this when you want to restart the sequence from the
beginning. Before you can run a deleted acquisition sequence, you
must resubmit the sequence.
Delete All Queued
Sequences
Pauses the current acquisition and deletes all sequences in the
queue. Use this when you want to restart all queued acquisitions.
Before you can run a deleted acquisition sequence, you must
resubmit the sequence.
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Shutting Down the LCquan Application While Acquiring
Shutting Down the LCquan Application While Acquiring
When you need to shut down the LCquan application while an acquisition is running, the
Shutdown While Acquiring dialog box (Figure 69) prompts you to select how the application
handles the acquisition.
• To quit the LCquan application and continue acquiring, select the Exit LCquan but
Continue Acquisition option.
• To quit the LCquan application and stop acquiring, select the Exit LCquan and Stop the
Acquisition option.
Figure 69. Shutdown While Acquiring dialog box
The acquisition for all submitted sequences stops. When you restart the LCquan
application and open the latest used workbook, the Acquisition Queue does not show any
sequences and the Acquisition History shows the Stop status for the sequence that was
acquiring when you exited the application.
Remote Acquisition
When acquiring raw files in a remote workbook, the LCquan application creates temporary
local folders for the files, sequences, and workbooks. It can either automatically time-stamp
raw files or never time-stamp raw files when you acquire data to a remote workbook.
Time Stamps
The time-stamped raw files have the following properties:
• Remotely stored raw files are time-stamped with the submission time.
• All raw files in a sequence share the same time stamp.
• Pausing during acquisition does not change the time stamp.
• The time stamp for the Rawfiles folder and the time stamp for the raw files are not
necessarily the same.
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Remote Acquisition
IMPORTANT The LCquan application can overwrite a raw file of the same name if
you turn off time-stamping.
 To time-stamp raw files automatically when acquiring data to a remote workbook
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager.
2. In the Authorization Manager, do the following (Figure 70):
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Acquisition Section folder.
e. Select Prevent Raw File Time-Stamping When Doing Remote Workbook
Acquisition.
The Permission Level options become available.
f.
Select the Disallowed option, and click OK.
Figure 70. Authorization Manager time-stamping permission disallowed
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Remote Acquisition
 To prevent raw file time-stamping when acquiring data to a remote workbook
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager (Figure 71).
Figure 71. Authorization Manager time-stamping permission allowed
2. In the Authorization Manager, do the following:
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Acquisition Section folder.
e. Select Prevent Raw File Time-Stamping When Doing Remote Workbook
Acquisition.
The Permission Level options become available.
f.
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Select the Allowed option, and click OK.
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Remote Acquisition
Local Folders
The LCquan application creates temporary local folders for the files, sequences, and
workbooks:
• During remote acquisition, the application creates a local temporary folder for the remote
workbook:
C:\Xcalibur\remote acquisition\workbook
When the workbook is closed, the application deletes this temporary workbook folder,
the instrument method file, and the sequence file.
• The LCquan application creates a local, rawfiles_timestamp folder for each sequence and
temporarily stores the raw files:
C:\Xcalibur\remote acquisition\workbook\rawfiles_timestamp
When the sequence is completed, the LCquan application deletes the rawfiles_timestamp
folder.
File Transfer
The LCquan application transfers raw files to the remote location:
• Raw files are tracked in the global database, the same as raw files used in local acquisition.
• When a sample is completed, the raw file is transferred to the remote location.
• When the user closes the LCquan application and no acquisition is running, it deletes the
local workbook folder.
The LCquan application cannot transfer files when it is not running.
Importing a Processing Sequence
During remote acquisition, use any of these methods to import a processing sequence:
• Import a saved sequence file or copy an acquisition sequence. For detailed descriptions of
the various commands and methods, see Chapter 5, “Creating a Processing Sequence.”
• Update the processing sequence with the most recently acquired samples. For detailed
instructions for copying files as they are acquired, see “Processing Data While Continuing
to Acquire Data” on page 107.
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3
Exploring the Data
This chapter describes the features of the Explore window. You can use the Explore window to
display a multi-component chromatogram and experiment with peak detection and
integration parameters to see how they affect the chromatogram.
Contents
• Introduction to the Explore Window
• Creating Explore Methods
• Exploring the Results
• Exporting the Active Raw File to Qual Browser
• Data Views
Introduction to the Explore Window
Use the Explore window to display a multi-component chromatogram and experiment with
peak detection and integration parameters to see how they affect the chromatogram. In the
Explore window, you can also create quan components and export them to the processing
method.
The Explore window of the LCquan application is similar to the Qual window of Processing
Setup in Xcalibur. From the Explore window, you can do the following:
• Automatically generate quan components by using the peak list function.
• Display the acquisition sequence history and select a sample from it.
• Import several sequences to review and select samples from any of the imported
sequences. Although you cannot edit sequences in the Explore window, you can import
them.
• Create methods that can later be applied to raw files in the Quantitate window.
• Use common tools to investigate acquired data and to produce a processing method.
• Perform actions that do not become part of the audit trail (except for exporting quan
components to the Quantitate window).
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Creating Explore Methods
Creating Explore Methods
Use the Create view of the Explore window to develop explore methods by specifying peak
integration and detection criteria (Figure 72).
Figure 72. Explore – Create window
The Create view of the Explore window contains the Chromatogram Definition, Peak
Integration, and Limit Peaks areas that you use to develop an explore method.
This section includes the following topics:
• Defining Chromatographic Parameters
• Defining Peak Integration Parameters
• Acquisition Sequence History
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 To open the Create view of the Explore window
When the left navigation is displayed:
a. Click Explore.
b. Click the Method icon.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Explore Section.
b. Choose View > Step Selector > Explore Method.
Defining Chromatographic Parameters
Use the Chromatogram Definition area (Figure 73) to define your chromatogram (see
Table 41).
 To define chromatographic parameters
1. In the Detector box, select the specific data stream.
Figure 73. Chromatogram Definition area
2. In the Smoothing box, enter the number of points to use for a moving mean filter to
smooth the chromatogram.
3. In the Trace box, select a type of chromatogram.
4. To use trace math, select an addition or a subtraction trace operator and select another
type of chromatogram in the second Trace box.
5. In the Mass1 (m/z) box, enter an initial mass value.
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6. When you are using trace operator math, enter a second mass value in the Range (min)
box to define the mass range.
7. In the Filter box, enter an existing filter or select a filter from a preloaded filter list.
Table 41. Chromatogram Definition area parameters (Sheet 1 of 2)
Parameter
Description
Detector
Specifies the specific data stream.
Smoothing
The number of points used for a moving mean filter to smooth
the chromatogram.
Format: whole numbers
Range: 1 to 15, odd numbers only
Note To disable filtering, set the parameter to 1.
Trace
Specifies the type of chromatogram:
• Mass Range: Specify up to 50 mass ranges. The masses are
added together to form the chromatogram.
• TIC: Full-scan acquisition resulting in a Total Ion Current
plot.
• Base Peak: In a differential chromatogram, the interpolation
of the baseline is derived from the distance between the
intersections of the tangents drawn to the peak sides and the
peak base.
Note This definition set is the same for the second Trace box.
The second trace box depends on which operators you select.
+/-/“ “
Trace operator used to specify a trace operation.
This trace operation matrix shows the combinations used to set up
a method:
Mass Range+Mass Range
– Mass Range
TIC+ Mass Range
– Base Peak
Base Peak+Mass Range
– Mass Range
Note If the operator box remains empty, the second trace choice
is disabled.
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Mass1 (m/z)
Specifies the initial mass value.
Mass2 (m/z)
Specifies the second mass value to define the mass range used for
trace operator math.
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Table 41. Chromatogram Definition area parameters (Sheet 2 of 2)
Parameter
Description
Filter
Specifies a scan filter to be applied to the acquired data. Enter a
filter or select a filter from a preloaded filter list (obtained from
the current raw file).
Note All filters are validated against the current set of filter
entry rules.
Defining Peak Integration Parameters
Use the Peak Integration area to select and define peak integration parameters. Use the Peak
Integration area to define Genesis, ICIS, and Avalon peak detection algorithms to be applied
to the active raw file.
Peak detection parameters are also available from the Quantitate window:
• The Peak Integration area on the Identification page
• The IRC Detection dialog box available from the ion ratio confirmation grid on the
Identification page
• The User Identification Settings dialog box available from the Chromatogram view in the
preview panes
This section contains instructions for specifying parameters for the following:
• Genesis Peak Integration
• ICIS Peak Integration
• Avalon Peak Integration
Note
• The Genesis peak detection algorithm has been provided for backward compatibility
with Xcalibur 1.0 studies.
• The ICIS peak detection algorithm has been designed for MS data and has superior
peak detection efficiency at low MS signal levels.
• The Avalon peak detection algorithm has been designed for UV data. Avalon also
supports negative peaks.
Genesis Peak Integration
Use the Genesis Peak Integration area to define Genesis peak detection algorithms to be
applied to the active raw file (see Table 42 on page 123). Table 43 on page 129 lists the
parameters for the Genesis Advanced Component Options dialog box.
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 To specify Genesis peak integration parameters
1. In the Peak Detection Algorithm box, select Genesis.
2. Type a multiplier value in the S/N Threshold box.
3. To detect unresolved peaks with the valley detection approximation method, select the
Valley Detection Enabled check box.
To set the expected peak width parameter and control the minimum width that a peak is
expected to have, enter a multiplier value in the Expected Width (sec) box.
4. To constrain the peak width of a component during the peak integration of a
chromatogram, select the Constrain Peak Width check box.
• To specify the minimum above the baseline before integration is turned on or off,
enter a percent of the total peak height in the Peak Ht (%) box.
• To constrain the peak width of an asymmetric chromatogram peak that has a tailing
trace, enter a peak integration multiplier in the Tailing Factor box.
5. To specify advanced component detection criteria, click Advanced (Figure 74).
Figure 74. Genesis Peak Integration area
Use these advanced criteria if the standard detection criteria do not provide the expected
results:
a. To specify a peak signal-to-noise cutoff, enter a Peak S/N Cutoff value.
b. To use a valley detection approximation method to detect unresolved peaks, enter
Rise Percentage value and a Valley S/N value.
c. Select whether the noise used in calculating S/N values is calculated using an RMS
calculation or Peak-to-Peak resolution threshold.
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Table 42. Genesis Peak Integration parameters (Sheet 1 of 2)
Parameter
Description
Advanced
Opens the Genesis Advanced Component Options dialog box
(Figure 75).
S/N Threshold
This multiplier specifies a signal-to-noise threshold for peak
integration. Only peaks with a signal-to-noise ratio greater than
this value are integrated.
Range: 0.0 to 999.0
Default multiplier: 0.5
Valley Detection
Enabled
Detects unresolved peaks with the valley detection approximation
method.
The LCquan application drops a vertical line from the apex of the
valley between unresolved peaks to the baseline. The intersection
of the vertical line and the baseline defines the end of the first peak
and the beginning of the second peak.
Expected Width (sec)
This multiplier specifies an expected peak width parameter that
controls the minimum width that a peak is expected to have when
valley detection is enabled.
With valley detection enabled, any valley points nearer than half
the expected width to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the LCquan
application ends the peak at that point. It always ends a peak when
the signal reaches the baseline, independent of the value set for the
expected peak width.
Range: 0.0 to 999.0
Default multiplier: 0.0
Units: seconds
Note Valid only when you select the Valley Detection Enabled
check box.
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
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Table 42. Genesis Peak Integration parameters (Sheet 2 of 2)
Parameter
Description
Peak Ht (%)
Specifies a percentage of the total peak height. This is the
minimum that a signal must be above the baseline before
integration is turned on or off. This option is available only when
you select the Constrain Peak Width option.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Tailing Factor
Specifies a value for the factor that controls how the application
integrates the tail of a peak. This factor is the maximum ratio of
the trailing edge to the leading side of a constrained peak and
calculates the retention time of the maximum extent of the right
edge of the tailing peak. This option is available only when you
select the Constrain Peak Width option.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Figure 75. Genesis Advanced Component Options dialog box
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Table 43. Genesis Advanced Component Options dialog box parameters
Parameter
Description
Peak Edge Detection
Chromatogram peak detection criteria using the peak signal-to-noise (S/N) cutoff value.
Peak S/N Cutoff
The peak edge is set to values below this defined S/N.
This test assumes an edge of a peak is found when the baseline
adjusted height of the edge is less than the ratio of the baseline
adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is
200, the application defines the right and left edges of the peak
when the S/N reaches a value less than 200.
Range: 50.0 to 10000.0
Valley Detection
Valley detection approximation method to detect unresolved peaks.
Rise Percentage
The percentage that the peak trace can rise above the baseline after
passing through a minimum (before or after the peak).
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the application applies
valley detection peak integration criteria.
This test is applied to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with
long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Range: 1.0 to 100.0
Default: 2.0
Report Noise As
RMS or
Peak to Peak
Thermo Scientific
Determines if the noise used in calculating S/N values is calculated
using an RMS calculation or peak-to-peak resolution threshold.
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ICIS Peak Integration
Use the ICIS Peak Integration area to define ICIS peak detection algorithms to be applied to
the active raw file (Figure 76).
 To specify ICIS peak integration parameters
1. In the Peak Detection Algorithm box, select ICIS.
Figure 76. ICIS Peak Integration area
2. In the Baseline Window box, enter the number of scans to use when searching for where
the minima are occurring.
3. In the Area Noise Factor box, enter a value to specify the noise-level multiplier that
determines the peak edge after the location of the possible peak.
4. In the Peak Noise Factor box, enter a value to specify the noise level multiplier that
determines the potential peak signal threshold.
5. To constrain the peak width of a component during the peak integration, select the
Constrain Peak Width check box.
• To specify the minimum above the baseline before integration is turned on or off,
enter a percent of the total peak height in the Peak Ht (%) box.
• To constrain the peak width of an asymmetric chromatogram peak that has a tailing
trace, enter a peak integration multiplier in the Tailing Factor box.
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6. To specify advanced component detection criteria, click Advanced to open the ICIS
Advanced Parameters dialog box (Figure 77).
Use the advanced component detection criteria if the standard detection criteria do not
provide the expected results:
Figure 77. ICIS Advanced Parameters dialog box
a. Select a noise method:
• To use a single-pass algorithm to determine the noise level, select the INCOS
Noise option.
• To use a multiple-pass algorithm to determine the noise level, select the
Repetitive Noise option.
b. To use an RMS calculation instead of the default ICIS noise method, select the
RMS Noise check box.
c. To specify the minimum number of scans required in a peak, enter a value in the
Min Peak Width box.
d. To specify the minimum separation in scans between the apexes of two potential
peaks, enter a value in the Multiplet Resolution box.
e. To specify the number of scans past the peak endpoint to use in averaging the
intensity, enter a value in the Area Tail Extension box.
f.
Thermo Scientific
To specify the number of allowable scans on each side of the peak apex, enter a value
in the Area Scan Window box.
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Table 44 lists the parameters for the ICIS Peak Integration area. Table 45 lists the advanced
parameters for ICIS.
Table 44. ICIS Peak Integration area parameters (Sheet 1 of 2)
Parameter
Description
Baseline Window
The number of scans used when searching for where the minima
are occurring. A local minimum becomes an anchor point,
making the entire curve locally reduced until these points are at
zero.
Range: 1 to 500
Default: 40
Area Noise Factor
The noise-level multiplier. This determines the peak edge after the
location of the possible peak, so that the peak can narrow or
broaden without affecting the baseline.
Range: 1 to 500
Default multiplier: 5
Peak Noise Factor
The noise level multiplier (a minimum S/N ratio). This
determines the potential peak signal threshold.
Range: 1 to 1000
Default multiplier: 10
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
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Table 44. ICIS Peak Integration area parameters (Sheet 2 of 2)
Parameter
Description
Peak Ht (%)
A percent of the total peak height. This is the minimum that a
signal must be above the baseline before integration is turned on
or off.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Note Valid only when you select the Constrain Peak Width
check box.
Tailing Factor
A peak integration multiplier that constrains the peak width of an
asymmetric chromatogram peak that has a tailing trace.
It is the maximum ratio of the trailing edge to the leading side of a
constrained peak and calculates the retention time of the
maximum extent of the right edge of the tailing peak.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Note Valid only when you select the Constrain Peak Width
check box.
Table 45. ICIS Advanced Parameters dialog box (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
INCOS Noise
A single-pass algorithm is used to determine the noise level.
Repetitive Noise
A multiple-pass algorithm is used to determine the noise level. In
general, this algorithm is more accurate in analyzing the noise
than the INCOS Noise algorithm, but it takes longer.
RMS Noise
A root mean square calculation is used to determine
signal-to-noise values instead of the default ICIS noise method.
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Table 45. ICIS Advanced Parameters dialog box (Sheet 2 of 2)
Parameter
Description
Peak Parameters
Units are in number of scans.
Min Peak Width
The minimum number of scans required in a peak.
Range: 0 to 100
Default: 3
Multiplet Resolution
The minimum separation in scans between the apexes of two
potential peaks. This is a criterion to determine if two peaks are
resolved. Use a larger number in a noisy environment when the
signal is bouncing around.
Range: 1 to 500
Default: 10 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging
the intensity.
Range: 0 to 100
Default: 5 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A
zero value defines all scans (peak-start to peak-end) to be included
in the area integration.
Range: 0 to 100
Default: 0 scans
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Avalon Peak Integration
Use the Avalon Peak Integration area to define Avalon peak detection algorithms to be applied
to the active raw file.
 To specify Avalon peak integration parameters
1. In the Peak Detection Algorithm list, select Avalon (Figure 78).
Avalon peak identification and integration criteria are applied to the active raw file. You
can add, modify, or delete (non-automated) timed events in the Avalon event list, but you
cannot delete an initial value. Table 47 on page 133 describes the initial and timed events.
Figure 78. Avalon Peak Integration area
2. To add a new event to the event list:
a. Specify the new values in the Time (min), Event, and Value boxes.
b. Click Add. The values are inserted into the Avalon event list.
3. To delete the entire row (except for an initial value row):
a. Select the row you want to delete. The selected row is highlighted.
b. Click Delete. The highlighted row is removed from the list.
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4. Change the values within a row as follows:
a. Select the row you want to change. The selected row is highlighted.
b. Specify the revised settings in some or all of these boxes: Time, Event, Value.
c. Click Change to automatically update the event list and the chromatogram display.
5. To estimate the initial values for the detection of peaks and display initial values in the
event list, click Auto Calculate.
Table 46 lists the parameters for the Avalon Peak Integration area. Table 47 lists the initial and
timed events.
Table 46. Avalon Peak Integration area parameters (Sheet 1 of 2)
Parameter
Description
Column Headings in the Event List
Time (min)
Displays the initial time value in minutes.
Event
Displays descriptions of detection parameters for initial events and
timed events. For details, see “Initial and Timed Events” on
page 133.
Note Start Threshold, End Threshold, Area Threshold,
P-P [Resolution] Threshold, Bunch Factor, Negative Peaks, and
Tension are defined with initial values.
Value
Displays the values associated with initial events or timed events.
Range: Factors are specific to each event.
Controls to Modify the Event List
Auto Calculate
Estimates the initial values for the detection of peaks—based on
the data in the current raw file—to display initial values in the
event list and searches for the best values of initial events that
detect peaks in the data. Any timed event in the event list is
unchanged when you click Auto Calculate.
Determines initial values for only: Start Threshold, End
Threshold, Area Threshold, P-P [Resolution] Threshold,
Bunch Factor, Negative Peaks, and Tension.
Note Valid only if a raw file is open.
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Time (Min)
Initial value or a time value in minutes.
Event
Descriptions of detection parameters for initial events and timed
events.
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Table 46. Avalon Peak Integration area parameters (Sheet 2 of 2)
Parameter
Description
Value
Values associated with the initial/timed events described in the
Event box.
The range of factors allowed for each value is specific to each
event.
Buttons
Add
Adds the Time, Event, and Value values to the Avalon Event List.
Delete
Deletes the selected row.
Change
Using the Time, Event, and Value values, updates the event list
and the chromatogram display.
Table 47. Initial and Timed Events (Sheet 1 of 2)
Event
Description
Start/End Threshold
Half of the result is a good estimate for the Start Threshold. You
can modify the Avalon estimates by entering your own values and
clicking Add to save your Start or End Threshold.
The Start Threshold depends on the RMS noise in the
chromatogram. It is the fundamental control used for peak
detection, so picking the best Start Threshold is essential for
high-quality data collection.
Units: Absolute value of peak area (counts x seconds)
Bunch Factor
The number of points grouped together during peak detection.
This method groups several chromatographic points during
integration without affecting the final area calculation of the peak.
Range: 1 to 6
Note A high bunch factor groups peaks into clusters.
Area Threshold
Controls the area cutoff. Any peak with a final area less than the
area threshold is not recorded.
Format: units of area for the data
Thermo Scientific
P-P Resolution
Defines how much peak overlap must be present before two or
more adjacent peaks create a peak cluster. Peak clusters have a
baseline drop instead of valley-to-valley baselines. This is specified
as a percent of peak height overlap.
Negative Peaks
Automatically resets after a negative peak has been found.
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Table 47. Initial and Timed Events (Sheet 2 of 2)
Event
Description
Tension
Controls how closely the baseline follows the overall shape of the
chromatogram.
A lower tension traces the baseline to follow changes in the
chromatogram more closely. A high baseline tension follows the
baseline less closely, over longer time intervals.
Units: minutes
Tangent Skim
Enables tangent skim on any peak clusters.
By default, the application selects the tallest peak in a cluster as the
parent (solvent) and detects peaks on either side (or both sides) of
the tallest peak. You can also identify which peak in the cluster is
the parent.
Tangent skim automatically resets at the end of the peak cluster.
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Integrate On/Off
Turns integration on or off at the set time.
Shoulders On
Turns on the detection of shoulders.
Shoulders Off
Turns off the detection of shoulders.
Force Cluster On
Turns on the grouping of peaks into a single peak.
Force Cluster Off
Turns off the grouping of peaks into a single peak.
Disable Cluster On
Enables the grouping effect in the specified time range.
Disable Cluster Off
Disables the grouping effect in the specified time range.
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Peak Limitations
In the Limit Peaks area (Figure 79), you can limit the number of peaks based on user-defined
thresholds (see Table 48).
Figure 79. Limit Peaks area
 To limit the number of peaks
1. To use only specific peaks, defined by either area or height:
a. In the Select Top Peaks area, select the Enable check box.
b. Select either option: Select By Area or Select By Height.
c. Type the maximum number of peaks to select.
2. To specify a threshold minimum:
a. In the Rel Peak Height Threshold area, select the Enable check box.
b. Specify the percentage of the highest peak to be used for classifying detected peaks.
Table 48. Limit Peaks area parameters (Sheet 1 of 2)
Parameter
Description
Select Top Peaks
Thermo Scientific
Enable
Specifies to use only specific (top) peaks: specific criteria defined
by either area or height.
Select by Area
Specifies peak areas as the only criteria for determining which
peaks to use.
Select by Height
Specifies peak heights as the only criteria for determining which
peaks to use.
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Table 48. Limit Peaks area parameters (Sheet 2 of 2)
Parameter
Description
Num to Select
The maximum number of peaks to include for consideration.
Rel Peak Height Threshold
Enable
Excludes all peaks that fall below the threshold percentage set
(for example, the maximum peak height of a [detected] group of
peaks).
% of Highest Peak
The percentage of the highest peak to be used for classifying
detected peaks.
Range: 0 to 100
Acquisition Sequence History
The Acquisition Sequence History pane (Figure 80) displays the history of all sequences (and
samples) acquired by the current workbook along with other relevant information, such as the
operator, start and end times, status, and comment. You can modify the Acquisition Sequence
History pane (see Table 49).
Figure 80. Acquisition Sequence History pane
Table 49. Acquisition Sequence History pane parameters (Sheet 1 of 2)
Parameter
Description
Info
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Operator
Displays the login ID of the person who is logged onto the system
and who is acquiring the sequence.
Start Time
Displays the time when the first sample (or startup method)
began.
End Time
Displays the time when the last sample (or shutdown method)
completed. When the application is closed before acquisition is
complete but the acquisition is allowed to complete in the
background, the end time is displayed as “Unknown.”
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Table 49. Acquisition Sequence History pane parameters (Sheet 2 of 2)
Parameter
Description
Comment
Displays a comment about the sequence, as entered in the Run
Sequence dialog box. For more information, see “Run Sequence
dialog box parameters” on page 78 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
Status
Displays the sequence status (one of the following):
• Waiting: Created but not yet submitted.
• Submitted: Submitted but not yet validated (data file has not
yet been accepted for acquisition) and not yet running.
• Queued: Submitted and validated.
• In Progress: Currently being acquired.
• Stopped: Stopped either at the request of the operator or
because of an error in acquisition.
• Complete: Successfully completed.
• Rejected: Failed validation; rejected and did not run.
Components
Displays the acquisition component names and their associated level amounts.
Samples
Displays all the sequence row information set at the time of the sample acquisition.
Shortcut Menu
Thermo Scientific
Show Sequence Items
Collapses the Acquisition Sequence History tree so that only the
first-level items (sequences) are shown.
Show
Info/Level/Sample
Items
Displays second-level items for each sequence in the Acquisition
Sequence History tree. These are Info, Levels, and Samples.
Show
Info/Level/Sample
Details
Displays third-level items for each sequence in the Acquisition
Sequence History tree. These are Info details, Level details, and
Sample details.
Show Info Details
Expands the Acquisition Sequence History tree to show details for
each Info item and collapse all other branches.
Show Level Details
Expands the Acquisition Sequence History tree to show details for
each Level item and collapse all other branches.
Show Sample Details
Expands the Acquisition Sequence History tree to show details for
each Sample item and collapse all other branches.
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Exploring the Results
In the Review view of the Explore window (Figure 81), you can create an explore method,
apply it to the raw data to create a peak list, and use the peak list to create components for the
processing method. Exploring the data helps you to construct a quantitative processing
method.
Figure 81. Explore – Review window
This section includes the following topics:
• Navigation Features
• Opening a Raw File and Displaying the Chromatogram
• Generating a Peak List
• Identifying Components
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 To open the Review view of the Explore window
When the left navigation pane is displayed:
a. Click Explore.
b. Click the Review icon.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Explore Section.
b. Choose View > Step Selector > Explore Review.
Navigation Features
You can use the following features of the Review view of the Explore window to navigate your
data:
• Sample Selector
• Locks
• Review Displays
• Current Review Display list parameters
Sample Selector
Three categories of sequences appear in the sample selector:
• Explore Sequences—sequences that you imported into Explore by using Load. You can
use Remove or Rename to delete or rename the selected sequence.
• Quantitate Sequences—processing sequences that you previously created in the
Quantitate window.
• Acquisition Sequence History—historical information about the sequences that were
used to acquire the data in the current workbook.
Note Raw files use absolute paths. When you move the workbook, the LCquan
application will not find the samples and will create an empty graph.
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 To process a raw file against the Explore Method
Click a raw file in the Sample Selector area (Figure 82).
The LCquan application automatically processes the data using the Explore method and
displays the results in the panes in the Explore window.
Figure 82. Sample Selector area
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Table 50 lists the parameters for the Sample Selector pane.
Table 50. Sample Selector pane parameters
Parameter
Description
Rawfile
Specifies the current a raw file.
Explore Sequences
Displays both loaded sequences and the acquisition history
sequence. The acquisition history is updated as samples are
acquired.
Quantitate Sequences
Displays a defined set of quantitative experiment parameters that
defines operating settings for a single sample or list of samples.
Each sample can be defined by the following settings: sample type,
file name, sample ID, QC or Standard level, ISTD correction
amount, dilution factor, vial position, injection volume, sample
volume, sample weight, sample name, and additional user-defined
parameters.
Acquisition Sequence
History
Displays a history of all sequences (and samples) that have been
acquired by the current workbook, along with other relevant
information for the acquisition such as operator, start and end
times, status, and comment.
 To use the sample selector shortcut menu
Right-click the Sample Selector pane to display the shortcut menu (Figure 83).
Figure 83. Shortcut menu for the Sample Selector pane
Table 51 describes these shortcut menu commands.
Table 51. Sample Selector shortcut menu commands (Sheet 1 of 2)
Thermo Scientific
Command
Description
Load New Sequence
Selects a sequence to load to the Explore Sequence area (even if the
Acquisition History is the active sequence).
Remove Active
Sequence
Deletes the selected sequence. The command is effective only if
the Explore Sequence is active.
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Table 51. Sample Selector shortcut menu commands (Sheet 2 of 2)
Command
Description
Rename Active
Sequence
Renames the selected sequence. The command is effective only if
the Explore Sequence is active.
Replace Active
Sequence
Replaces the currently selected sequence, A file selection dialog
box opens where you can select the replacement file. This
command is not available when any of the sequences under
Quantitate Sequence or Acquisition Sequence History are
selected.
The contents of the sequence are replaced, but the name does not
change.
Show Sequence Items
Collapses the currently selected sequence to display the sequence
name only.
Show
Info/Level/Sample
Items
Expands the currently selected sequence to display the sample
names.
Locks
Use locks to simultaneously compare data from different raw files, for example, to see how the
acquisition progressed from sample to sample. You can compare a plot from one sample to the
plots of other samples by locking one plot and clicking down the sequence in the sample
selector.
Change the state of the lock by clicking it. The lock can be in one of three different states:
• Unlocked (green),
• Locked against raw file change (yellow),
• Absolute lock (red),
When a plot is unlocked, every change of raw file or parameter is reflected in the plot.
Parameters, such as retention time, are sent out from unlocked plots, for example, when you
click a chromatogram.
Plots that are locked against raw file change respond to changes in parameters, but not to a
change of raw file. Parameters are not sent out from plots that are locked against raw file
change.
Plots that are absolutely locked do not respond to changes in parameters or raw files.
Parameters are not sent out from plots that are absolutely locked.
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Review Displays
You can define the location, number, and size of the individual graphic or table windows in
the results area. Select one of the five predefined sets of displays. Each choice displays the data
in multiple panes in the Explore window.
 To display a window layout
Select a layout from the Current Review Display list (Figure 84).
Figure 84. Current Review Display list
Table 52 lists the parameters for the Current Review Display list.
Table 52. Current Review Display list parameters
View
Layout
Multi Peak View
Opens on the left side of the page with the default Chromatogram
and Spectrum. Opens on the right side of the page with the
default Multi Peak Plot.
Comparison View
Displays three stacked panes: Chromatogram, Spectrum, and
Peak List (as the defaults).
Peak List View
Displays two tall panes side by side: Chromatogram and Peak List
(as the defaults).
Large Chro View
Displays a large, single pane: Chromatogram (as the default).
Sample Info View
Displays four panes: one pane in the top row, Chromatogram
(as default), and three small, side-by-side panes in the bottom row:
Sample Info, Instrument Method List, and Status Plot (as the
defaults).
Note You can change the contents of the panes but not their sizes, shapes, or positions.
 To change the name of the layout
1. Select the name in the Review Display list.
2. Type the new name.
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 To import a layout
1. Choose Files > Layout Configuration > Import Layout Configuration to display the
LCquan Config File dialog box.
2. Browse to the LCquan configuration file and click Open.
The application places the configuration file in the Imports folder.
 To save a layout
1. Choose Files > Layout Configuration > Export Layout Configuration to open the
LCquan Config File dialog box (Figure 85).
Figure 85. LCquan Config File dialog box
2. Type a name for the exported configuration file.
Type only the file name. You cannot change or enter the path. The LCquan application
saves the exported file in the Exports folder for the current workbook.
3. Click OK.
The LCquan application places the config file in the Exports folder.
Note When you change the properties of a display and save the workbook, the new
properties will be active when you reopen the workbook.
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Opening a Raw File and Displaying the Chromatogram
Open a raw file that is representative of your data set to determine suitable peak detection and
integration parameters.
 To open a raw file
Do one of the following in the Explore – Review view:
• Click the Browser button and select a raw file.
• Choose File > Open Raw File.
• Click a sample in the Sample Selector.
For more information, see “Sample Selector” on page 139.
The application imports the raw data for the raw file sample and displays the raw
chromatogram on the Explore – Create view.
 To see the mass spectrum
1. In the Current Review Display Layouts, select the type of layout to display.
For more information, see “Current Review Display list parameters” on page 143.
In the Chromatogram pane, peaks that correspond to the components are displayed with
their retention times (Figure 86).
2. Click a peak in the chromatogram.
The Spectrum view displays the corresponding spectrum.
Figure 86. Chromatogram pane
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Generating a Peak List
The LCquan application can generate a peak list, a table of peak properties such as retention
times, and peak areas of the major peaks in the chromatogram. You can use the peak list to
identify and name quan components and export the component names and properties to the
Quantitate window. Creating quan components is the first step in creating a processing
method.
The components that the LCquan application creates out of the peak list are based on the
Explore method define in the Create view of the Explore window. In general, you want to
filter first to get one peak in the peak list, generate its quan component, and add quan
components to the processing method one at a time.
 To create a peak list
1. Select Peak List from the view selector in the right pane (Figure 87).
Figure 87. Peak List in the right pane
2. In the Limit Peaks area, specify the peak list parameters:
a. Enable Select Top Peaks (Figure 88).
Figure 88. Limit Peaks area
b. Select either the Select By Area or Select By Height option.
c. Specify a number to select.
This limits the listed peaks to the n most significant.
d. Click Apply.
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The application generates a peak list for the peaks in the chromatogram (Figure 89).
Note In Explore, only the peak name is editable in the peak list.
Figure 89. Generated peaks list
3. To generate names for the peaks, right-click the peak list and choose
Create Peak Names > For All Peaks in List from the shortcut menu.
The application generates peak names in the form “Peak @ x.xxxx” where x.xxxx is the
retention time at the peak apex (Figure 90). (The component name is the same as the
peak name.)
Figure 90. Peak list
4. To change peak names, do one of the following:
• Select the current name and type a new name.
• Use the Peak Name List Editor.
5. To export all the component names and settings to the Quantitate window, right-click the
peak list and choose Create Quan Components > For All Peaks in List from the
shortcut menu.
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6. To export selected component names and settings to the Quantitate window:
a. Select the peaks for which you want to create quan components.
b. Right-click the peak list and choose Create Quan Components > For Selected
Peaks in the List from the shortcut menu (Figure 91).
Figure 91. Shortcut menu for the peak list
 To use the Peak Name List Editor
1. To open the Peak Name List Editor (Figure 92), right-click the peak list and choose
Modify Peak Names from the shortcut menu.
Table 53 lists the parameters for the Peak Name List Editor dialog box.
Figure 92. Peak Name List Editor dialog box
2. To create a new peak:
a. Type a new name on the last line of the grid.
You can use alphanumeric entries.
b. Specify values for the Apex RT and the Delta RT.
There is never any range checking on the Apex RT or the Delta RT.
3. To import a peak list, click Import and browse for your list.
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4. To export the peak list, click Export and enter a name for the file in the Peak Name List
File dialog box (Figure 93).
Figure 93. Peak Name List File dialog box
Note You can load the Peak Name List from any available location. A copy of the file
is created in the Import folder, and .hss tracks entries created for it.
Table 53. Peak Name List Editor dialog box parameters
Parameter
Description
Peak Name
Displays a column of label names for the explore peak.
Apex RT
Displays a column of the expected retention times for the peak.
Delta RT
Displays a column of the allowable ranges from the Apex RT.
Identifying Components
When the LCquan application acquires data, it creates unique scan filters according to the
type of experiment you specify in the instrument method. When you load a raw file, it lists
the scan filters associated with the raw file in the Filter box.
 To relate the chromatogram peaks with the components
From the Filters box, select a scan filter and click Apply.
The application displays the filtered chromatogram (Figure 94).
It is important to know the parent ion mass for your components. In this example, the
parent ion mass for methyltestosterone is m/z 303 and the scan filter is:
+ c Full ms2 [email protected] [100.00-310.00]
The methyltestosterone corresponds to the peak named Peak @ 1.991 in the peak list.
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Figure 94. Filtered chromatogram
 To review the filtered chromatograms and mass spectra
1. Click the Review icon.
The application displays the Review view of the Explore window.
2. Select Multi Peak Plot in the right pane.
3. Click a chromatogram peak in the multipeak plot.
The application displays the product ion mass spectrum at the maximum intensity, and
the mass-to-charge ratios of the first several ions of highest intensity in the mass spectrum.
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Exporting the Active Raw File to Qual Browser
Exporting the Active Raw File to Qual Browser
The LCquan application provides a direct link to Qual Browser from the Explore view. Qual
Browser provides for more sophisticated qualitative review than what is available in the
LCquan application, which is mainly concerned with quantitative, rather than qualitative,
analysis. With Qual Browser, you can perform library searches, formula searches for spectra,
background subtraction, and other data manipulation.
 To open Qual Browser
Click the Qual Browser icon in the navigation pane.
When you open Qual Browser, the LCquan application retrieves the currently selected
raw file.
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Data Views
Data Views
For each sample, you can display various types of data. The Explore – Create and Explore –
Review views let you preview or display your data in any of the following views:
• Chromatogram View
• Chromatogram List View
• Error Report View
• Filter List View
• General Parameters Plot View
• Instrument Method View
• Mass List View
• Peak List View
• Sample Info View
• Spectrum View
• Status Plot View
• Status Report View
• Tune Method View
• Multi Peak Plot View for Review Only
Each preview pane contains a Toolbar for Selectable Views at the top of the pane.
Toolbar for Selectable Views
Use the Toolbar for Selectable Views (Figure 95) to select the view you want to display in the
preview pane. Not all views display all the toolbar options. At a minimum, the toolbar
contains the View Selector list and a lock icon.
Figure 95. Toolbar for Selectable Views
Arrows
Item Selector
View Selector
Lock
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Table 54 lists the controls for the Toolbar for Selectable Views.
Table 54. Toolbar for Selectable Views controls (Sheet 1 of 3)
Control
Description
Arrows
Moves forward or backward through a range of possible selections:
for example, to display the next or previous chromatogram peak.
The arrows are not selectable (grayed out) when either of these
cases exists:
• A particular directional move is not possible; for example, the
arrows move through a list and the current selection is at the
top of the list, so the left (backward) arrow is grayed out.
• The yellow or red lock is set, so no changes can be made in the
red-locked pane and only changes other than raw file or
component changes can be made in yellow-locked panes.
Both arrows are grayed out.
Note The actions of the arrows vary in some instances between
the Explore and Quantitate windows. For example, in the
Chromatogram pane in Explore, the arrows can move through
multiple peaks for one sample. In the same pane in Quantitate,
they can move through different samples.
Lock
Allow changes (or prevent changes) to a raw file or parameters.
The color of the lock indicates the lock status of a pane.
Red = Locked Against All Changes. The lock icon is a closed lock.
• You cannot make any changes in panes that have red locks.
• No changes you make are reflected in panes that have red
locks.
• All shortcut menu commands that can change the pane or the
data are unavailable.
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Table 54. Toolbar for Selectable Views controls (Sheet 2 of 3)
Control
Description
Yellow = Locked Against Raw file (or Component) Changes. The
lock icon is a closed lock.
• You cannot make changes to a raw file (or to a component, in
the Calibration Curve pane) in panes that have yellow locks.
• When you make changes other than raw file changes in any
pane, those changes are reflected in panes that have yellow or
green locks. For example, if you click a Chromatogram pane,
the focal point moves in a Chromatogram List pane even if
the latter pane has a yellow lock.
• All shortcut menu commands that can change the raw file or
components in the pane are unavailable.
Green = Unlocked. The lock icon is an open lock.
Any changes you make in any panes are reflected in panes that
have green locks.
Note When you apply a yellow or a red lock to a pane, you
essentially capture (take a “snapshot” of ) that pane as it was just
before you locked it.
Play/Pause
Runs an automated action for the current pane.
Item Selector list
Displays a list of selectable items for the current pane.
Detector Selector list
The detector stream for the data type of interest.
When a raw file is currently selected for the pane, the detector box
contains a list of the detector streams in the raw file in the form:
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
When redisplaying, only the current selection (and any other
selection available from the raw file) is displayed.
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Table 54. Toolbar for Selectable Views controls (Sheet 3 of 3)
Control
Description
View Selector list
Select from the list of selectable views for the current section.
Chromatogram View
The Chromatogram view displays a chromatogram and all detected peaks for a sample and
Explore method (Figure 96). The displayed chromatogram is based on the range specified in
the Explore method. All detected peaks are displayed but cannot be edited. Click the
chromatogram to set the Retention Time marker. All spectrum, spectrum list, chromatogram
list, and multi-peak plot views that are not locked receive the selected time and update.
Figure 96. Chromatogram view
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock), or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 152.
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Table 55 lists the parameters for the Chromatogram view.
Table 55. Chromatogram view parameters
Parameters
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single sample peak.
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock Against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Display Options
Opens the Chromatogram Display Options dialog box. For more
information, see “Chromatogram Display Options.”
Reset Scaling
Resets both x and y axes to display the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Chromatogram Display Options
Use Chromatogram Display Options dialog box to modify the appearance of the
chromatogram (Figure 97).
These display options are also used when creating a processing method. For more information
about using these options to create a processing method, see “Chromatogram Display
Options” on page 268 in Chapter 4, “Creating a Processing Method.”
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Table 56 lists the parameters for the Chromatogram Display Options dialog box.
Figure 97. Chromatogram Display Options dialog box
 To display this dialog box
When the left navigation pane is displayed:
a. Click Explore.
b. Click the Method or Review icon.
c. Right-click the data pane of the Chromatogram view, and choose Display Options
from the shortcut menu.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Explore Section.
b. Choose View > Step Selector > Explore Method or Explore Review.
c. Right-click the Chromatogram pane, and choose Display Options.
Table 56. Chromatogram Display Options dialog box parameters (Sheet 1 of 2)
Parameter
Description
Label With
Select the data attributes you want to show in the data plots.
Thermo Scientific
Retention Time
Displays the peak apex retention time (RT) above the
chromatogram peaks. RT is displayed on all peaks that meet the
selection criteria set in the Label Threshold box.
Name
Displays the peak name above the peak.
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Table 56. Chromatogram Display Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Base Peak
Displays the base peak mass for the scan above the chromatogram
peak.
Signal to Noise
Displays the peak signal-to-noise (S/N) value above the
chromatogram peak.
Note When RMS S/N is selected in the Peak Detection Settings
options set, “<RMS>” appears after the S/N value.
Decimals
Sets the number of decimal places for the peak apex retention time
label.
Area
Displays the peak area.
Height
Displays the peak height.
Label Styles
Stylize the labeling displayed with the data.
Offset
Moves the label a defined distance from the data.
Rotated
Rotates the labels above the peaks to 90 degrees.
Boxed
Displays boxes around the labels above the peaks.
Size
Defines the distance the label is offset from the data.
Label Threshold (%)
Sets a threshold so that peaks above this level can show labels.
Plotting
Select one style to display your data.
Point to Point
Select a graphic style to display the active chromatogram or
spectrum using point-to-point peak profile.
Stick
Select a graphic style to display the active chromatogram using
vertical lines.
On/Off Labeling Option—When No Peak Found
Show Apex Time
Labels
Selects to always display maxima labels.
Axis Offset
Select one or both to offset the displayed plot from the x axis, y axis or both.
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X
Select to have the x-axis offset move the y axis slightly above the
x axis so that you can see baseline details.
Y
Select to have the y-axis offset move the x axis slightly to the right
of the y axis so that you can see plot details at low x-axis values.
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Chromatogram List View
The Chromatogram List view displays the chromatographic data points in tabular format
(Figure 98).
Figure 98. Chromatogram List view
The contents of the grid are read-only.
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock), or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 152. Table 57 lists the
parameters for the Chromatogram List view.
Table 57. Chromatogram List view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single scan.
Column Headings
Thermo Scientific
RT
Displays the retention time of the given data point.
Intensity
Displays the absolute intensity of the given data point.
%Relative Intensity
Displays the intensity of the data point relative to the most intense
data point in the chromatogram.
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Table 57. Chromatogram List view parameters (Sheet 2 of 2)
Parameter
Description
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Error Report View
The Error Report view displays the error log information stored in the current raw file
(Figure 99).
Figure 99. Error Report view
The contents of the grid are read-only.
When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
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Table 58 lists the parameters for the Error Report view.
Table 58. Error Report view parameters
Parameter
Description
Arrows
The left and rights arrows move through the list of detectors and
devices, incrementing or decrementing by a single item.
Detector Selector List Options
MS
Displays the error log of a mass spectrometer.
Status
Displays the error log of a device that does not log data.
[Detector Streams in
Current Raw File]
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Filter List View
The Filter List view displays the list of unique filters that are stored in the current raw file in
table format (Figure 100).
Figure 100. Filter List view
The contents of the grid are read-only.
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When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
Table 59 lists the parameters for the Filter List view.
Table 59. Filter List view parameters
Parameter
Description
Arrows
The arrows are not used in Explore window.
Column Heading
Filters
Displays the list of unique filters that are stored in the current raw
file.
Shortcut Menu
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Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard where you can paste the
data from the Clipboard buffer into a document.
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General Parameters Plot View
The General Parameters Plot view displays the selected parameters for all detected Explore
peaks for a sample and Explore method (Figure 101). Select the parameters you want to see
plotted from the Item Selector list. You can lock the general parameters plot for one sample
and click through the other samples to look for trends or inconsistencies in the data.
Figure 101. General Parameters Plot view
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 152.
Table 60 lists the parameters for the General Parameters Plot view.
Table 60. General Parameters Plot view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the item list,
incrementing or decrementing by a single item.
Item Selector List Options
RT
Displays retention time for the detected peaks.
Area
Displays areas for the detected peaks.
Units: count-seconds
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Table 60. General Parameters Plot view parameters (Sheet 2 of 2)
Parameter
Description
Height
Displays heights of the detected peak apexes.
Units: counts
Peak Width
Displays peak widths for the detected peaks.
Shortcut Menu
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Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Reset Scaling
Resets x and y axes to display the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Instrument Method View
The Instrument Method view displays the instrument method parameters (Figure 102). To
view an instrument’s method, select the instrument from the Item Selector list.
Figure 102. Instrument Method view
The contents of the grid are read-only.
When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock), or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 152.
Table 61 lists the parameters for the Instrument Method view.
Table 61. Instrument Method view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
Switches between instrument methods in the current raw file.
Instrument Selector List Options
[Instrument Name]
Displays the method for the selected instrument.
Shortcut Menu
Open Raw File
Thermo Scientific
Opens the Select Raw File dialog box where you can select the raw
file to load.
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Table 61. Instrument Method view parameters (Sheet 2 of 2)
Parameter
Description
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Mass List View
The Mass List view displays the spectral mass intensity list for a sample at the selected
retention time (Figure 103).
Figure 103. Mass List view
The contents of the grid are read-only.
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock), or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 152.
Table 62 lists the parameters for the Chromatogram List view.
Table 62. Mass List view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single scan.
Column Headings
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Mass
Displays the mass value above the spectral line column.
Intensity
Displays the intensity of the spectral data point column.
%Base
Displays the relative percentage this data point has to the largest
data point in the Intensity column.
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Table 62. Mass List view parameters (Sheet 2 of 2)
Parameter
Description
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Peak List View
The Peak List view displays a list of detected Explore peaks for a sample and an Explore
method (Figure 104). You can edit the peak name in the view.
You can also modify the peak names using the Peak Name List Editor dialog box.
Figure 104. Peak List view
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Table 63 lists the parameters for the Peak List view.
Table 63. Peak List view parameters (Sheet 1 of 4)
Parameter
Description
Arrows
The left and right arrows move through the peak list,
incrementing or decrementing by a single peak.
Column Headings
Peak Name
The name to apply to the explore peak column.
Apex RT
The expected RT for the peak column.
Area
The calculated peak area column.
% of Largest Area
The area of this peak relative to the area of the peak with the
biggest area in the list column.
% of Total Area
The area of this peak relative to the summed total area of all peaks
in this list column.
Shortcut Menu
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Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
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Table 63. Peak List view parameters (Sheet 2 of 4)
Parameter
Description
Create Peak Names –
For Selected Peaks in
List
Create peak names for the selected peaks in the list based on the
current detected set of peaks. Each peak name is auto-generated in
the form “Peak @ x.xxxx” where x.xxxx is the RT at the peak apex.
A peak apex value is created corresponding to the detected peak’s
apex and a delta value defined by the lesser value of either of these
two calculations:
• Apex RT minus the Peak Left endpoint
–or–
• Peak Right endpoint minus the Apex RT
The Peak Apex and Delta values are used to determine which label
to apply to the peak.
When a peak is located within the range:
• Peak Apex minus Delta to Peak Apex plus Delta, the
corresponding label is used.
Note Delta RT is the range that is allowed from the Apex RT.
Create Peak Names –
For All Peaks in List
Create peak names for all peaks in the list based on the current
detected set of peaks. Each peak name is auto-generated in the
form “Peak @ x.xxxx” where x.xxxx is the RT at the peak apex.
A peak apex value is created corresponding to the detected peak’s
apex and a delta value defined by the lesser value of either of these
two calculations:
• Apex RT minus the Peak Left endpoint
–or–
• Peak Right endpoint minus the Apex RT
The Peak Apex and Delta values are used to determine which label
to apply to the peak.
When a peak is located within the range:
• Peak Apex minus Delta to Peak Apex plus Delta, the
corresponding label is used.
Note Delta RT is the range that is allowed from the Apex RT.
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Table 63. Peak List view parameters (Sheet 3 of 4)
Parameter
Description
Modify Peak Names
Opens the Peak Name List Editor dialog box where you can
manage the current peak name list. Entries are not validated in
this dialog box. You can create duplicate names or location
parameters. For more information, see “Generating a Peak List”
on page 146.
The application use the first item in the list that matches the
criteria of a peak.
Import Peak Name List Opens a file-selection dialog box where you can import the
naming list to a text file (.txt or .csv).
A copy of the file is created in the Import folder, and both an
event record and a file tracking record are created. After the file is
accepted, the application relabels any peak list or chromatogram as
required.
Export Peak Name List Opens an export-name dialog box where you can export a naming
list to a text file. You specify the file name in the export-name
dialog box. The file is created in the Export folder of the current
workbook. The application creates both an event and a file
tracking record.
Create Quan
Components – For
Selected Peaks in List
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Creates a quantitation component for each selected peak in the
list. If no peaks are selected, the application uses all peaks.
The component name is the same as the peak name. The
component parameters are defaulted to a common set of values
with the exception of the following: Expected RT and RT
Window are peak dependent; the Mass Filter and Scan Filter are
obtained from the Explore method. All components are assumed
to be target components, and the level tables are copied from
existing components. After the components have been created, a
confirmation dialog box is displayed.
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Table 63. Peak List view parameters (Sheet 4 of 4)
Parameter
Description
Create Quan
Components – For
All Peaks in List
Creates a quantitation component for each peak in the list.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
The component name is the same as the peak name. The
component parameters are defaulted to a common set of values
with the exception of the following: Expected RT and RT
Window are peak dependent; the Mass Filter and Scan Filter are
obtained from the Explore method. All components are assumed
to be target components, and the level tables are copied from
existing components. After the components have been created, a
confirmation dialog box is displayed.
Sample Info View
The Sample Info view displays sample information stored in the current raw file during
acquisition (Figure 105).
Figure 105. Sample Info view
The contents of the grid are read-only.
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When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
Table 64 lists the parameters for the Sample Info view.
Table 64. Sample Info view parameters
Parameter
Description
Arrows
The arrows are not used in the Explore windows.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Spectrum View
The Spectrum view displays a spectrum for a sample at the selected retention time
(Figure 106).
 To make changes to the spectrum display
Right-click the spectrum view and choose Display Options from the shortcut menu.
For more information, see “Chromatogram Display Options” on page 156.
When the view is locked (lock icon is yellow or red), you cannot select any menu item in
the shortcut menu that changes the raw file (with the yellow lock), or the raw file and
parameters (with the red lock). Menu items that would cause changes are grayed out. For
more information about locks, see “Toolbar for Selectable Views” on page 152.
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Figure 106. Spectrum view
Table 65 lists the parameters for the Spectrum view.
Table 65. Spectrum view parameters
Parameter
Description
Arrows
The left and right arrows move through the scans, incrementing or
decrementing by a single scan.
Shortcut Menu
Thermo Scientific
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Display Options
Opens the Chromatogram Display Options dialog box. For more
information, see “Chromatogram Display Options dialog box
parameters” on page 157.
Reset Scaling
Resets the x and y axes to display the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Status Plot View
The Status Plot view displays status data that the instruments store during the acquisition of
the selected raw file (Figure 107). The list contains all the parameters for the selected
instrument.
Figure 107. Status Plot view
The contents of the plot are read-only.
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
Table 66 lists the parameters for the Status Plot view.
Table 66. Status Plot view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the item list,
incrementing or decrementing by a single item.
Item Selector List Options
Parameter
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Specifies the parameter plotted on the y axis.
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Table 66. Status Plot view parameters (Sheet 2 of 2)
Parameter
Description
Detector Selector List Options
MS
Displays status information for a mass spectrometer.
Status
Displays status information for a device that does not log data.
Detector Streams in
Current Raw File
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Shortcut Menu
Thermo Scientific
Open Raw File
Opens the Select Raw File dialog box, which you can select
the raw file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Reset Scaling
Resets the x and y axes to display the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Status Report View
The Status Report view displays the status information stored in the current raw file in table
format (Figure 108). A status report is a list of status information for all parameters at one
retention time. Use the arrows to move between time points of the chromatogram. Notice
that status information is acquired less frequently than the chromatogram, so the status
information does not always change.
Figure 108. Status Report view
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock), or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 152.
Table 67 lists the parameters for the Status Report view.
Table 67. Status Report view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the status item list,
incrementing or decrementing by a single status item.
Detector Selector List Options
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MS
Displays status information for a mass spectrometer.
Status
Displays status information for a device that does not log data.
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Table 67. Status Report view parameters (Sheet 2 of 2)
Parameter
Description
[Detector Streams in
Current Raw File]
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Thermo Scientific
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Tune Method View
The Tune Method view displays the tune method stored in the current raw file during
acquisition (Figure 109).
Figure 109. Tune Method view
When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
Table 68 lists the parameters for the Tune Method view.
Table 68. Tune Method view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The arrows are not used in the Explore window.
Column Headings
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Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
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Table 68. Tune Method view parameters (Sheet 2 of 2)
Parameter
Description
Shortcut Menu
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Reset Scaling
Resets scaling to the default pane.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Multi Peak Plot View for Review Only
The Multi Peak Plot view is a data view that is available only from the Explore – Review view
and displays all detected Explore peaks for a sample/method combination (Figure 110).
Figure 110. Multi Peak Plot view
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You can set the number of rows and columns, define the number of peak graphics displayed
on the screen, and change chromatographic display options.
• You can define a maximum of 50 cells.
• The x-axis range for each peak is 2.0 times the detected peak width, 50% on either side.
• The peak baseline endpoints are displayed as blue circles.
Note When the endpoints appear as blue circles, you cannot select and drag them to
manually integrate the peak.
 To set the number of rows and columns
1. Right-click the plot and choose Options from the shortcut menu.
The Multi-Peak Options dialog box opens. For more information, see “Multi-Peak
Options dialog box parameters” on page 182.
2. In the Arrangement box, enter the number of columns and rows.
You can set the normalization level to be the same for all peaks, or you can normalize each
peak individually.
 To set the normalization levels
1. Right-click the plot and choose Options from the shortcut menu.
The Multi-Peak Options dialog box opens. For more information, see “Multi-Peak
Options dialog box parameters” on page 182.
2. In the Intensity Scale box, select either the Normalize to Largest Peak or Use Fixed
Intensity Range option.
 To set label and plotting styles
From the window menu, choose Options > Display Options > Chromatogram.
The Chromatogram Display Options dialog box opens. These label and plotting styles
apply to the multi-peak views. For more information, see “Chromatogram Display
Options dialog box parameters” on page 157.
When the view is locked (lock icon is yellow), you cannot select any menu item in the
shortcut menu that changes the raw file. Menu items that would cause changes are grayed out.
For more information about locks, see “Toolbar for Selectable Views” on page 152.
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Table 69 lists the parameters for the Multi Peak Plot view.
Table 69. Multi Peak Plot view parameters
Parameter
Description
Arrows
The left and right arrows move through the grid, incrementing or
decrementing by a single sample peak.
Play / Pause
Starts or pauses the timed review of the samples.
Play causes the peaks for the given sample to be displayed for the
specified time interval (see Multi-Peak Options); then the next set
of peaks is displayed for the specified time interval until there are
no more peaks in the list. When the Repeat Playback box is
selected, the playback restarts at the beginning of the list until
manually stopped. Switching panes also stops the timed display.
Shortcut Menu
Lock Against Raw File
Change
Prevents changes to a raw file. The lock icon is yellow and the lock
is closed.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Use User Defined Time Resets the time scale to the user-defined range as entered in the
Range
Realtime Display Settings dialog box. For more information, see
“Realtime Display Settings” on page 87.
Thermo Scientific
Options
Opens the Multi-Peak Options dialog box. For more information,
see “Multi-Peak Options.”
Reset Scaling
Resets x and y axes to show the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Multi-Peak Options
Use the Multi-Peak Options dialog box to determine how the peaks are arranged and to
change chromatographic display options (Figure 111). Table 70 lists the parameters for the
Multi-Peak Options dialog box.
Figure 111. Multi-Peak Options dialog box
Table 70. Multi-Peak Options dialog box parameters
Parameter
Description
Arrangement
Range: 1 to 50
Note The product of columns and rows must be equal to or less than 50.
Number of Display
Columns
Number of peaks displayed left to right.
Number of Display
Rows
Number of peaks displayed top to bottom.
Playback
Playback options are unavailable in the Explore window.
Intensity Scale
Normalize to Largest
Peak
Overrides the settings defined in the Display Options dialog box.
This option disables the fixed intensity range edit box.
Use Fixed Intensity
Range
Overrides the settings defined in the Display Options dialog box.
This option disables the fixed intensity range edit box.
Time Scale
Use User Defined Time Select to enter a user specified time range to use for all plots.
Range
Time Range (mins)
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Sets the time base, in minutes, for all plots.
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4
Creating a Processing Method
A processing method provides instructions to the LCquan application about how to perform
quantitative analysis on raw data. A processing method contains component identification,
detection, integration, and calibration information. This chapter describes how to create a
processing method by using the Create Method views of the Quantitate window.
Contents
• Creating a Processing Method with the New Method Wizard
• Importing Information for a Q Exactive Mass Spectrometer
Quantitation Method
• Specifying Method Identification
• Specifying Method Calibration
• Saving the Processing Method
• Importing a Processing Method
• Exporting Components and Levels to an Acquisition Sequence
• Data Views
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Creating a Processing Method with the New Method Wizard
Creating a Processing Method with the New Method Wizard
From the Create Method view in the Quantitate window, you can construct a processing
method. The LCquan application requires component identification information to associate
the internal standard and target compounds with chromatogram peaks (Figure 113). To
import processing information for the Q Exactive mass spectrometer from an exported
inclusion list, see “Importing Information for a Q Exactive Mass Spectrometer Quantitation
Method” on page 188.
Start the Wizard
Use the New Method Wizard to create a processing method.
 To start the Wizard
1. From any window, click Quantitate in the navigation pane.
The Create Method view opens.
2. Open the New Method Wizard (see Figure 112).
• When you have not previously defined a processing method, the New Method
Wizard automatically opens and leads you through the initial steps of creating a
method.
• When you have already defined a processing method, use the Options >
New Processing Method menu command to open the wizard.
Figure 112. Welcome page for the New Method Wizard
3. Click Next.
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Create or Import a Method
Create a new processing method or importing an existing one from a file (see Table 71).
 To define a processing method
1. Do one of the following:
• Select the Create New Method option and the Initialize with Acquisition
Component Names check box.
• Select the Import Existing Method option.
Note The Initialize with Acquisition Component Names check box is available only
when you have defined component names (Figure 113).
When you create a new acquisition sequence, you can assign temporary component
names using a sequenced base component name, such as Comp1-Comp4.
To assign custom component names, use the Acquisition Levels dialog box available
from the Acquisition Sequence grid shortcut menu. Refer to the Standard and QC
Levels command on the shortcut menu.
Figure 113. Create or import method page
2. Click Next.
• If you chose to create a new method, go to Specify Calibration Standards.
• If you chose to import an existing method, go to Import a Processing Method.
Table 71. Options for the create or import method page
Thermo Scientific
Parameter
Description/Condition
Create New Method
Creates a new processing method.
Initialize with
Acquisition
Component Names
Creates default processing method components with the
names from the acquisition sequence component list.
Import Existing
Method
Select to specify an existing processing method.
Note This check box is enabled only when the components
are defined in the acquisition sequence.
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Import a Processing Method
Import a saved processing method file.
 To import a processing method file
1. Type the path to a processing method file or click Browse and find a file (Figure 114).
Figure 114. Import processing method page
2. Click Next.
Specify Calibration Standards
Specify the type of standards you are using to calibrate (Figure 115).
 To specify the standards
1. Select a standard.
• To use an internal standard, select the Calibrate Using Internal Standards option.
• To use an external standard, select the Calibrate Using External Standards option.
Figure 115. Internal or external standards page
2. Click Next.
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Creating a Processing Method with the New Method Wizard
Select a Raw File
Select a raw file to test the peak detection and integration parameters.
 To select a raw file
1. Click Browse.
2. Browse to find the raw file in the raw files folder in your workbook.
3. Click Open.
Note In general, open a raw file that corresponds to a low-concentration calibration
standard.
Note To help you determine the parameters of the processing method, use a raw file
from a similar past experiment.
4. Click Next.
Complete the Wizard
Click Finish to exit the New Method Wizard.
The Create Method view in the Quantitate window opens to the Identification page.
You are now ready to begin building the processing method.
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Importing Information for a Q Exactive Mass Spectrometer Quantitation Method
Importing Information for a Q Exactive Mass Spectrometer
Quantitation Method
Using the Q Exactive mass spectrometer within the LCquan application, you can easily create
quantitation experiments. Starting with Exactive Series 2.3, you can import compound
information, including targeted SIM mass lists, for a processing method from the inclusion
list in the method editor for the Q Exactive mass spectrometer. By importing, you can update
your quantitation methods without manually entering method parameter information. For
information about importing information automatically from an inclusion list, see “To
automatically import method values into the LCquan application” on page 189.
To create methods and acquire data, you must have the Q Exactive mass spectrometer
installed and configured (see “Configuring Instruments” on page 115) and have added the
necessary component information to the inclusion list.
A successful import requires the following information:
• Component name
• Mass value
• Start and stop time
After you export a file from the inclusion list editor, the application places a file containing
parameter information for a quantitation method in the LCquan workbook temp folder.
Exported inclusion list information is available from either the acquisition workstation or a
processing workstation when you access the Quantitate > Method section of the Workbook.
• To export the inclusion list, see To manually import method values from an exported
inclusion list. Then the next time you open the LCquan application, your file is available
for import.
• To import the inclusion list, see To automatically import method values into the LCquan
application.
 To manually import method values from an exported inclusion list
1. To create an inclusion list in the method editor, open the application and click Inclusion
from the Instrument Setup page.
The application displays a table where you can add or change mass information. To
import the information successfully, you must enter the following:
• Mass [m/z]
• Start time
• End time
• Comment (Use this field for the component name.)
Note You can also import information from an Excel spreadsheet by saving the file as
a CSV file. Save the CSV file to the location listed in step 5.
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2. To export the inclusion list as a CSV file, click File > Export to display the Save dialog
box.
3. In the File Name box, type LCquan_Component_List.csv.
If you type the wrong name, the application saves the file in the correct folder, but it does
not prompt you when you click Quantitate and then click the Method icon. The file
remains until you exit the application. You can export the file again using the correct
name. When you click Quantitate and then click the Method icon, the application
prompts you to import the information.
4. In the Save as Type list, select Comma-separated Files (*.CSV) as the file type.
5. In the file area, browse to the temp directory of your workbook. To save the file, click
Save.
 To automatically import method values into the LCquan application
1. Click
to open the LCquan application.
2. From the list on the opening screen, select a workbook to open or select New Workbook.
The LCquan application opens.
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3. In the left navigation pane, click Quantitate and then click the Method icon (see
Figure 116).
Figure 116. Method before importing data from the inclusion list
The application prompts you to import instrument method information contained in the
exported method editor inclusion list.
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4. Do one of the following:
• To import the information and merge it with your LCquan method information,
click OK.
If your file does not have the required information, the application displays a message
and deletes the file. Return to the navigation pane, and click Instruments. Use the
method editor to add the required information, and then export the file again (see
step 2 on page 189 for detailed information).
• To define your own parameter values, click Cancel.
The application deletes the file.
5. To restore the file, return to the navigation pane and click Instruments. Use the method
editor to add the required information to the inclusion list, and then save the target mass
information.
6. Export the file again (see step 2 on page 189 for detailed information).
7. Open the LCquan application.
A message box appears again prompting you to import the data.
If you already entered values with matching compound names, the file overwrites those
values. The application updates the related values for matching compounds.
The LCquan application imports the following information to the Identification page:
• Component name
• Mass (m/z) (updated if already defined)
• Retention Time parameters (updated if already defined)
The application does not import peak identification or peak integration information.
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The next figure (Figure 117) shows the imported information for Figure 116 on
page 190.
Figure 117. Method after importing data from the inclusion list
The application displays imported target mass information that has been added to the
Explore and Quantitate sections of the navigation pane.
You must still enter all information on the Calibration page. (See “Specifying Method
Calibration” on page 242 for more information.)
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Specifying Method Identification
The LCquan application requires component identification information to associate the
internal standard and target compounds with chromatogram peaks (Figure 118). To import
processing information for the Q Exactive mass spectrometer from an exported inclusion list,
see “Importing Information for a Q Exactive Mass Spectrometer Quantitation Method” on
page 188.
Figure 118. Quantitate – Create Method – Identification window
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Specifying Method Identification
 To open the Identification page of the Create Method view
When the left navigation pane is displayed:
a. Click Quantitate.
b. Click the Method icon.
c. Click the Identification tab.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Quantitate Section.
b. Choose View > Step Selector > Quantitate Method.
c. Click the Identification tab.
The Identification page of the Create Method view includes these functional areas:
• Chromatogram Definition Area
• Retention Time Area
• Peak Integration Area
• Peak Identification Area
• Ion Ratio Confirmation Area
This section contains instructions for performing the following:
• Summing Ions Dialog Box
• Defining Peak Integration Parameters
Chromatogram Definition Area
Use the Chromatogram Definition area to specify the chromatographic parameters used to
create a chromatogram (Figure 119). Table 72 lists the parameters for the Chromatogram
Definition area.
Figure 119. Chromatogram Definition area
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Table 72. Chromatogram Definition area parameters (Sheet 1 of 2)
Parameter
Description
Detector
Specifies the specific data stream.
Smoothing
The number of points used for a moving mean filter to smooth
the chromatogram.
Format: whole numbers
Range: 1 to 15, odd numbers only
Note To disable filtering, set the parameter to 1.
Trace
Specifies the type of chromatogram:
• Mass Range: Specify up to 50 mass ranges. The masses are
added together to form the chromatogram.
• TIC: Full-scan acquisition resulting in a Total Ion Current
plot.
• Base Peak: In a differential chromatogram, the interpolation
of the baseline is derived from the distance between the
intersections of the tangents drawn to the peak sides and the
peak base.
• Summed: Uses ion summing to create a chromatogram that is
the sum of the chromatograms of related compounds. Ion
summing can increase sensitivity because it sums up to five
chromatograms of related masses, for example, water loss,
adducts, isotopes, or multiply charged peptides.
Note This definition set is the same for the second Trace box.
The second Trace box depends on which operators you select.
There is no second Trace box or trace operators for Trace:
Summed.
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Table 72. Chromatogram Definition area parameters (Sheet 2 of 2)
Parameter
Description
Trace: Mass Range, TIC, or Base Peak
+/-/“ “
Trace operator used to specify a trace operation.
This trace operation matrix shows the combinations used to set up
a method:
Mass Range+Mass Range
– Mass Range
TIC+ Mass Range
– Base Peak
Base Peak+Mass Range
– Mass Range
Note If the operator box remains empty, the second trace choice
is disabled.
Mass1 (m/z)
Specifies the initial mass value.
Mass2 (m/z)
Specifies the second mass value to define the mass range used for
trace operator math.
Filter
Specifies a scan filter to be applied to the acquired data. Enter a
filter or select a filter from a preloaded filter list (obtained from
the current raw file).
Note All filters are validated against the current set of filter
entry rules.
Trace: Summed
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Edit Summed
Opens the Summing Ions Dialog Box. Use the Summing Ions
dialog box to specify the mass-to-charge ratios and scan filters of
up to five ions for ion summing.
Summed Ions table
Displays the filters and mass-to-charge ratios of the ions you
specified for ion summing in the Summing Ions Dialog Box.
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Mass Tolerance and Precision
Use the Masses dialog box to specify tolerance and precision settings for the mass data
displayed in the Chromatogram and Spectrum panes (Figure 120). Table 73 lists the
parameters for the Masses dialog box.
To open the Masses dialog box, choose Options > Masses.
Figure 120. Masses dialog box
Table 73. Masses dialog box parameters
Parameter
Description
Mass Tolerance
Mass Tolerance
Type the mass tolerance value.
Range: 0.1 to 50 000
Note Mass ± mass tolerance is summed for each scan.
Units
Select one unit of measurement for data display.
• mmu = millimass units
• ppm = parts per million
Mass Precision
Decimals
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Type the number of decimal places for mass values display.
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Retention Time Area
Use the Retention Time area to specify a search window or corrections for retention time drift
(Figure 121). Table 74 lists the parameters for the Retention Time area.
Figure 121. Retention Time area
Table 74. Retention Time area parameters (Sheet 1 of 2)
Parameter
Description
Expected (min)
The expected elution time of the component (peak apex).
Range: 0.0 to 999.0
Units: minutes
Window (sec)
The time boundaries for the expected peak apex occurrence.
Range: 1.0 to 999.0
Units: seconds
Use as RT Ref
Specifies that the active component peak is to be used as a
retention time reference. (This component’s actual retention time
is used to adjust the expected retention times of other components
automatically during processing.)
All RT References appear in the Adjust Using list.
View Width (min)
The amount of time to display the Chromatogram pane.
Range: [Expected RT – (View Width/2)] through [Expected RT +
(View Width/2)]
Range: 0.10 to 999.0
Units: minutes
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Table 74. Retention Time area parameters (Sheet 2 of 2)
Parameter
Description
Adjust Using
Specifies that the retention time for this component be adjusted
based on the actual RT of another component that has been
designated an RT Reference.
Retention time references are automatically created if you select
the Use as RT Reference option when the component is active.
The processing method must have at least one retention time
reference for this box to be active.
All RT References appear in the Adjust Using list.
Adjust Using list
Specifies the RT Reference from the list to be used to adjust the
expected retention time of the current component.This list is
active only when you select the Adjust Using check box. The
actual retention time of the RT Reference component is used to
adjust the retention time of the active component automatically
during processing. The adjustment to the expected retention time:
Corrected RT Component Expected = RT Component Expected × RT
Reference Actual / RT Reference Expected
Peak Integration Area
Use the Peak Integration area to select and define peak integration parameters. Use the
Peak Integration area to define Genesis, ICIS, and Avalon peak detection algorithms to be
applied to the active raw file.
The Peak Integration area is dynamic, displaying criteria for the selected peak detection
method (Figure 122): Genesis, ICIS, or Avalon.
Figure 122. Peak Detection Algorithm list
The parameters for each of these peak integration methods is described in detail in “Defining
Peak Integration Parameters” on page 211.
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Peak Identification Area
Use the Peak Identification area (see Figure 123) to specify criteria for identifying peaks in
other raw files of the data set that correspond to the current component. Table 75 lists the
parameters for the Peak Identification area.
Figure 123. Peak Identification area
Table 75. Peak Identification area parameters
Parameter
Description
Highest Peak
Specifies that the highest (most intense) peak in the spectrum is
used as the component identification criterion.
Nearest RT
Specifies that the peak with the retention time in the
chromatogram that is closest to the expected retention time is used
as the component identification criterion.
Min Peak Height (S/N) For Genesis or ICIS only: Specifies a value for the minimum
S/N ratio. This criterion specifies that only peaks that meet or
exceed this minimum S/N are displayed.
Range (all peaks): 1.0 to 999.0
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Ion Ratio Confirmation Area
Use the Ion Ratio Confirmation area to confirm the presence of an analyte by comparing the
response of the quantitate ion (or ions) with the responses of one to five qualifier ions
(Figure 124). Table 76 lists the parameters for the Ion Ratio Confirmation area.
Figure 124. Ion Ratio Confirmation area
Table 76. Ion Ratio Confirmation area parameters (Sheet 1 of 2)
Parameter
Description
Enabled
Places the IRC table in a usable state so that confirmation
processing can take place.
To open the IRC Detection Method dialog box, select a row (not a
cell) and right-click the grid. For a detailed description of the IRC
detection method parameters, see “IRC Detection Method” on
page 224.
Note When this check box is cleared, the data fields are grayed
out.
Mass
Specifies the mass of the ion to be used in the confirmation
process. Type a new mass value into an empty row to generate a
new table row.
Target Ratio (%)
Specifies the ratio of the qualifier ion response to the quan ion
response.
Range: 0 to 200%
Window (+/–%)
Thermo Scientific
Specifies the amount (as a percentage) that the measured ratio can
vary from the target window value for the ion to still be considered
confirmed.
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Table 76. Ion Ratio Confirmation area parameters (Sheet 2 of 2)
Parameter
Description
Qualifier Ion
Coelution
Specifies the time the retention time can vary from the expected
retention time for the ion to still be considered confirmed.
Range: 0.000 to 0.100
Units: minutes
Shortcut Menu
Delete Selected Rows
Deletes all currently selected rows. You must select entire rows (by
clicking the leftmost column) before you can delete them.
Edit Selected Rows
Processing Info
Opens the IRC Detection Method dialog box where you can
change IRC peak detection settings. The settings for each IRC are
independent. When multiple rows are selected when you choose
this command, the first IRC in the list is selected for editing. For
detailed information about IRC peak detection settings, see “IRC
Detection Method” on page 224.
Window %
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Relative
Uses the target ratio tolerances in the Window ±% column as
relative percentages of the target ratio.
Absolute
Uses the target ratio tolerances in the Window ±% column as
absolute percentages of the target ratio.
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Summing Ions Dialog Box
Use the Summing Ions dialog box to specify for ion summing the mass-to-charge ratios and
scan filters of up to five ions (Figure 125). Ion summing creates a single chromatogram by
summing together up to five chromatograms. Ion summing can increase sensitivity because it
sums the chromatograms of related masses, for example, water loss, adducts, isotopes, or
multiply charged peptides. Ion summing provides the best results when chromatographic
peaks have similar retention times and peak shapes, and are identified by a unique scan filter,
mass filter, or both. Ion summing is data processing only and does not affect the original raw
data. The LCquan application can easily reconstruct and report the original chromatograms
that are part of the summed chromatogram. You cannot use ion summing and ion ratio
chromatograms together with the same component.
Figure 125. Summing Ions dialog box
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Table 77 lists the parameters for the Summing Ions dialog box.
Table 77. Summing Ions dialog box parameters
Parameter
Description
Mass (m/z)
Specifies one or more mass-to-charge ratios or ranges of
mass-to-charge ratios of an ion whose chromatogram the
LCquan application uses for ion summing.
Filter
Specifies the scan filter of an ion whose chromatogram the
LCquan application uses for ion summing.
+ (add ions)
Adds an ion for ion summing. To add an ion, select a scan filter
in the Filter box and enter an ion mass-to-charge ratio in the
Mass box. You can add the chromatograms of up to five ions.
– (subtract ions)
Removes an ion from the ion summing list. When you subtract
an ion, the LCquan application grays out the entry, but does not
delete it.
Apply
Populates the Summed Ions table on the Identification page of
the Create Method view with the scan filters and mass-to-charge
ratios of the ions you specified in the Summing Ions dialog box.
The Apply button does not close the dialog box.
OK
Populates the Summed Ions table on the Identification page of
the Create Method view with the scan filters and mass-to-charge
ratios of the ions you specified in the Summing Ions dialog box.
The OK button closes the dialog box.
 To open the Summing Ions dialog box
In the Chromatogram Definition Area of the Create Method – Identification page, select
Trace: Summed, and click Edit Summed.
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Chromatogram Normalization
In the Quantitate window, the LCquan application can normalize the chromatogram plot, so
either the height of the detected peak is 100% or the height of the highest peak is 100%
(Figure 126). You select which normalization to use in the Authorization Manager.
Note In the Explore window, the LCquan application normalizes the chromatogram so
that the height of the highest peak is 100%.
Figure 126. Multi Peak Plot view
Normalized to detected peak
Normalized to highest peak
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 To normalize the chromatogram plot so that the detected peak is 100%
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager dialog box (Figure 127).
Figure 127. Normalize Quan Chromatogram Plots to Detected Peak permission set to Allowed
2. In the Authorization Manager, do the following:
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Quantitate Section folder.
e. Select Normalize Quan Chromatogram Plots to Detected Peak.
The Permission Level options become available.
f.
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Select the Allowed option, and click OK.
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 To normalize the chromatogram plot so that the highest peak is 100%
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager (Figure 128).
Figure 128. Normalize Quan Chromatogram Plots to Detected Peak permission set to
Disallowed
2. In the Authorization Manager, do the following:
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Quantitate Section folder.
e. Select Normalize Quan Chromatogram Plots to Detected Peak.
The Permission Level options become available.
f.
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Select the Disallowed option, and click OK (Figure 128).
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Specifying Component ID Parameters and Integrating the Peaks
When the LCquan application acquires data, it creates unique scan filters according to the
type of experiment you specify in the instrument method. When you load a raw file, it lists
the scan filters associated with the raw file in the Filter list. To quantitate components, you
must filter the chromatogram.
Use the Peak Detection Algorithm list in the Peak Integration Area to specify the type of peak
detection algorithm (ICIS, Genesis, or Avalon) you want to use to analyze the raw data. These
algorithms apply smoothing, construct a chromatogram using the scan or mass filters, assign
peak numbers, generate a peak list, and determine the peak start and peak end points. All
algorithms provide component peak detection and chromatographic peak detection.
For detailed instructions on selecting peak detection algorithms, see “Defining Peak
Integration Parameters” on page 211.
 To detect and integrate a component peak in the current raw file
1. In the Component list, select a component.
The Component list is ordered by increasing retention time (Figure 129).
Figure 129. Component list
2. Specify these parameters in the Chromatogram Definition Area:
a. In the Mass box, enter ion masses from the Spectrum pane that correspond to the
selected component.
Only these ions are included in the chromatogram.
b. In the Filter list, select a scan filter for the selected component and click Apply.
The LCquan application applies the scan filter to the data in the raw file and displays
the resulting filtered chromatogram data in the Chromatogram pane.
Note The LCquan application created these scan filters from the instrument
method parameters that were defined and used to obtain the selected raw file. It
displays all scan filters in the raw file.
For a detailed description of the Chromatogram Definition area, see “Chromatogram
Definition Area” on page 194.
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3. In the Chromatogram pane:
a. To specify the expected retention time and retention time window for the selected
component, right-click and choose Auto Update Expected RT from Spectrum
Marker from the shortcut menu.
b. Right-click again and choose Set Spectrum to Peak Apex from the shortcut menu.
The LCquan application automatically does the following:
• Determines the peak apex scan (maximum) or selected scan and draws a vertical
red bar in the component peak in the Chromatogram pane.
• Displays the spectrum for the apex peak scan or selected scan in the Spectrum
pane.
• Displays the chromatogram for all ion masses displayed in the Spectrum pane.
• Specifies the retention time corresponding to the selected scan in the Expected
box in the Retention Time Area.
c. Display the starting and ending points and (shaded) area of the component peak.
The LCquan application shades the peak gray and displays the current baseline (blue)
with square handles at the starting and ending points of the peak.
d. To adjust the x-axis and y-axis ranges to improve the display of the peak, activate the
Chromatogram pane by clicking the square button in the upper-right corner of the
pane.
Adjust the x-axis range by doing one of the following:
• Drag the cursor horizontally over the x-axis range that you want displayed.
• Use the
,
, and
buttons.
Adjust the y-axis range by doing one of the following:
• Drag the cursor vertically over the y-axis range that you want displayed.
• Use the
,
, and
buttons.
e. Inspect the component peak: Verify that the peak has the proper symmetry and that
the grayed area (between the blue handles and above the blue baseline) accurately
represents the contribution of the component to the chromatogram.
• When necessary, repeat steps a through c.
• When you have problems with noise in the peak, unresolved peaks, or peak
tailing, see “Defining Peak Integration Parameters” on page 211.
• When baseline noise is interfering with peak identification or integration, see the
advanced features for Genesis or ICIS in “Defining Peak Integration Parameters”
on page 211.
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 To specify peak detection criteria
The Peak Integration Area is dynamic, displaying criteria for the selected peak detection
method: Genesis, ICIS, or Avalon (Figure 130).
Figure 130. Peak Detection Algorithm list
For detailed descriptions of the peak detection parameters, see Defining Peak Integration
Parameters.
 To automatically identify the current component in other raw files
1. In the Peak Identification area, select criteria for identifying peaks in the other raw files of
the data set that correspond to the current component.
• Select the Highest Peak option (default) to identify the highest peak as the peak that
corresponds to the current component (after the filters and settings of the current
component have been applied to the raw file).
• Select the Nearest RT option to identify the peak with a retention time nearest the
value shown in the Expected box—in the Retention Time area—as the peak that
corresponds to the current component (after the filters and settings of the current
component have been applied to the raw file). The peak must have a height greater
than the value you specify in the Min Peak Height box.
2. To add qualifier ions, select the Enabled check box in the Ion Ratio Confirmation Area
and enter settings for up to five qualifier ions into the table.
For an example of ion ratio confirmation, see “Ion Ratio Confirmation of Analytes
Example” on page 241.
3. In the Retention Time Area, specify a search window or retention time criteria.
• To specify a search window, enter the value for the peak detection time search in the
Window (sec) box. When the apex of the detected peak is outside this window, the
peak will not be detected using retention time peak detection criteria. A search
window is defined as: [Expected (min) ± Window (sec)] / 2.
• To use the retention time of the current component to adjust for retention time drift
of other components, select the Use as RT Ref check box.
• To correct for retention time drift, select the Adjust Using check box and select a
previously defined retention time reference from the list.
4. Click Apply to save the settings for the current component.
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 To finish identifying components
1. (Optional) Save the current settings as the default settings—when settings for the
following components are similar to the current settings—by clicking Save As Default.
2. Repeat the previous steps for all components in the raw file.
Defining Peak Integration Parameters
Use the Peak Integration Area to select and define peak integration parameters. Use the
Peak Integration area to define Genesis, ICIS, and Avalon peak detection algorithms to be
applied to the active raw file.
Peak detection parameters are also available from these locations:
• The Peak Integration area in the Create view of the Explore window
• The IRC Detection dialog box available from the ion ratio confirmation grid on the
Identification page in the Create Method view of the Quantitate window
• The User Identification Settings dialog box available from the Chromatogram view in the
preview panes
This section contains instructions for specifying parameters for the following:
• Genesis Peak Integration
• ICIS Peak Integration
• Avalon Peak Integration
Note
• The Genesis peak detection algorithm has been provided for backward compatibility
with Xcalibur 1.0 studies.
• The ICIS peak detection algorithm has been designed for MS data and has superior
peak detection efficiency at low MS signal levels.
• The Avalon peak detection algorithm has been designed for UV data. Avalon also
supports negative peaks.
Genesis Peak Integration
Use the Genesis Peak Integration area to define Genesis peak detection algorithms to be
applied to the active raw file (Figure 131). Table 78 on page 213 lists the parameters for the
Genesis Peak Integration area.
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 To specify Genesis peak integration parameters
1. In the Peak Detection Algorithm box, select Genesis.
Figure 131. Genesis Peak Integration area
2. Type a multiplier value in the S/N Threshold box.
3. To detect unresolved peaks with the valley detection approximation method, select the
Valley Detection Enabled check box.
• To set the expected peak width parameter and control the minimum width that a
peak is expected to have, enter a multiplier value in the Expected Width (sec) box.
4. To constrain the peak width of a component during the peak integration of a
chromatogram, select the Constrain Peak Width check box.
• To specify the minimum above the baseline before integration is turned on or off,
enter a percent of the total peak height in the Peak Ht (%) box.
• To constrain the peak width of an asymmetric chromatogram peak that has a tailing
trace, enter a peak integration multiplier in the Tailing Factor box.
5. To specify advanced component detection criteria, click Advanced.
Use these advanced criteria if the standard detection criteria do not provide the expected
results:
a. To specify a peak signal-to-noise cutoff, enter a Peak S/N Cutoff value.
b. To use a valley detection approximation method to detect unresolved peaks, enter
Rise Percentage value and a Valley S/N value.
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c. Select whether the noise used in calculating S/N values is calculated using an RMS
calculation or Peak-to-Peak resolution threshold.
For a detailed description of advanced parameters, see Table 79.
Table 78. Genesis Peak Integration area parameters (Sheet 1 of 2)
Parameter
Description
Advanced
Opens the Genesis Advanced Component Options dialog box
(Figure 75).
S/N Threshold
This multiplier specifies a signal-to-noise threshold for peak
integration. Only peaks with a signal-to-noise ratio greater than
this value are integrated.
Range: 0.0 to 999.0
Default multiplier: 0.5
Valley Detection
Enabled
Detects unresolved peaks with the valley detection approximation
method.
The LCquan application drops a vertical line from the apex of the
valley between unresolved peaks to the baseline. The intersection
of the vertical line and the baseline defines the end of the first peak
and the beginning of the second peak.
Expected Width (sec)
This multiplier specifies an expected peak width parameter that
controls the minimum width that a peak is expected to have when
valley detection is enabled.
With valley detection enabled, any valley points nearer than half
the expected width to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the LCquan
application ends the peak at that point. It always ends a peak when
the signal reaches the baseline, independent of the value set for the
expected peak width.
Range: 0.0 to 999.0
Default multiplier: 0.0
Units: seconds
Note Valid only when you select Valley Detection Enabled.
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
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Table 78. Genesis Peak Integration area parameters (Sheet 2 of 2)
Parameter
Description
Peak Ht (%)
Specifies a percentage of the total peak height. This is the
minimum that a signal must be above the baseline before
integration is turned on or off. This option is available only when
you select the Constrain Peak Width option.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Tailing Factor
Specifies a value for the factor that controls how the LCquan
application integrates the tail of a peak. This factor is the
maximum ratio of the trailing edge to the leading side of a
constrained peak and calculates the retention time of the
maximum extent of the right edge of the tailing peak. This option
is available only when you select the Constrain Peak Width
option.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Figure 132. Genesis Advanced Component Options dialog box
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Table 79. Genesis Advanced Component Options parameters
Parameter
Description
Peak Edge Detection
Chromatogram peak detection criteria using the peak signal-to-noise (S/N) cutoff value.
Peak S/N Cutoff
The peak edge is set to values below this defined S/N.
This test assumes an edge of a peak is found when the baseline
adjusted height of the edge is less than the ratio of the baseline
adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is
200, the LCquan application defines the right and left edges of the
peak when the S/N reaches a value less than 200.
Range: 50.0 to 10 000.0
Valley Detection
Valley detection approximation method to detect unresolved peaks.
Rise Percentage
The percentage that the peak trace can rise above the baseline after
passing through a minimum (before or after the peak).
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the LCquan application
applies valley detection peak integration criteria.
This test is applied to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with
long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Range: 1.0 to 100.0
Default: 2.0
Report Noise As
RMS or
Peak to Peak
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Determines if the noise used in calculating S/N values is calculated
using an RMS calculation or peak-to-peak resolution threshold.
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ICIS Peak Integration
Use the ICIS Peak Integration area to define ICIS peak detection algorithms to be applied to
the active raw file. Table 80 on page 218 lists the parameters for the ICIS Peak Integration
area. Table 81 on page 219 lists advanced parameters for ICIS Peak Integration.
 To specify ICIS peak integration parameters
1. In the Peak Detection Algorithm box, select ICIS (Figure 133).
Figure 133. ICIS Peak Integration area
2. In the Baseline Window box, enter the number of scans to use when searching for where
the minima are occurring.
3. In the Area Noise Factor box, enter a value to specify the noise-level multiplier that
determines the peak edge after the location of the possible peak.
4. In the Peak Noise Factor box, enter a value to specify the noise level multiplier that
determines the potential peak signal threshold.
5. To constrain the peak width of a component during the peak integration, select the
Constrain Peak Width check box.
• To specify the minimum above the baseline before integration is turned on or off,
enter a percent of the total peak height in the Peak Ht (%) box.
• To constrain the peak width of an asymmetric chromatogram peak that has a tailing
trace, enter a peak integration multiplier in the Tailing Factor box.
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6. To specify advanced component detection criteria, click Advanced.
The application displays the ICIS Advanced Parameters dialog box (Figure 134).
Figure 134. ICIS Advanced Parameters dialog box
Use the advanced component detection criteria if the standard detection criteria do not
provide the expected results:
a. Select a noise method:
• To use a single-pass algorithm to determine the noise level, select the INCOS
Noise option.
• To use a multiple-pass algorithm to determine the noise level, select the
Repetitive Noise option.
b. To use an RMS calculation instead of the default ICIS noise method, select the RMS
Noise check box.
c. To specify the minimum number of scans required in a peak, enter a value in the
Min Peak Width box.
d. To specify the minimum separation in scans between the apexes of two potential
peaks, enter a value in the Multiplet Resolution box.
e. To specify the number of scans past the peak endpoint to use in averaging the
intensity, enter a value in the Area Tail Extension box.
f.
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To specify the number of allowable scans on each side of the peak apex, enter a value
in the Area Scan Window box.
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Table 80. ICIS Peak Integration area parameters (Sheet 1 of 2)
Parameter
Description
Advanced
Opens the ICIS Advanced Parameters dialog box (see Table 81).
Baseline Window
The number of scans used when searching for where the minima
are occurring. A local minimum becomes an anchor point,
making the entire curve locally reduced until these points are at
zero.
Range: 1 to 500
Default: 40
Area Noise Factor
The noise-level multiplier used to determine the peak edge after
the location of the possible peak, so that the peak can narrow or
broaden without affecting the baseline.
Range: 1 to 500
Default multiplier: 5
Peak Noise Factor
The noise level multiplier (a minimum S/N ratio) used to
determine the potential peak signal threshold.
Range: 1 to 1000
Default multiplier: 10
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
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Table 80. ICIS Peak Integration area parameters (Sheet 2 of 2)
Parameter
Description
Peak Ht (%)
A percent of the total peak height. This is the minimum that a
signal must be above the baseline before integration is turned on
or off.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Note Valid only when you select the Constrain Peak Width
check box.
Tailing Factor
A peak integration multiplier that constrains the peak width of an
asymmetric chromatogram peak that has a tailing trace.
It is the maximum ratio of the trailing edge to the leading side of a
constrained peak and calculates the retention time of the
maximum extent of the right edge of the tailing peak.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Note Valid only when you select the Constrain Peak Width
check box.
Table 81. ICIS Advanced Parameters dialog box (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
INCOS Noise
A single-pass algorithm is used to determine the noise level.
Repetitive Noise
A multiple-pass algorithm is used to determine the noise level. In
general, this algorithm is more accurate in analyzing the noise
than the INCOS Noise algorithm, but it takes longer.
RMS Noise
A root mean square calculation is used to determine
signal-to-noise values instead of the default ICIS noise method.
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Table 81. ICIS Advanced Parameters dialog box (Sheet 2 of 2)
Parameter
Description
Peak Parameters
Units are in number of scans.
Min Peak Width
The minimum number of scans required in a peak.
Range: 0 to 100
Default: 3
Multiplet Resolution
The minimum separation in scans between the apexes of two
potential peaks. This is a criterion to determine if two peaks are
resolved. Use a larger number in a noisy environment when the
signal is bouncing around.
Range: 1 to 500
Default: 10 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging
the intensity.
Range: 0 to 100
Default: 5 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A
zero value defines all scans (peak-start to peak-end) to be included
in the area integration.
Range: 0 to 100
Default: 0 scans
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Avalon Peak Integration
Use the Avalon Peak Integration area to define Avalon peak detection algorithms to be applied
to the active raw file.
 To specify Avalon peak integration parameters
1. In the Peak Detection Algorithm box, select Avalon (Figure 135).
Avalon peak identification and integration criteria are applied to the active raw file. You
can add, modify, or delete (non-automated) timed events in the Avalon event list, but you
cannot delete an initial value.
Figure 135. Avalon Peak Integration area
2. To add a new event to the event list:
a. Specify the new values in the Time (min), Event, and Value boxes.
b. Click Add. The values are inserted into the Avalon event list.
3. To delete the entire row (except for an initial value row):
a. Select the row you want to delete. The selected row is highlighted.
b. Click Delete. The highlighted row is removed from the list.
4. To change the values within a row:
a. Select the row you want to change. The selected row is highlighted.
b. Specify the revised settings in some or all of these boxes: Time, Event, Value.
c. Click Change to automatically update the event list and the chromatogram display.
5. To estimate the initial values for the detection of peaks and display initial values in the
event list, click Auto Calculate.
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Table 82 lists the parameters for the Avalon Peak Integration area. Table 83 lists the
parameters for Initial and Timed Events.
Table 82. Avalon Peak Integration area parameters
Parameter
Description
Column Headings in the Event List
Time (min)
Displays the initial time value in minutes.
Event
Displays descriptions of detection parameters for initial events and
timed events. For details, see Table 90 on page 237.
Note Start Threshold, End Threshold, Area Threshold,
P-P [Resolution] Threshold, Bunch Factor, Negative Peaks, and
Tension are defined with initial values.
Value
Displays the values associated with initial events or timed events.
Range: Factors are specific to each event.
Controls to Modify the Event List
Auto Calculate
Estimates the initial values for the detection of peaks—based on
the data in the current raw file—to display initial values in the
event list and searches for the best values of initial events that
detect peaks in the data. Any timed event in the event list is
unchanged when you click Auto Calculate.
Determines initial values for only: Start Threshold,
End Threshold, Area Threshold, P-P [Resolution] Threshold,
Bunch Factor, Negative Peaks, and Tension.
Note Valid only if a raw file is open.
Time (Min)
Initial value or a time value in minutes.
Event
Descriptions of detection parameters for initial events and timed
events.
Value
Values associated with the initial/timed events described in the
Event box.
The range of factors allowed for each value is specific to each
event.
Buttons
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Add
Adds the Time, Event, and Value values to the Avalon Event List.
Delete
Deletes the selected row.
Change
Using the Time, Event, and Value values, updates the event list
and the chromatogram display.
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Table 83. Initial and Timed Events (Sheet 1 of 2)
Event
Description
Start/End Threshold
Half of the result is a good estimate for the Start Threshold. You
can modify the Avalon estimates by entering your own values and
clicking Add to save your Start or End Threshold.
The Start Threshold depends on the RMS noise in the
chromatogram. It is the fundamental control used for peak
detection, so picking the best Start Threshold is essential for
high-quality data collection.
Units: Absolute value of peak area (counts x seconds)
Bunch Factor
The number of points grouped together during peak detection.
This method groups several chromatographic points during
integration without affecting the final area calculation of the peak.
Range: 1 to 6
Note A high bunch factor groups peaks into clusters.
Area Threshold
Controls the area cutoff. Any peak with a final area less than the
area threshold is not recorded.
Format: units of area for the data
P-P Resolution
Defines how much peak overlap must be present before two or
more adjacent peaks create a peak cluster. Peak clusters have a
baseline drop instead of valley-to-valley baselines. This is specified
as a percent of peak height overlap.
Negative Peaks
Automatically resets after a negative peak has been found.
Tension
Controls how closely the baseline follows the overall shape of the
chromatogram.
A lower tension traces the baseline to follow changes in the
chromatogram more closely. A high baseline tension follows the
baseline less closely, over longer time intervals.
Units: minutes
Tangent Skim
Enables tangent skim on any peak clusters.
By default, the application selects the tallest peak in a cluster as the
parent (solvent) and detects peaks on either side (or both sides) of
the tallest peak. You can also identify which peak in the cluster is
the parent.
Tangent skim automatically resets at the end of the peak cluster.
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Table 83. Initial and Timed Events (Sheet 2 of 2)
Event
Description
Integrate On/Off
Turns integration on or off at the set time.
Shoulders On
Turns on the detection of shoulders.
Shoulders Off
Turns off the detection of shoulders.
Force Cluster On
Turns on the grouping of peaks into a single peak.
Force Cluster Off
Turns off the grouping of peaks into a single peak.
Disable Cluster On
Enables the grouping effect in the specified time range.
Disable Cluster Off
Disables the grouping effect in the specified time range.
IRC Detection Method
Use the IRC Detection Method dialog box to specify additional peak detection criteria when
the standard detection criteria on the Identification page do not provide the expected results.
Peak detection parameters are also available from these locations:
• The Peak Integration area in the Create Method view of the Explore window
• The Peak Integration area on the Identification page in the Create Method view of the
Quantitate window
• The User Identification Settings dialog box available from the Chromatogram view in the
preview panes
To open the IRC Detection Method dialog box (Figure 136), right-click the Ion ratio
confirmation grid and choose Edit Selected Rows Processing Info from the shortcut menu.
Figure 136. Ion Ratio Confirmation area
The IRC Detection Method dialog box includes these tabs:
• IRC Detection Method – Identification
• IRC Detection Method – Genesis Integration
• IRC Detection Method – Genesis Advanced
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• IRC Detection Method - ICIS Integration
• IRC Detection Method – ICIS Advanced
• IRC Detection Method - Avalon Integration
The tabs are dynamic depending on the selected peak detection algorithm (ICIS, Genesis, or
Avalon).
IRC Detection Method – Identification
Use this page (Figure 137) to set up advanced chromatographic parameters and select the peak
detection algorithm (Genesis, ICIS, or Avalon). Table 84 lists the parameters for the
Identification page of the IRC Detection Method dialog box.
Figure 137. IRC Detection Method dialog box showing the Identification page
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Table 84 lists the parameters for the Identification page of the IRC Detection Method dialog
box.
Table 84. IRC Detection Method dialog box, Identification page parameters (Sheet 1 of 2)
Parameter
Description
Component
Specifies the mass value of the selected compound. This parameter
is read-only.
Smoothing Points
Specifies the number of points to use for a moving mean filter to
smooth the chromatogram.
Format: integers
Range: 1 to 15, odd numbers only
Note Set the parameter to 1 to disable filtering.
Trace
Specifies the type of chromatogram: TIC, Mass Range, or Base
Peak. This parameter is read-only.
• Mass Range: Specify up to 50 mass ranges. The masses are
added together to form the chromatogram.
• TIC: Full-scan acquisition resulting in a Total Ion Current
plot.
• Base Peak: In a differential chromatogram, the interpolation
of the baseline is derived from the distance between the
intersections of the tangents drawn to the peak sides and the
peak base.
Note This definition set is the same for the second Trace field.
The second trace field depends on which operators are chosen.
+/-/“ “
Specifies an addition or a subtraction trace operator when you are
using trace math. This parameter is read-only.
This Trace Operation matrix shows the combinations used to set
up an Explore Method:
Mass Range+Mass Range
– Mass Range
TIC+ Mass Range
– Base Peak
Base Peak+Mass Range
– Mass Range
Note If the Operator box is empty, the second trace choice is
disabled.
Mass (m/z)
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Specifies the initial mass value. This parameter is read-only.
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Table 84. IRC Detection Method dialog box, Identification page parameters (Sheet 2 of 2)
Parameter
Description
Filter
Specifies an existing filter or a filter from a preloaded filter list
(obtained from the current raw file). This parameter is read-only.
Note All filters are validated against the current set of filter
entry rules.
Peak Detection
Algorithm
Specifies the peak detection algorithm used: Avalon, Genesis, or
ICIS. The tabs in this dialog box reflect the value chosen here.
IRC Detection Method – Genesis Integration
Use this page to set up advanced chromatographic parameters (see Figure 138).
Figure 138. IRC Detection Method dialog box showing the Genesis Integration page
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Table 85 lists the parameters for the Genesis Integration page of the IRC Detection Method
dialog box.
Table 85. IRC Detection Method, Genesis Integration page parameters (Sheet 1 of 2)
Parameter
Description
S/N Threshold
This multiplier specifies a signal-to-noise threshold for peak
integration. Only peaks with a signal-to-noise ratio greater than
this value are integrated.
Range: 0.0 to 999.0
Default multiplier: 0.5
Valley Detection
Enabled
Specifies the valley detection approximation method to detect
unresolved peaks. This method drops a vertical line from the apex
of the valley between unresolved peaks to the baseline. The
intersection of the vertical line and the baseline defines the end of
the first peak and the beginning of the second peak.
To turn this method on, select the Valley Detection check box. To
turn this method off, clear the check box.
Expected Width (sec)
This multiplier specifies an expected peak width parameter that
controls the minimum width that a peak is expected to have when
valley detection is enabled.
With valley detection enabled, any valley points nearer than half
the expected width to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the application
ends the peak at that point. It always ends a peak when the signal
reaches the baseline, independent of the value set for the expected
peak width.
Range: 0.0 to 999.0
Default multiplier: 0.0
Units: seconds
Note Valid only when you select the Valley Detection Enabled
check box.
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
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Table 85. IRC Detection Method, Genesis Integration page parameters (Sheet 2 of 2)
Parameter
Description
Peak Ht (%)
Specifies a percentage of the total peak height. This is the
minimum that a signal must be above the baseline before
integration is turned on or off. This option is available only when
you select the Constrain Peak Width option.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Tailing Factor
Specifies a value for the factor that controls how the application
integrates the tail of a peak. This factor is the maximum ratio of
the trailing edge to the leading side of a constrained peak and
calculates the retention time of the maximum extent of the right
edge of the tailing peak. This option is available only when you
select the Constrain Peak Width option.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
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IRC Detection Method – Genesis Advanced
Use this page (Figure 139) to set up advanced chromatographic parameters. Table 86 lists the
parameters for the Genesis Advanced page of the IRC Detection Method dialog box
Figure 139. IRC Detection Method dialog box showing the Genesis Advanced page
Table 86. IRC Detection Method, Genesis Advanced page parameters (Sheet 1 of 2)
Parameter
Description
Report Noise As
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RMS
Specifies that noise is calculated using an RMS calculation based
on the noise data points.
Peak to Peak
Specifies that noise is calculated using the peak-to-peak variation
of the noise data points.
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Table 86. IRC Detection Method, Genesis Advanced page parameters (Sheet 2 of 2)
Parameter
Description
Rise Percentage
The percentage that the peak trace can rise above the baseline after
passing through a minimum (before or after the peak).
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the application applies
valley detection peak integration criteria. This test is applied to
both the left and right edges of the peak. The rise percentage
criteria is useful for integrating peaks with long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Range: 1.0 to 100.0
Default: 2.0
Peak S/N Cutoff
Specifies the value for the signal-to-noise cutoff below which the
application defines the peak edge; the box displays the current
cutoff value that it uses for defining the peak edge. For example, if
the signal-to-noise at the apex is 500 and the Peak S/N Cutoff
value is 200, the application defines the right and left edges of the
peak when the S/N reaches a value of less than 200.
Range: 50.0 to 10 000.0
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IRC Detection Method - ICIS Integration
Use this page (Figure 140) to set up advanced chromatographic parameters. Table 87 lists the
parameters for the ICIS Integration page of the IRC Detection Method dialog box.
Figure 140. IRC Detection Method dialog box showing the ICIS Integration page
Table 87. IRC Detection Method dialog box, ICIS Integration page parameters (Sheet 1 of 2)
Parameter
Description
Baseline Window
The number of scans used when searching for where the minima
are occurring. A local minimum becomes an anchor point,
making the entire curve locally reduced until these points are at
zero.
Range: 1 to 500
Default: 40
Area Noise Factor
The noise-level multiplier used to determine the peak edge after
the location of the possible peak, so that the peak can narrow or
broaden without affecting the baseline.
Range: 1 to 500
Default multiplier: 5
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Table 87. IRC Detection Method dialog box, ICIS Integration page parameters (Sheet 2 of 2)
Parameter
Description
Peak Noise Factor
The noise level multiplier (a minimum S/N ratio) used to
determine the potential peak signal threshold.
Range: 1 to 1000
Default multiplier: 10
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
Peak Ht (%)
A percent of the total peak height. This is the minimum that a
signal must be above the baseline before integration is turned on
or off.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Note Valid only when you select the Constrain Peak Width
check box.
Tailing Factor
A peak integration multiplier that constrains the peak width of an
asymmetric chromatogram peak that has a tailing trace.
It is the maximum ratio of the trailing edge to the leading side of a
constrained peak and calculates the retention time of the
maximum extent of the right edge of the tailing peak.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Note Valid only when you select the Constrain Peak Width
check box.
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IRC Detection Method – ICIS Advanced
Use this page (Figure 141) to set up advanced chromatographic parameters. Table 88 lists the
parameters for the ICIS Advanced page of the IRC Detection Method dialog box.
Figure 141. IRC Detection Method dialog box showing the ICIS Advanced page
Table 88. IRC Detection Method dialog box, ICIS Advanced page parameters (Sheet 1 of 2)
Parameter
Description
Noise Method
Incos Noise
A single-pass algorithm is used to determine the noise level.
Repetitive Noise
A multiple-pass algorithm is used to determine the noise level. In
general, this algorithm is more accurate in analyzing the noise
than the INCOS Noise algorithm, but it takes longer.
RMS Noise
A root mean square calculation is used to determine
signal-to-noise values instead of the default ICIS noise method.
Min Peak Width
The minimum number of scans required in a peak.
Range: 0 to 100
Default: 3 scans
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Table 88. IRC Detection Method dialog box, ICIS Advanced page parameters (Sheet 2 of 2)
Parameter
Description
Multiplet Resolution
The minimum separation in scans between the apexes of two
potential peaks. This is a criterion to determine if two peaks are
resolved. Use a larger number in a noisy environment when the
signal is bouncing around.
Range: 1 to 500
Default: 10 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging
the intensity.
Range: 0 to 100
Default: 5 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A
zero value defines all scans (peak-start to peak-end) to be included
in the area integration.
Range: 0 to 100
Default: 0 scans
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IRC Detection Method - Avalon Integration
Use this page (Figure 142) to specify advanced component detection criteria. Use these
additional criteria when the standard detection criteria do not provide the expected results.
Table 89 lists the parameters for the Avalon Integration page of the IRC Detection Method
dialog box. Table 90 lists the parameters for initial and timed events.
Note To detect peaks, Avalon uses the settings for initial events and user-defined timed
events in the event list.
Figure 142. IRC Detection Method dialog box showing the Avalon Integration page
Table 89. RC Detection Method dialog box, Avalon Integration page parameters (Sheet 1 of 2)
Parameter
Description
Auto Calculate Initial
Events
Estimates the initial values for the detection of peaks—based on
the data in the current raw file—to display initial values in the
event list and searches for the best values of initial events that
detect peaks in the data. Any timed event in the event list is
unchanged when you click Auto Calculate.
Determines initial values for only: Start Threshold, End
Threshold, Area Threshold, P-P [Resolution] Threshold,
Bunch Factor, Negative Peaks, and Tension.
Note Valid only when a raw file is open.
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Table 89. RC Detection Method dialog box, Avalon Integration page parameters (Sheet 2 of 2)
Parameter
Description
Time (Min)
Displays the initial time value in minutes.
Event
Displays descriptions of detection parameters for initial events and
timed events. For details, see Table 90.
Note Start Threshold, End Threshold, Area Threshold,
P-P [Resolution] Threshold, Bunch Factor, Negative Peaks, and
Tension are defined with initial values.
Value
Displays the values associated with initial events or timed events.
Range: Factors are specific to each event.
Add
Adds the Time, Event, and Value values to the Avalon Event List.
Delete
Deletes the selected row.
Change
Using the Time, Event, and Value values, updates the event list
and the chromatogram display.
Table 90. Initial and Timed Events (Sheet 1 of 2)
Event
Description
Start/End Threshold
Half of the result is a good estimate for the Start Threshold. You
can modify the Avalon estimates by entering your own values and
clicking Add to save your Start or End Threshold.
The Start Threshold depends on the RMS noise in the
chromatogram. It is the fundamental control used for peak
detection, so picking the best Start Threshold is essential for
high-quality data collection.
Units: Absolute value of peak area (counts x seconds)
Bunch Factor
The number of points grouped together during peak detection.
This method groups several chromatographic points during
integration without affecting the final area calculation of the peak.
Range: 1 to 6
Note A high bunch factor groups peaks into clusters.
Area Threshold
Controls the area cutoff. Any peak with a final area less than the
area threshold is not recorded.
Format: units of area for the data
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Table 90. Initial and Timed Events (Sheet 2 of 2)
Event
Description
P-P Resolution
Defines how much peak overlap must be present before two or
more adjacent peaks create a peak cluster. Peak clusters have a
baseline drop instead of valley-to-valley baselines. This is specified
as a percent of peak height overlap.
Negative Peaks
Automatically resets after a negative peak has been found.
Tension
Controls how closely the baseline follows the overall shape of the
chromatogram.
A lower tension traces the baseline to follow changes in the
chromatogram more closely. A high baseline tension follows the
baseline less closely, over longer time intervals.
Units: minutes
Tangent Skim
Enables tangent skim on any peak clusters.
By default, the application selects the tallest peak in a cluster as the
parent (solvent) and detects peaks on either side (or both sides) of
the tallest peak. You can also identify which peak in the cluster is
the parent.
Tangent skim automatically resets at the end of the peak cluster.
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Integrate On/Off
Turns integration on or off at the set time.
Shoulders On
Turns on the detection of shoulders.
Shoulders Off
Turns off the detection of shoulders.
Force Cluster On
Turns on the grouping of peaks into a single peak.
Force Cluster Off
Turns off the grouping of peaks into a single peak.
Disable Cluster On
Enables the grouping effect in the specified time range.
Disable Cluster Off
Disables the grouping effect in the specified time range.
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Identification Options
Use the Identification Options dialog box to select a baseline and noise window for peak
identification purposes. The Genesis Baseline parameters in the dialog box apply to all
samples in a sequence, not just component by component. They apply only when you use the
Genesis peak detection algorithm. Table 91 lists the parameters for the Identification Options
dialog box.
 To open the Identification Options dialog box
From the window menu, choose Options > Identification.
The Identification Options dialog box opens (Figure 143).
Figure 143. Identification Options dialog box
Table 91. Identification Options parameters (Sheet 1 of 2)
Parameter
Description
Baseline
Baseline & Noise
Window
Set the width of the chromatographic piece that is sent to the
analysis routines during peak detection and integration.
The piece created is centered around the Expected Retention
Time ± window width.
Genesis Baseline
These global parameters apply to all samples in a sequence. They apply only when you use
the Genesis peak detection algorithm.
Baseline Noise
Tolerance
This value controls how the baseline is drawn in the noise data.
The higher the baseline noise tolerance value, the higher the
baseline is drawn through the noise data.
Range: 0.0 to 100.0
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Table 91. Identification Options parameters (Sheet 2 of 2)
Parameter
Description
Minimum Number of
Scans in Baseline
Minimum number of scans to calculate a baseline. A larger
number includes more data in an averaged baseline.
Range: 2 to 100.0
Baseline Noise
Rejection Factor
Current baseline noise rejection factor.
This factor controls the width of the RMS noise band above and
below the peak detection baseline and is applied to the raw RMS
noise values to raise the effective RMS noise during peak
detection. The left and right peak boundaries are assigned above
the noise and, therefore, are closer to the peak apex value in
minutes.
This action effectively raises the peak integration baseline above
the RMS noise level.
Range: 0.1 to 10.0
Default: 2.0
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Ion Ratio Confirmation of Analytes Example
With Ion Ratio Confirmation (IRC) you can confirm the presence of an analyte by
comparing the response of the quantitate ion (or ions) with the responses of one to five
qualifier ions. When any of the qualifier ion/quantitate ion response ratios are outside of the
upper or lower bounds that you specify, or if the quantitate and qualifier ions do not coelute,
the LCquan application marks the analyte as Not Found in the Review All Results view in the
Quantitate window.
Specify the masses, target area ratios, and area ratio windows of the qualifier ions in the Ion
Ratio Confirmation table of the processing method. The application displays the mass
chromatograms of the qualifier and quantitate ions in the IRC Chromatogram pane.
In the following example (Figure 144), the application divides the area of the m/z 327.1 mass
chromatogram peak by the area of the m/z 309.2 + 267.2 mass chromatogram peak and
multiplies this value by 100. If the value is less than 50% or greater than 70%, the application
marks hydrocortisone as Not Found. Also, the peak maximum of the qualifier ion
chromatogram must be within 0.1 minutes of the peak maximum of the quantitate ion
chromatogram.
Figure 144. Identification page
m/z 309.2 + 267.2
m/z 327.1
50–70%
hydrocortisone
0.1 minutes
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Specifying Method Calibration
After importing the component names and calibration levels from the acquisition sequence
into the processing method, use features on the Calibration page to specify the identification
settings for the internal standard and target compounds (Figure 145).
Figure 145. Quantitate – Create Method – Calibration window
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 To open the Calibration page of the Create Method view
When the left navigation pane is displayed:
a. Click Quantitate.
b. Click the Method icon.
c. Click the Calibration tab.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Quantitate Section.
b. Choose View > Step Selector > Quantitate Method.
c. Click the Calibration tab.
Use this page to enter calibration information for each of your components.
The Calibration page of the Create Method view includes these areas and functions:
• Component Type Area
• Target Compound Area
• Component List Pane
• Calibration Shortcut Menu
• Correction for Isotope Contribution
This section contains instructions for performing the following:
• Specifying Calibration Options
• Specifying Internal Standards and Target Compounds
• Reviewing the Integrated Peaks
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Component Type Area
Use the Component Type area (Figure 146) to specify the type of component: internal
standard or target. Table 92 lists the parameters for the Component Type area.
Figure 146. Component Type area
Table 92. Component Type area parameters
Parameter
Description
Target Compound
Specifies that the component you are calibrating is a target
compound. This option disables ISTD Amount and ISTD Units
and enables all elements in the Target Compound box.
ISTD
Specifies that the component you are calibrating is an internal
standard. This option enables ISTD Amount and ISTD Units and
disables all elements in the Target Compound box except Isotope
and the response group.
Note ISTD, ISTD Amount, and ISTD Units are not available
when you perform an external calibration.
Target Units
The unit type for the target compound. This option is available
only when Target Compound is the compound type.
ISTD Amount
The amount of the selected internal standard. This option is
available only when ISTD is the compound type.
Range: 0.001 to 100 000.000.
ISTD Units
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The unit type for the internal standard. This option is available
only when ISTD is the compound type.
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Target Compound Area
Use the Target Compound area to specify parameters for the target compound (Figure 147).
 To edit the level tables
1. To remove a level, select the entire row, and click Delete.
You can select multiple rows and delete them all at once.
2. To change a level name, select the name and type the new one over it.
When you enter a name that already exists, a warning message is displayed and you must
enter a different name.
3. To move from cell to cell, press TAB. To move backward through the cells, press
SHIFT+TAB.
4. To enter a new level, click the empty row at the end of the grid, enter a new name, and
enter an amount.
Note For QCs, you can also enter the % Test amount.
Figure 147. Target Compound area
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Table 93 lists the parameters for the Target Component area.
Table 93. Target Compound area parameters (Sheet 1 of 2)
Parameter
Description
General Controls
ISTD
Specifies the ISTD to associate with the current target compound.
All defined ISTDs are in the list.
Isotope%
Opens the Correction for Isotope Contribution dialog box, so you
can correct for an impurity in the internal standard compound
that elutes at the same time as the target compound, correct for an
impurity in the target compound that elutes at the same time as
the internal standard, or both. For more information, see
“Correction for Isotope Contribution” on page 253.
Calibration Curve
Type
Specifies the calibration curve type to be used for the current
component. Not all Response, Origin, and Weighting selections
are available with every calibration curve type.
For details, see Table 94.
Response
Area
Specifies that this area value will be used in response calculations.
Height
Specifies that this height value will be used in response
calculations.
Origin
Determine how to use the origin when the calibration curve is generated.
Ignore
Specifies that the origin is not included as a valid point in the
calibration curve when the curve is generated. When you select
this option, the calibration curve might or might not pass through
the origin.
Force
Specifies that the calibration curve passes through the origin of the
data point plot when the calibration curve is generated.
Include
Specifies that the origin is included as a single data point in the
calculation of the calibration curve. When you select this option,
the calibration curve might or might not pass through the origin.
Weighting
Specify how the individual data points are weighted in calculating the calibration curve.
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Equal
Weights all calibration data points equally during the least-squares
regression calculation of the calibration curve.
1/X
Specifies a weighting of 1/X for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants are weighted by the inverse of their quantity.
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Table 93. Target Compound area parameters (Sheet 2 of 2)
Parameter
Description
1/X^2
Specifies a weighting of 1/X^2 for all calibration data points
during the least-squares regression calculation of the calibration
curve. Calibrants are weighted by the inverse of the square of their
quantity.
1/Y
Specifies a weighting of 1/Y for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants are weighted by the inverse of their response (or
response ratio).
1/Y^2
Specifies a weighting of 1/Y^2 for all calibration data points
during the least-squares regression calculation of the calibration
curve. Calibrants are weighted by the inverse of the square of their
response (or response ratio).
1/s^2
Specifies a weighting of 1/s^2 for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants at a given level are weighted by the inverse of the
standard deviation of their responses (or response ratios). For this
weighting factor to be used, there must be two or more replicates
at each level. When only one calibrant is available for any level,
1/s^2 weighting cannot be used.
Table Headings
Cal Level
Displays calibration levels for this compound.
Amount
Displays the amount of the calibration level compound.
QC Level
Displays QC levels for this compound.
Amount
Displays the amount of the QC level compound.
%Test
Displays the acceptable difference (as a percentage) between the
known amount and calculated (measured) amount of each QC
level.
Table 94. Calibration Curve Type area parameters (Sheet 1 of 2)
Thermo Scientific
Calibration curve type
Allowable settings for response, origin, and weighting
Linear
All settings are allowed with this exception: When Origin is set to
Include, all Weighting values are grayed out and Weighting is set
to Equal.
Quadratic
All settings are allowed with this exception: When Origin is set to
Include, all Weighting values are grayed out and Weighting is set
to Equal.
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Table 94. Calibration Curve Type area parameters (Sheet 2 of 2)
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Calibration curve type
Allowable settings for response, origin, and weighting
Linear Log-Log
No Weighting or Origin selections are allowed. All Weighting and
Origin values are grayed out. Weighting is set to Equal and Origin
is set to Ignore.
Quadratic Log-Log
No Weighting or Origin selections are allowed. All Weighting and
Origin values are grayed out. Weighting is set to Equal, and
Origin is set to Ignore.
Average RF
No Weighting or Origin selections are allowed. All Weighting and
Origin values are grayed out. Weighting is set to Equal, and
Origin is set to Ignore.
Point-to-Point
No Weighting selections are allowed. All Weighting values are
grayed out. Weighting is set to Equal. Only the Ignore and Force
Origin options are allowed. The Include Origin option is grayed
out. When Origin is set to Include, it changes to Ignore.
Cubic Spline
No Weighting selections are allowed. All Weighting values are
grayed out. Weighting is set to Equal. Only the Ignore and Force
Origin options are allowed. The Include Origin option is grayed
out. When Origin is set to Include, it changes to Ignore.
Locally Weighted
No Weighting or Origin selections are allowed. All Weighting and
Origin values are grayed out. Weighting is set to Equal, and
Origin is set to Ignore.
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Component List Pane
Use the Component List pane to add, delete, or rename a component (Figure 148). Table 95
lists the parameters for the Component List pane.
Figure 148. Component List pane
Table 95. Component list functions
Function
Description
Buttons
Adds a component.
Deletes a component.
Renames a component.
Shortcut Menu
Thermo Scientific
Add
Adds a component name.
Delete
Deletes a component name.
Rename
Renames a component.
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Calibration Shortcut Menu
Right-click anywhere in the Calibration page to display the shortcut menu.
Command
Description
Shortcut Menu
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Delete Selected Rows
Deletes the currently selected rows in the Cal or QC grid.
You must select each row to be deleted by clicking the row
indicator to the left of the row.
Copy Current Component
Levels to All Target
Components
Copies the current Cal and QC level tables to all other
defined target components.
Copy Current Calibration
Parameters to All Target
Components
Copies all calibration parameters defined in this
component to other defined target components.
Copy Current Calibration
Parameters & Level Tables to
all Target Components
Copies all calibration parameters defined in this
component and in the current Cal and QC level tables to
other defined target components.
Copy Selected Acquisition
Levels to All Target
Components
Opens the Select Component dialog box where you can
copy the Cal and QC level tables defined for the
acquisition components to all defined target components.
The level tables are a composite of all levels for all
acquisition components. For more information, see
“Select Component Dialog Box.”
Load Default Levels for This
Component
Loads the default level tables for the current component.
Load Selected Acquisition
Levels for this Component
Opens the Select Component dialog box where you can
select acquisition components. The levels from the
selected component are copied for both the Cal and QC
levels. For more information, see “Select Component
Dialog Box.”
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Select Component Dialog Box
Use the Select Component dialog box to select the component with the level tables you want
to use to copy acquisition levels to all target components or load acquisition levels for the
selected component (Figure 149). Table 96 lists the parameters for the Select Component
dialog box.
Figure 149. Select Component dialog box
Table 96. Select Component dialog box parameters (Sheet 1 of 2)
Parameter
Description
Component Table
Component
Select the component with the level tables you want to use from
the list of components in the sequence.
Cal Level Table
Thermo Scientific
Cal Level
Displays the calibration levels for the selected component.
Amount
Displays the amounts of the target compound used for each
calibration level.
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Table 96. Select Component dialog box parameters (Sheet 2 of 2)
Parameter
Description
QC Level Table
Use QC samples containing known amounts of a component to help ensure the accuracy of
an analysis. The application measures the quantity of the QC component in the same
manner as it measures that of unknown components. The measured quantity is then
compared with a user-defined expected quantity and a user-defined percent test.
QC Level
Displays the quality control levels for the selected component.
The application can accommodate up to 15 QC levels.
Amount
Displays the amounts of the target compound used for each QC
(quality control) level.
%Test
Displays a value for the acceptable difference (as a percent)
between the known amount and calculated (measured) amount of
each QC level.
Button
Select
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Selects the component name you highlighted in the Component
table.
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Correction for Isotope Contribution
Use the Correction for Isotope Contribution dialog box to correct for an impurity in the
internal standard compound that elutes at the same time as the target compound, correct for
an impurity in the target compound that elutes at the same time as the internal standard, or
correct for both (Figure 150). Table 97 lists the parameters for the Correction for Isotope
Contribution dialog box.
Figure 150. Correction for Isotope Contribution dialog box
Table 97. Correction for Isotope Contribution dialog box parameters
Parameter
Description
Contribution of ISTD
to Target Compound
Displays the ratio: (ISTD [impurity] / ISTD [pure]) × 100%.
• ISTD [impurity] is an impurity compound in the internal
standard reagent that elutes at the same time as the target
compound.
• ISTD [pure] is the pure internal standard compound.
Range: 0.00 to 100.00%
Contribution of Target Displays the ratio: (TM [impurity] / TM [pure]) × 100%
Compound to ISTD
• TM [impurity] is an impurity compound in the target
molecule reagent that elutes at the same time as the internal
standard.
• TM [pure] is the pure target compound.
Range: 0.00 to 100.00%
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Specifying Calibration Options
 To set global calibration options
1. Choose Options > Calibration.
The Calibration Options dialog box opens (Figure 151). Table 98 lists the parameters for
the Calibration Options dialog box.
Figure 151. Calibration Options dialog box
2. Select Internal or External standards.
3. (Optional) Save your calibration standards choice as the default.
Table 98. Calibration Options dialog box parameters
Parameter
Description
Calibrate By
Internal Standard
Specifies that the method use internal standard calibration.
External Standard
Specifies that the method use external standard calibration.
Specifying Internal Standards and Target Compounds
An internal standard (ISTD) component acts as a response reference for the target
components in the sample.
Note When creating an internal standard Processing Method, you must define at least
one component to be an internal standard before you can define any other components as
target compounds.
 To specify the internal standard settings
1. In the Component list (Figure 152), select the component that you want to identify as an
internal standard.
2. In the Component Type area, select the ISTD option.
The Internal Standard area becomes active.
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3. Specify the internal standard settings:
a. In the ISTD Amount box, enter the amount of the internal standard injected into
each sample.
b. In the ISTD Units box, enter the units of the internal standard injected into each
sample.
4. Click Apply to accept the internal standard settings.
5. To identify other components as internal standards, repeat steps 1 through 4.
Figure 152. Internal standard interface example
 To specify the calibration curve parameters for the target compounds
1. In the Component list, select the component that you want to identify as a target
compound.
2. In the Component Type area, select the Target Compound option.
The Target Compound area becomes active.
3. To create an internal standard method, in the ISTD list, select the internal standard for
the target compound.
4. In the Response area, specify the LCquan application response by selecting the Area
option or Height option.
5. In the Target Units box, enter the units that you want to appear under the x axis of the
calibration curve plot.
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6. In the Calibration Curve Type list, select the calibration curve type.
When you select Linear or Quadratic, the Weighting area becomes active. Do the
following:
• In the Weighting area, select the weighting option that the LCquan application
applies to the correct regression weighting method when it calculates the least-squares
regression calibration curve.
• In the Origin area, select how to treat the origin in the calibration curve calculation:
• To exclude the origin in the calibration curve calculation, select the Ignore
option.
• To require that the calibration curve pass through the origin, select the Force
option.
• To include the origin as one data point, select the Include option.
When you select any of the other curve types, the Weighting area is not active.
7. Specify calibration level data:
• Use the Cal Level boxes to enter calibration levels.
• Use the Amount boxes to enter the amount of internal standard added at each level.
The LCquan application automatically adds another row to the table when you click
the Amount box after filling in the Cal Level box.
8. Specify quality control level data:
• Use the QC Level boxes to enter quality control levels. Use the down-arrow key to
add more levels.
• Use the Amount boxes to enter the amount of internal standard added at each level.
• Use the % Test boxes to enter a value for the acceptable difference (as a percent)
between the known amount and calculated (measured) amount of each quality
control level.
The LCquan application automatically adds another row to the table when you click
the % Test box after filling in the QC Level and Amount boxes.
9. To correct for isotope contribution, click Isotope%.
Use the Correction for Isotope Contribution dialog box to correct for an impurity in the
internal standard compound that elutes at the same time as the target compound, correct
for an impurity in the target compound that elutes at the same time as the internal
standard, or both. For more information, see “Correction for Isotope Contribution dialog
box parameters” on page 253.
10. To accept the calibration settings for this component, click Apply.
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11. To save the current settings as the default settings—when settings for the following
components are similar to the current settings—click Save As Default.
Peak detection type, mass range, and scan filters are not saved.
12. Repeat steps 1 through 10 for each target component.
13. To save the current component identification and calibration settings in a new or existing
Processing Method (.pmd) file, choose File > Export > Processing Method.
 To watch an animation of these procedures
Click the play button.
Note To watch this animation, you must have Adobe™ Flash™ Player version 10 or
later. To download the latest Adobe Flash Player, go to get2.adobe.com/flashplayer/.
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Saving the Processing Method
Reviewing the Integrated Peaks
When you have finished entering the component identification and integration settings for
the target compounds and the internal standard, review the integrated peaks.
 To review the integrated peaks
• When the peaks have been correctly integrated, go to “Ion Ratio Confirmation of
Analytes Example” on page 241.
• When there is excessive noise in a peak, unresolved peaks, or peak tailing, return to
“Summing Ions Dialog Box” on page 203 and change the peak identification and
integration parameters.
• When baseline noise is interfering with peak identification or integration, change the
settings in the Advanced Parameters dialog box for the appropriate peak detection
method.
For details about displaying and viewing data in the preview panes, see “Data Views” on
page 259.
Saving the Processing Method
When you have finished creating the processing method, choose File > Save to save the
settings in the workbook.
Importing a Processing Method
When you are doing routine quantitative analysis experiments, you might save time by
importing an existing processing method into your current workbook instead of creating a
new method. You can use the method as is or you can edit it.
Use any of these options to import a processing method:
• New Study Wizard
When you create a new workbook, the New Study Wizard gives you the option of
importing instrument methods, acquisition sequences, and processing parameters to
initialize the new workbook. You can import all this data from an existing workbook, or
you can import a processing method from an individual legacy file (.pmd) or from an
LCquan file (.lqn).
• New Method Wizard in the Quantitate window
When you use the New Method Wizard in the Quantitate window, you have the option
of importing a previously saved processing method. You can import a processing method
from an individual legacy file (.pmd) or from an LCquan file (.lqn).
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Exporting Components and Levels to an Acquisition Sequence
• Processing Method command from within the Quantitate window
From the Create Method view in the Quantitate window, you can choose File > Import >
Processing Method to display the Import Quantitation Method dialog box. Use this
dialog box to import a processing method from an individual legacy file (.pmd) or from
an LCquan file (.lqn).
Exporting Components and Levels to an Acquisition Sequence
Just as you can import the component names and calibration levels from an acquisition
sequence into a processing method, you can also do the reverse—that is, export component
names and calibration levels from a processing method into an acquisition sequence.
To export component names and calibration levels from the processing method to the
acquisition sequence, follow the instructions “To change or import calibration and QC levels”
on page 64 in Chapter 2, “Preparing to Perform Quantitative Analysis.”
Data Views
This chapter describes the preview panes in the Quantitate window that contain a list of views
used to display the data in various forms. The preview panes appear on the following views:
• Create Method
• Survey
• Review All Results
In the preview panes, select from the following views to display the data:
• Calibration Curve View for Survey or Review All Results Only
• Chromatogram View for Create Method Only
• Chromatogram View for Survey or Review All Results Only
• Spectrum View
• IRC Chromatogram View
• Chromatogram List View
• Error Report View
• Filter List View
• General Parameters Plot View for Survey or Review All Results Only
• Instrument Method List View
• Mass List View
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Data Views
• Peak List View for Survey or Review All Results Only
• Sample Info View
• Status Plot View
• Status Report View
• Tune Method View
• Multi Peak Plot View for Survey or Review All Results Only
Each preview pane contains a Toolbar for Selectable Views at the top of the pane.
Toolbar for Selectable Views
Each preview pane contains a Toolbar for Selectable Views (Figure 153) at the top of the pane.
Use the Toolbar for Selectable Views to select the view you want to display in the preview
pane. Not all views display all the toolbar options. At a minimum, the toolbar contains the
View Selector list and a lock icon.
Figure 153. Toolbar for Selectable Views
Arrows
Item Selector
View Selector
Lock
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Table 99 lists the controls for the Toolbar for Selectable Views.
Table 99. Toolbar for Selectable Views controls (Sheet 1 of 3)
Control
Description
Arrows
Moves forward or backward through a range of possible selections:
for example, to display the next or previous chromatogram peak.
The arrows are not selectable (grayed out) when either of these
cases exists:
• A particular directional move is not possible; for example, the
arrows move through a list and the current selection is at the
top of the list, so the left (backward) arrow is grayed out.
• The yellow or red lock is set, so no changes can be made in the
red-locked pane and only changes other than raw file or
component changes can be made in yellow-locked panes.
Both arrows are grayed out.
Note The actions of the arrows vary in some instances between
the Explore and Quantitate windows. For example, in the
Chromatogram pane in Explore, the arrows can move through
multiple peaks for one sample. In the same pane in Quantitate,
they can move through different samples.
Lock
Allow changes (or prevent changes) to a raw file or parameters.
The color of the lock indicates the lock status of a pane.
Red = Locked Against All Changes. The lock icon is a closed lock.
• You cannot make any changes in panes that have red locks.
• No changes you make in any panes are reflected in panes that
have red locks.
• All shortcut menu commands that can change the pane or the
data are unavailable.
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Table 99. Toolbar for Selectable Views controls (Sheet 2 of 3)
Control
Description
Yellow = Locked Against raw file (or Component) Changes. The
lock icon is a closed lock.
• You cannot make changes to a raw file (or to a component, in
the Calibration Curve pane) in panes that have yellow locks.
• When you make changes other than raw file changes in any
panes, those changes are reflected in panes that have yellow or
green locks. For example, when you click a Chromatogram
pane, the focal point moves in a Chromatogram List pane
even if the latter pane has a yellow lock.
• All shortcut menu commands that can change the raw file or
components in the pane are unavailable.
Green = Unlocked. The lock icon is an open lock.
Any changes you make in any panes are reflected in panes that
have green locks.
Note When you apply a yellow or a red lock to a pane, you
essentially capture (take a “snapshot” of ) that pane as it was just
before you locked it.
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Play/Pause
Runs an automated action for the current pane.
Item Selector list
Displays a list of selectable items for the current pane.
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Table 99. Toolbar for Selectable Views controls (Sheet 3 of 3)
Control
Description
Detector Selector list
The detector stream for the data type of interest.
When a raw file is currently selected for the pane, the detector box
contains a list of the detector streams in the raw file in the form:
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name. When no raw file is available when specifying the
detector stream, MS is the only option available.
When a new selection is made from the list, the selection list
continues to have the initial selection in the list until the current
pane is changed. When redisplaying, only the current selection
(and any other selection available from the raw file) is displayed.
View Selector list
Select from the list of selectable views for the current section.
Calibration Curve View for Survey or Review All Results Only
The Calibration Curve view is available from the Survey or Review All Results views in the
Quantitate window (Figure 154).
This view displays a calibration curve for the selected component. The replicates list is created
by adding all the integrated standards from the result rows. There is a one-to-one
correspondence between each result row (in the Standards tab) and the replicates list.
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Data Views
Figure 154. Calibration Curve view
When the view is locked (lock icon is yellow or red), you cannot select any menu item in the
shortcut menu that changes the raw file (with the yellow lock) or the raw file and parameters
(with the red lock). Menu items that would cause changes are grayed out. For more
information about locks, see “Toolbar for Selectable Views” on page 260. Table 100 lists the
parameters for the Calibration Curve view.
Table 100. Calibration Curve view parameters (Sheet 1 of 3)
Parameter
Description
Arrows
The left and right arrows move through the sequence list,
incrementing or decrementing by a single sample.
Shortcut Menu
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Lock against All
Change
Specifies that changes to a raw file or parameters (such as retention
time selection) in other panes have no effect on this pane. The
lock icon is red and the lock is closed.
Unlock
Specifies that changes to raw files and relevant parameters cause an
update to occur in this pane, using the new settings. The lock icon
is green and the lock is open.
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Table 100. Calibration Curve view parameters (Sheet 2 of 3)
Parameter
Exclude/Include
Description
Note This menu item appears only when you click a data point
in the curve. When the data point you click has already been
excluded, the menu item is “Include” instead of “Exclude.”
When Exclude is displayed: Forces the calibration curve to be
recalculated without the selected data point. The Exclude entry in
the results grid and Cal Exclusion List dialog box are updated to
show that this point is excluded, and the excluded data point is
redrawn as an unfilled square on the calibration curve.
When Include is displayed: Includes the data point and forces the
calibration curve to be recalculated. The Exclude entry in the
results grid and Cal Exclusion List dialog box are updated to show
that this point is now included, and the included data point is
redrawn as a filled square on the calibration curve. You can
include or exclude samples that are shared between brackets. Their
status is unique to the bracket (that is, excluding a shared sample
in bracket 1 has no effect on its inclusion status in bracket 2).
For more information, see “Modifying Calibration Settings” on
page 344 in Chapter 6, “Processing the Raw Files and Reviewing
the Analytical Results.”
Calibration Settings
Opens the Calibration Settings dialog box with Type, Curve,
Levels, and Isotope% tabs. For more information, see “Modifying
Calibration Settings” on page 344 in Chapter 6, “Processing
the Raw Files and Reviewing the Analytical Results.”
The Type tab is available for both ISTDs and target compounds.
All other tabs are shown only for target compounds.
Thermo Scientific
Exclusion List
Opens the Cal Exclusion List dialog box, which displays all
replicates used in creating the current calibration curve and their
exclusion status and also is where you can change that status. For
more information, see “Excluding a Calibration Standard from the
Calibration Curve” on page 350 in Chapter 6, “Processing
the Raw Files and Reviewing the Analytical Results.”
Larger Symbols
Increase the size of the replicate data points (the square markers).
Five sizes are available. The marker size doubles each time you
select this command, until the maximum size is reached. The
current size setting is stored in the registry and is used for all
workbooks when you open them.
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Table 100. Calibration Curve view parameters (Sheet 3 of 3)
Parameter
Description
Smaller Symbols
Reduces the replicate data points (the square markers). Five sizes
are available. The marker size is halved each time you select this
command, until the minimum size is reached. The current size
setting is stored in the registry and is used for all workbooks when
you open them.
Reset Scaling
Resets the graph axes to the maximum limits, so the entire plot is
displayed. The limits for the calibration plot are set to allow the
display of all measured samples, not just the calibration replicates.
When you select an Unknown sample, the intersection lines
drawn on the plot are visible.
Copy to Clipboard
Copies the current calibration curve graph to the Clipboard
buffer. You can then paste it from the buffer into a document.
Chromatogram View for Create Method Only
This view is available from the Create Method view in the Quantitate window.
This view displays a chromatogram and all detected peaks for a
sample/component/integration type and method (Figure 155).
The displayed chromatogram is based on the range specified in the method. All detected
peaks are displayed but cannot be edited. Click the chromatogram to set the Retention Time
marker. All spectrum and spectrum list views that are not locked receive the selected time and
update.
Figure 155. Chromatogram view for Create Method
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260.
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Table 101 lists the parameters for the Calibration Curve view.
Table 101. Chromatogram parameters
Parameter
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single peak.
Shortcut Menu
Thermo Scientific
Open Raw File
Opens the Select Raw File dialog box where you can select the raw
file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Display Options
Opens the Chromatogram Display Options dialog box, where you
can select pane options. For more information, see
“Chromatogram Display Options dialog box parameters” on
page 269.
Set Spectrum to Peak
Apex
Select this menu item to set Selected RT at the peak apex. Other
panes might be updated (depending on status).
Auto Update Expected
RT From Spectrum
Marker
When selected, makes the cursor active within a chromatogram by
copying the RT position to the “Expected RT” box.
Reset Scaling
Resets scaling to the default pane.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
The menu item is selected, indicating it is enabled.
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Chromatogram Display Options
Use the Chromatogram Display Options dialog box to modify the appearance of the
chromatogram (Figure 156).
Figure 156. Chromatogram Display Options dialog box
 To display this dialog box
When the left navigation pane is displayed:
a. Click Quantitate.
b. Click the Method icon.
c. Right-click the data pane of the Chromatogram view, and choose Display Options
from the shortcut menu.
When the left navigation pane is hidden:
a. Choose View > Section Selection > Quantitate Section.
b. Choose View > Step Selector > Quantitate Method.
c. Right-click the Chromatogram pane, and choose Display Options.
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Table 102 lists the parameters for the Chromatogram Display Options dialog box.
Table 102. Chromatogram Display Options dialog box parameters (Sheet 1 of 2)
Parameter
Description
Label With
Select the data attributes you want to show in the data plots.
Retention Time
Displays the peak apex retention time (RT) above the
chromatogram peaks. RT is displayed on all peaks that meet the
selection criteria set in the Label Threshold box.
Name
Displays the peak name above the peak.
Base Peak
Displays the base peak mass for the scan above the chromatogram
peak.
Signal to Noise
Displays the peak signal-to-noise (S/N) value above the
chromatogram peak.
Note When RMS S/N is selected in the Peak Detection Settings
options set, “rms” appears after the S/N value.
Decimals
Sets the number of decimal places for the peak apex retention time
label.
Area
Displays the peak area.
Height
Displays the peak height.
Label Styles
Stylize the labeling displayed with the data.
Offset
Moves the label a defined distance from the data.
Rotated
Rotates the labels above the peaks to 90 degrees.
Boxed
Displays boxes around the labels above the peaks.
Size
Defines the distance the label is offset from the data.
Label Threshold (%)
Sets a threshold so that peaks above this level can show labels.
Plotting
Select one style to display your data.
Point to Point
Select a graphic style to display the active chromatogram or
spectrum using point-to-point peak profile.
Stick
Select a graphic style to display the active chromatogram using
vertical lines.
On/Off Labeling Option—When No Peak Found
Show Apex Time
Labels
Thermo Scientific
Selects to always display maxima labels.
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Table 102. Chromatogram Display Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Axis Offset
Select one or both to offset the displayed plot from the x axis, y axis or both.
X
Select to have the x-axis offset move the y axis slightly above the
x axis so that you can see baseline details.
Y
Select to have the y-axis offset move the x axis slightly to the right
of the y axis so that you can see plot details at low x axis values.
Chromatogram View for Survey or Review All Results Only
This view is available from the Survey or Review All Results views in the Quantitate window.
This view displays a chromatogram and all detected peaks for a sample (Figure 157). The Item
Selector List options for this view are identical to those for the Chromatogram List view, so
you can compare the two views side by side.
 To add a peak
1. Right-click the pane and choose Set Peak to Not Found Status.
2. Right-click the pane and choose Manually Add Peak. The pointer changes to
.
3. Right-click the pane and choose Add or Change Peak Comment.
The Chromatogram Comment dialog box opens.
4. To enter comments about the manually added peak, see “Adding Comments to the
Chromatogram Display” on page 382 in Chapter 6, “Processing the Raw Files and
Reviewing the Analytical Results.”
5. Click OK or Apply as appropriate.
6. To draw the new peak, drag the peak baseline, defining the start and end of the peak.
7. To manually adjust the peak baseline and endpoints, grab the square blue handles and
drag them.
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Figure 157. Chromatogram view for Survey or Review All Results
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 103 lists the parameters for the Chromatogram view.
Table 103. Chromatogram view parameters (Sheet 1 of 4)
Parameter
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single scan.
Item Selector List Options
ISTD
Displays the chromatogram from the current component’s ISTD.
Method
Displays the method-derived chromatogram (regardless of which
integration type is currently in use) for the current component.
Selected
Displays the chromatogram from the current component.
Shortcut Menu
Thermo Scientific
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Method Settings
Resets the integration method to those methods specified in the
original processing method.
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Table 103. Chromatogram view parameters (Sheet 2 of 4)
Parameter
Description
User Settings
Applies a set of user-defined peak detection parameters to the
integration of this peak. For more information, see “Specifying
Additional Peak Detection Criteria” on page 354 in Chapter 6,
“Processing the Raw Files and Reviewing the Analytical Results.”
Note Selecting this menu item automatically places the current
sample into User Integration mode.
Manual Integration
Denotes that you have adjusted the integration baseline by
dragging the control boxes on the plot or by typing new numbers
in the Baseline dialog box. This option is grayed out until you
have made baseline changes at least one time. For more
information, see “Manually Integrating Peaks” on page 371 in
Chapter 6, “Processing the Raw Files and Reviewing the
Analytical Results.”
Show Peak Info
Opens the Peak Information dialog box where you can view peak
information that reflects the settings for the currently displayed
chromatogram. For more information, see “User Identification
Settings – ICIS Integration” on page 364 in Chapter 6,
“Processing the Raw Files and Reviewing the Analytical Results.”
The compound identification name is displayed in the title bar.
When the component peak is not found, the dialog box displays a
single tab labeled “No Peak.”
The tabs available and their order depend on the type of peak
being examined. For typical peaks, three tabs provide access to the
following: Peak Information – Info, Peak Information – Flags, and
Peak Information – Spectrum. When IRCs are used, an additional
tab appears for the Peak Information – IRC Tests. For more
information, see “User Identification Settings – ICIS Integration”
on page 364 in Chapter 6, “Processing the Raw Files and
Reviewing the Analytical Results.”
Each IRC has a separate menu item; only one Peak Info box is
allowed for each IRC. The selected peak in the plot is updated to
reflect the selection in the menu. Additional Show Peak Info
menu items are available for each qualifier ion.
Change Peak Baseline
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Opens the Baseline dialog box where you can enter peak baseline
coordinates directly. For more information, see “Manually
Integrating Peaks” on page 371 in Chapter 6, “Processing the Raw
Files and Reviewing the Analytical Results.”
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Table 103. Chromatogram view parameters (Sheet 3 of 4)
Parameter
Description
Add or Change Peak
Comment
Opens the Chromatogram Comment dialog box where you can
enter a comment to be associated with the selected chromatogram.
There is a separate comment for each sample, component, or
integration type chromatogram. For more information, see
“Adding Comments to the Chromatogram Display” on page 382
in Chapter 6, “Processing the Raw Files and Reviewing the
Analytical Results.”
User Peak Detection
Settings
Opens the User Identification Settings dialog box where you can
change some of the detection and integration parameters without
returning to the Identification page of the Create Method view in
the Quantitate window. For more information, see “Specifying
Additional Peak Detection Criteria” on page 354 in Chapter 6,
“Processing the Raw Files and Reviewing the Analytical Results.”
Note Selecting User Identification Settings automatically sets
the integration type in the corresponding row in the grid to User
Integration.
Thermo Scientific
Display Options
Opens the Chromatogram Display Options dialog box where you
can select view options. For more information, see
“Chromatogram Display Options” on page 268.
Manually Add Peak
Manually places a baseline on the plot and sets the current
integration method to Manual Integration. Use this option if no
peak has been detected for the currently selected compound and
there is no integration baseline on the chromatogram plot for you
to adjust manually.
Set Peak to Not Found
Status
Discards the currently detected peak. All panes are updated to
reflect the fact that no peak exists. When no peak is currently
available, this command is grayed out. ISTD peaks cannot be set
to Not Found status; the command is grayed out. After you use
this command, the Manually Add Peak command is available.
Update Expected
Retention Time Update User Settings
for Component in
Current Row
Updates the expected elution time (point of maximum signal) of
the current component in the current row from the retention time
specified in the user-defined peak-detection settings to the
detected retention time.
Update Expected
Retention Time Update User Settings
for All Components in
Current Row
Updates the expected elution time (point of maximum signal) of
all components in the current row from the retention time
specified in the user-defined peak-detection settings to the
detected retention time.
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Table 103. Chromatogram view parameters (Sheet 4 of 4)
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Parameter
Description
Update Expected
Retention Time Update Method
Settings for
Component Using
Current Row
Updates the expected elution time (point of maximum signal) of
the current component in the current row from the retention time
specified in the processing method to the detected retention time.
Update Expected
Retention Time Update Method
Settings for All
Components Using
Current Row
Updates the expected elution time (point of maximum signal) of
all components in the current row from the retention time
specified in the processing method to the detected retention time.
Reset Scaling
Resets both x and y axes to display the maximum amount of data.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
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Spectrum View
This view displays a spectrum for a sample at the selected retention time (Figure 158).
In the Survey or Review All Results views in the Quantitate window, the Item Selector List
options for this view are identical to those for the Mass List view so you can compare the two
views side by side. Table 104 lists the parameters for the Spectrum view.
 To make changes to the spectrum display
Right-click the spectrum view and choose Display Options from the shortcut menu.
The Spectrum Display Options dialog box opens. For more information, see “Spectrum
Display Options dialog box parameters” on page 95 in Chapter 2, “Preparing to Perform
Quantitative Analysis.”
Figure 158. Spectrum view
When the view is locked (lock icon is red), you cannot select any menu item in the
shortcut menu that changes the raw file or parameters. Menu items that would cause
changes are grayed out. For more information about locks, see “Toolbar for Selectable
Views” on page 260.
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Table 104. Spectrum view parameters
Parameter
Description
Arrows
The left and right arrows move through scans in the raw file,
incrementing or decrementing by a single scan.
Item Selector List Options (Survey and Review All Results views only)
ISTD
Displayed spectrum is from the current component’s ISTD.
Component
Displayed spectrum is from the current component.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Specifies that changes to a raw file or parameters (such as retention
time selection) in other panes have no effect on this pane. The
lock icon is red and the lock is closed.
Unlock
Specifies that changes to raw files and relevant parameters cause an
update to occur in this pane, using the new settings. The lock icon
is green and the lock is open.
Spectrum at Peak Apex Displays the spectrum at the selected component peak’s apex.
When more than one chromatogram peak is currently displayed in
the pane, the first chromatogram in the list is used for setting the
RT.
Spectrum at Peak Left
Edge
Displays the spectrum at the selected component peak’s left edge.
When more than one chromatogram peak is currently displayed in
the pane, the first chromatogram in the list is used for setting the
RT.
Spectrum at Peak Right Displays the spectrum at the selected component peak’s right edge.
Edge
When more than one chromatogram peak is currently displayed in
the pane, the first chromatogram in the list is used for setting the
RT.
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Display Options
Displays the Spectrum Display Options dialog box where you can
modify the appearance of the spectrum in the Spectrum pane. For
more information, see “Spectrum Display Options dialog box
parameters” on page 95 in Chapter 2, “Preparing to Perform
Quantitative Analysis.”
Reset Scaling
Resets the x-axis and y-axis ranges in the Chromatogram pane or
the Spectrum pane to their default values.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
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IRC Chromatogram View
This view displays up to six side-by-side IRC chromatograms, with the last (rightmost)
chromatogram being an overlay of all the IRCs and the component chromatogram
(Figure 159). The chromatograms have color-coded borders: Green = Ion passed both IRC
tests; Red = Ion did not pass at least one of the tests. IRC does not support user peak
integration settings.
Figure 159. IRC Chromatogram view
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 105 lists the parameters for the IRC Chromatogram view.
Table 105. IRC Chromatogram view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
In the Create Method view, the left and right arrows move
through the IRC peaks, incrementing or decrementing by a single
peak.
In the Survey or Review All Results views, the left and right arrows
move through the samples, incrementing or decrementing by a
single sample.
Note When you open the Peak Info dialog box, its content
reflects the current selection.
Shortcut Menu
Thermo Scientific
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
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Table 105. IRC Chromatogram view parameters (Sheet 2 of 2)
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Parameter
Description
Show Peak Info
Opens the Peak Information dialog box. The selected peak in the
plot is updated to reflect the selection in the menu. Additional
Show Peak Info menu items are available for each qualifier ion.
For more information, see “User Identification Settings – ICIS
Integration” on page 364 in Chapter 6, “Processing the Raw Files
and Reviewing the Analytical Results.”
Load Raw File
[Create Method view only] Opens the Select Raw File dialog box.
All panes are updated using the new raw file.
Method Settings
[Survey or Review All Results views only] Selects the Method peak
for the currently selected IRC chromatogram. When Method
Settings is selected, a check mark appears to the left of the menu
item.
Manual Integration
[Survey or Review All Results views only] Selects the Manual peak
for the currently selected IRC chromatogram. When Manual
Integration is selected, a check mark appears to the left of the
menu item. This item is only available when there is a manually
selected peak; otherwise, it is grayed out.
Change Peak Baseline
[Survey or Review All Results views only] Opens the Baseline
dialog box, so you can review and modify peak baseline properties.
For more information, see “Manually Integrating Peaks” on
page 371 in Chapter 6, “Processing the Raw Files and Reviewing
the Analytical Results.”
Display Options
Opens the Ion Ratio Chromatogram Display Options dialog box
where you can select view options. For more information, see “Ion
Ratio Chromatogram Display Options.”
Reset Scaling
Resets scaling to the default pane.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
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Ion Ratio Chromatogram Display Options
Use this dialog box (Figure 160) to modify the appearance of the IRC chromatogram view.
Table 106 lists the parameters for the Ion Ratio Chromatogram Display Options dialog box.
Figure 160. Ion Ratio Chromatogram Display Options dialog box
Table 106. Ion Ratio Chromatogram Display Options dialog box parameters (Sheet 1 of 2)
Parameter
Description
Label With
Select the data attributes you want to show in the data plots.
Retention Time
Displays the peak apex retention time (RT) above the
chromatogram peaks. RT is displayed on all peaks that meet the
selection criteria set in the Label Threshold box.
Name
Displays the peak name above the peak.
Base Peak
Displays the base peak mass for the scan above the chromatogram
peak.
Signal to Noise
Displays the peak signal-to-noise (S/N) value above the
chromatogram peak.
Note When RMS S/N is selected in the Peak Detection Settings
options set, “rms” appears after the S/N value.
Thermo Scientific
Decimals
Sets the number of decimal places for the peak apex retention time
label.
Area
Displays the peak area.
Height
Displays the peak height.
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Table 106. Ion Ratio Chromatogram Display Options dialog box parameters (Sheet 2 of 2)
Parameter
Description
Label Styles
Stylize the labeling displayed with the data.
Offset
Moves the label a defined distance from the data.
Rotated
Rotates the labels above the peaks to 90 degrees.
Boxed
Displays boxes around the labels above the peaks.
Size
Defines the distance the label is offset from the data.
Label Threshold (%)
Sets a threshold so that peaks above this level can show labels.
Plotting
Select one style to display your data.
Point to Point
Select a graphic style to display the active chromatogram or
spectrum using point-to-point peak profile.
Stick
Select a graphic style to display the active chromatogram using
vertical lines.
On/Off Labeling Option—When No Peak Found
Show Apex Time
Labels
Selects to always display maxima labels.
Axis Offset
Select one or both to offset the displayed plot from the x axis, y axis or both.
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X
Select to have the x axis offset move the y axis slightly above the
x axis so that you can see baseline details.
Y
Select to have the y-axis offset move the x axis slightly to the right
of the y axis so that you can see plot details at low x axis values.
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Chromatogram List View
This view displays the chromatographic data points in table format (Figure 161).
In the Survey or Review All Results views in the Quantitate window, the Item Selector List
options for this view are identical to those for the Chromatogram view so that you can
compare the two views side by side.
Figure 161. Chromatogram List view
The contents of the grid are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 107 lists the parameters for the Chromatogram List view.
Table 107. Chromatogram List view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the selection,
incrementing or decrementing by a single sample peak.
Item Selector List Options (Survey and Review All views only)
ISTD
Displayed chromatogram is from the current component’s ISTD.
Method
Displayed chromatogram is the method-derived chromatogram
(regardless of which integration type is currently in use) for the
current component.
Selected
Displayed chromatogram is from the current component.
Column Headings
Thermo Scientific
RT
Displays the retention time of the given data point.
Intensity
Displays the absolute intensity of the given data point.
%Relative Intensity
Displays the intensity of the data point relative to the most intense
data point in the chromatogram.
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Table 107. Chromatogram List view parameters (Sheet 2 of 2)
Parameter
Description
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box,
so you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Error Report View
This view displays the error log information stored in the current raw file (Figure 162).
Figure 162. Error Report view
The contents of the grid are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 108 lists the parameters for the Error Report view.
Table 108. Error Report view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the list of detectors,
incrementing or decrementing by a single detector.
Detector Selector List Options
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Displays the error log of a mass spectrometer.
Status
Displays the error log of a device that does not log data.
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Table 108. Error Report view parameters (Sheet 2 of 2)
Parameter
Description
[Detector Streams in
Current Raw File]
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box,
so you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Filter List View
This view displays the list of unique filters that are stored in the current raw file in table
format (Figure 163).
Figure 163. Filter List view
The contents of the grid are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260.
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Table 109 lists the parameters for the Filter List view.
Table 109. Filter List view parameters
Parameter
Description
Arrows
[Not used in the Create Method view] The left and right arrows
move through the sequence list, incrementing or decrementing by
a single sample.
Column Heading
Filters
Displays the list of unique filters that are stored in the current raw
file.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box,
so you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
General Parameters Plot View for Survey or Review All Results Only
This data view is available from the Survey or Review All Results views in the Quantitate
window (Figure 164).
This data view displays the selected parameters over the sequence for all detected peaks in the
current view (All, Standards, QCs, Blanks, or Unknowns). Select the parameters you want to
see plotted from the Item Selector list.
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Figure 164. General Parameters Plot view
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 110 lists the parameters for the General Parameters Plot view.
Table 110. General Parameters Plot view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the item list,
incrementing or decrementing by a single item.
Item Selector List Options
RT
Displays retention times for the current component.
Area
Displays areas for the component peaks.
Units: count-seconds
Height
Displays heights of the current component peak apexes.
Units: counts
Thermo Scientific
Response
Displays the ratios of sample peak areas or heights to ISTD areas
or heights.
Peak Width
Displays peak widths for the current component.
Calculated Amount
Displays the sample amounts, as calculated with the response ratio
and calibration curve.
% Difference
Displays the percent difference as defined by 100 × (calculated
amount – specified amount) / specified amount.
% RSD
Displays the percent relative standard deviation.
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Table 110. General Parameters Plot view parameters (Sheet 2 of 2)
Parameter
Description
Shortcut Menu
Lock against All
Change
Prevents changes to a raw file or parameters.The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable.The lock icon is green and the lock is
open.
Reset Scaling
Resets scaling to the default pane.
Copy to Clipboard
Copies selected data to the Clipboard. You can then paste the data
from the Clipboard buffer into a document.
Instrument Method List View
This view displays the instrument method parameters for the selected sample (Figure 165).
When you select Instrument Method List, an instrument selector list appears in the toolbar of
the preview pane. To view an instrument’s method, select the instrument from the instrument
selector list. When you select a TSQ Quantum™ mass spectrometer, the LCquan application
appends the source parameters from the tune method to the end of the instrument method
parameters.
Figure 165. Instrument Method List view
Note Use the arrows,
, to change the preview to display the parameters for the other
types of instrument methods associated with the current sample (.raw file).
To display the shortcut menu for the Instrument Method List, right-click the Instrument
Method preview pane.
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When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 111 lists the parameters for the Instrument Method List view.
Table 111. Instrument Method List view parameters
Command
Description
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the sample file to load.
Lock against All
Change
Disables the Open Raw File command for the Instrument Method
preview pane. The lock icon is red and the lock is closed.
Unlock
Enables the Open Raw File command for the Instrument Method
preview pane. The lock icon is green and the lock is open.
Copy to Clipboard
Copies the contents of the Instrument Method preview pane to
the Clipboard. To create a report, you can paste the copy into
other software.
Mass List View
This view displays the spectral mass and intensity list for a sample at the selected retention
time (Figure 166).
In the Survey or Review All Results views in the Quantitate window, the Item Selector List
options for this view are identical to those for the Chromatogram view so you can compare
the two views side by side.
Figure 166. Mass List view
The contents of the grid are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260.
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Table 112 lists the parameters for the Mass List view.
Table 112. Mass List view parameters
Parameter
Description
Arrows
The left and right arrows move through the chromatogram,
incrementing or decrementing by a single scan.
Item Selector List Options (Survey and Review All Results views only)
ISTD
Displayed values are from the current component’s ISTD.
Component
Displayed values are from the current component.
Column Headings
Mass
Displays the mass value above the spectral line column.
Intensity
Displays the intensity of the spectral data point column.
%Base
Displays the relative percentage this data point has to the largest
data point in the Intensity column.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Spectrum at Peak Apex Selects the spectrum at the selected component peak’s apex. The
first chromatogram in the list sets the RT.
Spectrum at Peak Left
Edge
Selects the spectrum at the selected component peak’s left edge.
The first chromatogram in the list sets the RT.
Spectrum at Peak Right Selects the spectrum at the selected component peak’s right edge.
Edge
The first chromatogram in the list sets the RT.
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Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
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Peak List View for Survey or Review All Results Only
This view is available from the Survey or Review All Results views in the Quantitate window.
The Peak List view displays a list of detected peaks for a sample (Figure 167).
Figure 167. Peak List view
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 113 lists the parameters for the Peak List view.
Table 113. Peak List view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the item list,
incrementing or decrementing by a single peak.
Column Headings
Thermo Scientific
Peak Name
The name to apply to the peak column.
Apex RT
The expected RT for the peak column.
Area
The calculated peak area column.
% of Largest Area
The area of this peak relative to the area of the peak with the
biggest area in the list column.
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Table 113. Peak List view parameters (Sheet 2 of 2)
Parameter
Description
% of Total Area
The area of this peak relative to the summed total area of all peaks
in this list column.
Shortcut Menu
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
Sample Info View
This view displays sample information stored in the current raw file during acquisition
(Figure 168).
Figure 168. Sample Info view
The contents of the grid are read-only.
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When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file or parameters. Menu items that would cause changes are
grayed out. For more information about locks, see “Toolbar for Selectable Views” on
page 260. Table 114 lists the parameters for the Sample Info view.
Table 114. Sample Info view parameters
Parameter
Description
Arrows
[Not used in the Create Method view] The left and right arrows
move through the sequence list, incrementing or decrementing by
a single sample.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
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Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
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Status Plot View
This view displays the status information stored in the current raw file in graphical form
(Figure 169).
Figure 169. Status Plot view
The contents of the plot are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file. Menu items that would cause changes are grayed out. For
more information about locks, see “Toolbar for Selectable Views” on page 260.
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Table 115 lists the parameters for the Status Plot view.
Table 115. Status Plot view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the item list,
incrementing or decrementing by a single item.
Item List
Item Selector List Options
[Parameter]
[Create Method view only] Select the parameter you want to plot
on the y axis.
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
8 kV Ionized Voltage
8 kV Ionized Current
Sheath Gas Flow Rate
Aux Gas Flow Rate
Ion Sweep Gas Flow Rate
API Temperature
Capillary Temperature
Capillary Offset
Tube Lens Offset
Forepressure
Q0 RF Power
Q0 RF Voltage
Q00 Offset
Lens 0 Offset
Q0 Offset
Detector Selector List Options
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MS
Displays status information for a mass spectrometer.
Status
Displays status information for a device that does not log data.
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Table 115. Status Plot view parameters (Sheet 2 of 2)
Parameter
Description
[Detector Streams in
Current Raw File]
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Shortcut Menu
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Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Reset Scaling
Resets scaling to the default pane.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
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Status Report View
This view displays the status information stored in the current raw file in table format
(Figure 170).
Figure 170. Status Report view
The contents of the grid are read-only.
When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file. Menu items that would cause changes are grayed out. For
more information about locks, see “Toolbar for Selectable Views” on page 260. Table 116 lists
the parameters for the Status Report view.
Table 116. Status Report view parameters (Sheet 1 of 2)
Parameter
Description
Arrows
The left and right arrows move through the status items in the raw
file, incrementing or decrementing by a single status item.
Detector Selector List Options
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MS
Displays status information for a mass spectrometer.
Status
Displays status information for a device that does not log data.
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Table 116. Status Report view parameters (Sheet 2 of 2)
Parameter
Description
[Detector Streams in
Current Raw File]
When a raw file is open, displays the list of detector streams that
are stored in the current raw file. The format of the list items is
Generic Detector Stream Name: Instrument Name: Model Name:
Channel Name.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is
open.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
Tune Method View
This view displays the tune method stored in the current raw file during acquisition
(Figure 171).
Figure 171. Tune Method view
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When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file. Menu items that would cause changes are grayed out. For
more information about locks, see “Toolbar for Selectable Views” on page 260. Table 117 lists
the parameters for the Tune Method view.
Table 117. Tune Method view parameters
Parameter
Description
Arrows
[Not used in the Create Method view] The left and right arrows
move through the sequence list, incrementing or decrementing by
a single status item.
Column Headings
Parameter
Displays a column of descriptive text for the item.
Value
Displays a column of data for the given parameter.
Shortcut Menu
Open Raw File
[Create Method view only] Opens the Select Raw File dialog box
where you can select the raw file to load.
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red
and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and open.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to
the Clipboard. You can then paste the data from the Clipboard
buffer into a document.
Multi Peak Plot View for Survey or Review All Results Only
The Multi Peak Plot view is available from the Survey or Review All Results views on the
Quantitate window (Figure 172).
This view displays all detected peaks for a sample/method combination.
You can set the number of rows and columns and define the number of peak graphics
displayed on the screen.
• You can define a maximum of 50 cells.
The x-axis range for each peak is 2.0 times the detected peak width, 50% on either side.
• The peak baseline endpoints are displayed as blue circles.
Note When the endpoints appear as blue circles, you cannot select and drag them to
manually integrate the peak.
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 To set the number of rows and columns
1. Right-click the plot and choose Options from the shortcut menu.
The Multi Peak Plot View dialog box opens where you can determine how peaks are
arranged and change chromatographic display options. For more information, see Multi
Peak Plot parameters.
2. In the Arrangement box, type the number of columns and rows.
You can set the normalization level to be the same for all peaks, or you can normalize each
peak individually.
 To set the normalization levels
1. Right-click the plot and choose Options from the shortcut menu.
The Multi Peak Plot View dialog box opens (Figure 172).
2. In the Intensity Scale list, select Normalize to Largest Peak or Use Fixed Intensity
Range.
Figure 172. Multi Peak Plot view for Survey or Review All Results
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When the view is locked (lock icon is red), you cannot select any menu item in the shortcut
menu that changes the raw file. Menu items that would cause changes are grayed out. For
more information about locks, see “Toolbar for Selectable Views” on page 260. Table 118 lists
the parameters for the Sample Info view.
Table 118. Multi Peak Plot parameters
Parameter
Description
Arrows
When you select All Samples for Selected Component in the Item Selector list, you can click
the left/right arrow to move the selection to the previous/next component until the first/last
component is selected.
When you select All Components for Selected Sample in the Item Selector list, you can click
the left/right arrow to move the selection to the previous/next sample in the sequence grid
until the first/last sample is selected.
Play/Pause
Click to start or pause the timed review of the samples.
Click the play button to cause the peaks for the given component or sample to be displayed
for the specified time interval. The next set of peaks is displayed for the specified time
interval until there are no more peaks in the list. When you select the Repeat Playback check
box, the playback restarts at the beginning of the list until stopped manually. Switching
panes also stops the timed display.
Item Selector List Options
All Samples for
Selected Component
Select this option so chromatographic peaks for each sample in the given tab (All, Standards,
QCs, Blanks and Unknowns) are produced and displayed in the grid-like arrangement.
All Components for
Selected Sample
Select this option so that chromatographic peaks for each component for the selected sample
are produced and displayed in the grid-like arrangement.
Shortcut Menu
Lock against All
Change
Prevents changes to a raw file or parameters. The lock icon is red and the lock is closed.
Unlock
Makes the pane editable. The lock icon is green and the lock is open.
Use User Defined
Time Range
Resets the time scale to the user-defined range, as entered in the Realtime Display Settings
dialog box. For more information, see “Realtime Display Settings” on page 87 in Chapter 2,
“Preparing to Perform Quantitative Analysis.”
Options
Opens the Multi-Peak Options dialog box.
Reset Scaling
Resets x and y axes to show the maximum amount of data.
Copy to Clipboard
Copies a chromatogram, mass spectrum, or calibration curve to the Clipboard. You can then
paste the data from the Clipboard buffer into a document.
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Creating a Processing Sequence
This chapter describes how to create a processing sequence by using the Sequence views of the
Quantitate window. A processing sequence provides instructions to the LCquan application
about what samples to process. It consists of a list of sample data files and includes
information about sample type and calibration or QC levels.
Contents
• Defining a Processing Sequence
• Editing a Processing Sequence
• Exporting a Processing Sequence
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Defining a Processing Sequence
From the Create Sequence views in the Quantitate window, you can create a new processing
sequence or edit an existing sequence.
• If you have not defined or imported a processing sequence, when you click the Sequence
icon, the application opens the New Processing Sequence Wizard. When you complete
the wizard, the Create Sequence (create) view opens (Figure 173).
Figure 173. Create Sequence (create) window
Opens the edit view.
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• If you already created a processing sequence, when you click the Sequence icon, the
application opens the current sequence in the Create Sequence (edit) view (Figure 174).
From this view, you can access the Create Sequence (create) view in the Quantitate
window.
Figure 174. Create Sequence (edit) window
Opens the create view.
Use any of these methods to create a processing sequence:
• Using the New Processing Sequence Wizard
• Copying an Acquisition Sequence
• Importing a Processing Sequence
• Copying the Last Acquired Sequence
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Using the New Processing Sequence Wizard
If you have not defined or imported a processing sequence, use the New Processing Sequence
Wizard to create a new sequence.
Start the Wizard
Use the New Processing Sequence Wizard to create a new sequence.
 To open the New Processing Sequence Wizard
1. Do one of the following:
• Click Quantitate, and then click the Sequence icon.
• Choose View > Section Selection > Quantitate Section, and then choose View >
Step Selector > Quantitate Sequence.
The New Processing Sequence Wizard opens (Figure 175).
Figure 175. Welcome page for the New Processing Sequence Wizard
2. Click Next.
Create or Import a Sequence
Create a new processing sequence, or import an existing sequence file (see Figure 176 and
Table 177).
 To create a processing sequence
1. Do one of the following:
• Select the Create New Sequence option.
• Select the Import Existing Sequence from File option.
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Figure 176. Create or import sequence page
Figure 177. Create or import a sequence page parameters
Option
Description/Condition
Create New Sequence
Select this to specify that you want to create a new processing
sequence.
Import Existing
Sequence from File
Select this to specify that you want to import an existing
processing sequence.
Import from
Acquisition Sequence
Select this to create default processing sequence components with
the names from the acquisition sequence component list and
import the sequence defined in the acquisition setup.
Note This option is enabled only if the acquisition sequence
exists.
2. Click Next.
• If you selected the Create New Sequence option, go to Complete the Wizard.
• If you selected the Import Existing Sequence from File option, go to Import a
Sequence File.
Import a Sequence File
Import a saved sequence file.
 To import a sequence file
1. Type the path for the sequence file, or click Browse and find a file (Figure 178).
Figure 178. Sequence file path page
2. Click Next.
Complete the Wizard
On the final Wizard page, click Finish to exit the New Processing Sequence Wizard and apply
all your settings.
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Note If you receive a warning about missing or mismatched level names, see “Resolving
Discrepancies in Level Names” on page 327.
When you complete the New Processing Sequence Wizard, the Create Sequence (create) view
in the Quantitate window opens. You are now ready to begin refining your processing
sequence.
Copying an Acquisition Sequence
Usually, instead of creating a processing sequence, it is more convenient to use your
acquisition sequence as your processing sequence. You can do this in either of two ways:
• Copying from the Acquisition Sequence History
• Copying from the Acquisition Sequence
Copying from the Acquisition Sequence History
Use the acquisition sequence history list on the Create Sequence (edit) view to copy sequences
to your sequence grid.
When you have already acquired data in the workbook, the acquisition sequence or sequences
that you used are listed in the acquisition sequence history list. To copy an acquisition
sequence, select it from the list and drag it into the processing sequence grid. To select
multiple sequences, hold down the SHIFT or CTRL keys.
The LCquan application will ask if you want to replace the current sequence and if you want
to overwrite the levels for matching component names.
Copying from the Acquisition Sequence
When an acquisition sequence already exists in the current workbook, you can use it to define
the processing sequence in the following ways:
• From the File > Import menu:
–
Choose Processing Sequence > Copy From Acquisition Sequence to copy the
acquisition sequence from the current workbook.
–
Choose Processing Sequence > Copy From Last Acquired Sequence to copy the
last-acquired sequence.
• Right-click anywhere in the Create Sequence (edit) view and use the commands on the
shortcut menu:
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Choose Import Processing Sequence > Copy From Acquisition Sequence to copy
the acquisition sequence from the current workbook.
–
Choose Import Processing Sequence > Copy From Last Acquired Sequence to
copy the last-acquired sequence.
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Defining a Processing Sequence
Importing a Processing Sequence
Use any of these methods to import an existing processing sequence into your current
workbook:
• New Study Wizard
When you create a new workbook, the New Study Wizard gives you the option of
importing instrument methods, acquisition sequences, and processing parameters to
initialize the new workbook. You can import all this data from an existing workbook, or
you can import an acquisition sequence from an individual legacy file (.sld, .ipp, or .csv)
or from an LCquan file (.lqn).
When you import an acquisition sequence from an individual legacy file into a workbook
that does not contain a processing sequence, the LCquan application uses the same
sequence for the acquisition sequence and the processing sequence in the current
workbook.
• New Processing Sequence Wizard in the Quantitate window
When you use the New Processing Sequence Wizard, you have the option to import a
previously saved sequence from an individual legacy file (.sld, .ipp, or .csv) or from an
LCquan file (.lqn).
• Menu commands from within the Quantitate window
From the Create Sequence views of the Quantitate window, choose
File > Import > Processing Sequence > From File to display the Load Sequence File
dialog box and import a sequence from an individual legacy file (.sld, .ipp, or .csv) or
from an LCquan file (.lqn).
From anywhere in the Create Sequence (edit) view, right-click and choose Import
Processing Sequence > From File from the shortcut menu to display the Load Sequence
File dialog box.
Note The level names in the processing sequence must match those defined in the
processing method:
• If the calibration or quality control level names in the sequence are different from
those in the processing method, the LCquan application displays the Standard
Level Names Association dialog box or the QC Level Names Association dialog
box. You can use these dialog boxes to associate the level names in the sequence
with the level names in the processing method.
• If the imported sequence contains calibration or QC levels but the processing
method does not, the LCquan application displays a warning box to inform you.
It then displays the Sample Type Assignment dialog box. You can change the
sample type of these samples to unknown in the processing sequence or discard
the samples that have these levels in the processing sequence.
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Editing a Processing Sequence
Copying the Last Acquired Sequence
You can replace the defined processing sequence with a shortened sequence that is based on
the data already acquired.
 To update the processing sequence with the most recent list of acquired samples:
1. Choose Options > Acquisition Sequence Info to open the Acquisition Sequence
dialog box.
2. To update the sequence, select Auto Update the Processing Sequence When Acquiring.
If you are currently acquiring data when you select this option, a message box prompts
you to update the current processing sequence with the most recent list of samples
acquired. If you do not respond to the message box after five seconds, the LCquan
application automatically updates the sequence.
–or–
Right-click the sequence grid and choose Import Processing Sequence > Copy from
Last Acquired Sequence from the shortcut menu.
For details about the Acquisition Sequence parameters, see “Processing Data While
Continuing to Acquire Data” on page 107 in Chapter 2, “Preparing to Perform Quantitative
Analysis.”
Editing a Processing Sequence
If you already created a processing sequence, use the Create Sequence views to edit the current
sequence or create a new one.
• Using the Create Sequence (edit) View, you can review the sequence information and edit
the information in many of the sequence columns.
• “Using the Create Sequence (create) View” on page 323, you can associate new raw files
with sample types or levels.
Using the Create Sequence (edit) View
When you use the LCquan application for quantitative analysis, you do not always have to
create a new processing sequence. Instead, you can copy the acquisition sequence from the
current workbook to use as the processing sequence or import an existing sequence from
another workbook or legacy file. With these techniques, you can quickly define your
processing sequence.
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Editing a Processing Sequence
After you copy or import a sequence, use the Create Sequence (edit) view to review the
processing sequence to ensure that it is correct and, if necessary, alter the processing sequence
in several different ways:
• To review the processing sequence
• To remove a raw file from the processing sequence
• To add a raw file to the processing sequence
• To change the sample type
• To change a range of cells
• To modify the arrangement of the processing sequence
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 To review the processing sequence
1. To open the Create Sequence (edit) view (Figure 179) and display the new processing
sequence, click Edit.
Figure 179. Create Sequence (edit) window
2. Inspect the processing sequence and verify that it contains the correct sample data files
(.raw) and that each raw file is properly associated with a blank, unknown, calibration
level, or QC level.
3. If you find an error in the processing sequence, correct the errors:
a. Click Create to return to the Create Sequence (create) view.
b. Click Remove and Add to reassociate the raw files.
c. Click Edit to return to the Create Sequence (edit) view.
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Figure 180 shows an example. When you are satisfied that the processing sequence is correct,
you are ready to process the raw files. For more information about processing the raw files, see
Chapter 6, “Processing the Raw Files and Reviewing the Analytical Results.”
Figure 180. Sample raw files and their calibration levels
To save the current sequence in the Exports folder of the workbook, choose File > Export >
Processing Sequence. The LCquan application saves the file with the .sld file extension.
 To remove a raw file from the processing sequence
1. To select the row in the sequence that you want to delete, click the row number.
You can select multiple rows to delete.
2. Right-click the sequence grid to display the shortcut menu.
3. Choose Delete Selected Samples.
 To add a raw file to the processing sequence
1. Right-click the sequence grid to display the shortcut menu.
2. Choose Add Sample.
The Select Raw File dialog box opens.
3. In the Select Raw File dialog box, select the files you want to add and click Open.
The LCquan application obtains the sample information from the selected files and adds
the samples to the last rows of the sequence.
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 To change the sample type
1. Click the Sample Type box to display the down arrow (Figure 181).
Figure 181. Sample Type list
2. Select the new sample type from the list to open the Select Level dialog box (Figure 182).
Figure 182. Select Level dialog box
3. Select the level you want to associate with the sample.
4. Click OK.
Note If no levels are defined in the selected processing method, the list of levels appears
blank.
 To change a range of cells
Fill selected columns of selected rows with duplicate text entries or appropriately
sequenced number entries:
a. Select the row that you want to copy.
b. Right-click the sequence grid, and choose Fill Down from the shortcut menu.
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c. In the Fill Down dialog box (Figure 183), specify the columns to be included and the
range of rows.
Figure 183. Fill Down dialog box
For detailed descriptions of the fill down parameters, see “Fill Down dialog box parameters”
on page 60 in Chapter 2, “Preparing to Perform Quantitative Analysis.”
 To modify the arrangement of the processing sequence
Use the shortcut menu commands. For example, you can change the sorting order of the
sequence.
For detailed descriptions of the processing sequence grid shortcut menu commands, see the
Processing Sequence Shortcut Menu.
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Processing Sequence Shortcut Menu
Right-click the sequence grid to display the shortcut menu (Figure 184). Table 119 lists the
commands for the processing sequence shortcut menu.
Figure 184. Processing sequence shortcut menu
Table 119. Processing sequence grid shortcut menu commands (Sheet 1 of 2)
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Command
Description
Fill Down
Opens the Fill Down dialog box where you can duplicate column
data from a selected row to other rows in the sequence. For more
information, see “Processing Sequence Fill Down Parameters.”
Set Sorting Order
Opens the Sequence Sorting Order dialog box where you can
change the sorting order of the rows in the sequence. For detailed
parameter definitions, see “Modifying the Column Sort Order” on
page 319.
Columns
Opens the Column Arrangement dialog box where you can
customize the column arrangement and display. See “Customizing
Column Arrangement” on page 320.
Add Sample
Opens the Select Raw File dialog box where you can select samples
to add to the Result list.
Delete Selected
Samples
Removes the selected samples (rows) from the Result list.
Duplicate Selected
Row
Copies the selected row and adds it to the Result list. The new row
is added to the sequence according to the current sort criteria.
Show Level Amounts
Opens the Review Level Amounts dialog box that displays the
amount of sample in a calibration level or quality control level.
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Table 119. Processing sequence grid shortcut menu commands (Sheet 2 of 2)
Command
Description
Import Processing
Sequence
From File: Opens the Load Sequence dialog box where you can
load a sequence (.sld, .ipp, .lqn, or .csv).
Copy from Last Acquired Sequence: Overwrites the processing
sequence with the last acquisition sequence.
Copy from Acquisition Sequence: Overwrites the processing
sequence with the acquisition sequence in the workbook.
For information about updating the processing sequence with the
most recent list of acquired samples, see “Processing Data While
Continuing to Acquire Data” on page 107 in Chapter 2,
“Preparing to Perform Quantitative Analysis.”
Processing Sequence Fill Down Parameters
From the processing sequence grid, you can duplicate or sequence column values. The
mechanism is the same as the Fill Down for the acquisition sequence grid, but different
columns are affected. Not all columns can be “filled down.” Figure 185 shows the processing
sequence Fill Down dialog box.
Figure 185. Processing sequence Fill Down dialog box
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Table 120 lists the parameters for the processing sequence Fill Down dialog box.
Table 120. Processing sequence Fill Down dialog box parameters
Parameter
Description
Select Columns
For descriptions of all column names and values, see “Processing
Sequence Grid Column Parameter Definitions.”
Row Controls
Fill From Row
Specifies the first row to receive new data.
To Row
Specifies the last row to receive new data.
Using Row
Specifies which row the initial data comes from.
Create Samples in
Selected Empty Rows
During Fill Down
Specifies that a new sample be created in an empty row during a
fill down that includes the row in its fill down range. When not
selected, specifies that the empty row is ignored during a fill down
that includes the row in its fill down range.
Buttons
Selects all the check boxes in the Select Columns area.
Clears all the check boxes in the Select Columns area.
Processing Sequence Grid Column Parameter Definitions
Figure 186 shows the processing sequence grid columns.
Figure 186. Processing sequence grid columns
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Table 121 lists the available columns for the processing sequence grid.
Table 121. Processing sequence grid column parameters (Sheet 1 of 3)
Parameter
Description
Sample Type
Displays the type of sample described by the sequence row. The
sample type defines how the LCquan application processes the
sample data. Each sample must be classified as one of the
following sample types:
•
•
•
•
FileName
Unknown
Blank
QC (quality control)
Standard
Displays the name of the raw file that contains the sample data.
The file name is a combination of the base file name prefix
assigned to the sequence and a sequential sequence number.
When the default sequence starting number 1 was not changed,
the suffix number is the same as the row number of the sequence:
001, 002, and so on.
When the default sequence starting number was changed to
another number, the first sample has the starting number and
subsequent rows in the sequence are incremented by 001. For
example, if the starting number was 100, the file name for the first
sample would have a suffix of 100, the second sample would have
a suffix of 101, and so on.
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Path
The path in the workbook from which raw files are loaded.
Sample ID
Displays the sample ID for each data file. The sample ID is an
alphanumeric string of characters that identifies a sample.
Level
Indicates the level defined for a calibration sample or quality
control sample. For details about calibration or QC levels, see
Chapter 4, “Creating a Processing Method.”
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Table 121. Processing sequence grid column parameters (Sheet 2 of 3)
Parameter
Description
ISTD Corr Amt
Specifies an updated amount of internal standard for the
corresponding sample. The default value is 0.0.
For each component defined as an internal standard, a bulk
adjustment factor can be applied to the base response of each
internal standard defined in the processing method. When no
adjustment is required, verify that a value of 0.000 is entered in
the ISTD Corr Amt box. When an adjustment is required, enter
the actual value of all internal standard amounts or concentrations
in the sample into the ISTD Corr Amt box for the sample row or
rows requiring adjustment.
The new value entered must use the same units as specified in the
processing method. Do not enter the units of measurement into
the box. For example, for 20 ng, type 20.
Dil Factor
Displays the dilution factor used to prepare the sample. The valid
range is 0.000 to 10 000.000. The application interprets a value of
0.000 as no dilution.
Vial Pos
Displays the sample’s position number in the autosampler. This
column value is read-only.
Inj Vol
Displays the injection volume in microliters of sample to be
injected.
When you are using an autosampler, you can set the default
injection volume in the Autosampler dialog box in the Instrument
Setup window. The minimum and maximum injection volumes
that you can use depends upon the Autosampler you select. The
usable range is dependent upon the injection mode and might be
smaller than the range displayed in the status bar. For more details,
consult your Autosampler manual.
Fill Down cannot be used on Inj Vol column values.
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Sample Vol
Displays the volume of a component that has been placed in the
sample. The unit for this volume is specified in the Xcalibur
Processing Setup window and is included only in LCquan reports.
The LCquan application does not convert units.
Sample Wt
Displays the amount of a component that has been placed in the
sample. The unit for this sample weight is specified in the
Xcalibur Processing Setup window and is included only in
LCquan reports. The LCquan application does not convert units.
Sample Name
Displays the sample name that you specified when you created the
sequence.
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Table 121. Processing sequence grid column parameters (Sheet 3 of 3)
Parameter
Description
Comment
Displays the comment entered for this sample.
Barcode
Displays the barcode for this sample.
Fill Down cannot be used on Barcode column values.
Barcode Status
Displays the status of the barcode reading.
User Columns
1–5
(User-defined) Displays information pertinent to the active
sample row in the acquisition sequence. Use these columns to
convey sample information to others or as a reminder to yourself.
Modifying the Column Sort Order
Use the Sequence Sorting Order dialog box to can change the sorting order of the rows in the
sequence (Figure 187). Table 122 lists the parameters for the Sequence Sorting Order dialog
box.
Figure 187. Sequence Sorting Order dialog box
Table 122. Sequence Sorting Order dialog box parameters (Sheet 1 of 2)
Parameter
Description
Sorting Options
The following sorting options are applicable to all three sort orders.
Thermo Scientific
File Name
Sorts the list so the file names are in alphabetical order.
Level Name
Sorts the list so the calibration standard and QC level names are in
alphabetical order.
Sample ID
Sorts the list so the sample IDs are in alphabetical or numerical
order.
Sample Type
Sample types are not sorted alphabetically. In ascending order, the
types are: Standards, QCs, Blanks, and Unknowns.
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Table 122. Sequence Sorting Order dialog box parameters (Sheet 2 of 2)
Parameter
Description
First Order
Specifies the first order of sorting for the sequence. The default
first order of sorting is by sample type.
Second Order
Specifies the second order of sorting for the sequence.
Third Order
Specifies the third order of sorting for the sequence.
Sort in Descending
Order
The application sorts the list in descending (n-to1) order. Clear
this option to have it sort the list in ascending order.
Customizing Column Arrangement
 To customize the column arrangement of a sequence
1. From the processing sequence grid shortcut menu, choose Columns.
The Column Arrangement dialog box opens (Figure 188). Table 123 lists the parameters
for the Column Arrangement dialog box.
Figure 188. Column Arrangement dialog box
2. To hide currently displayed columns, select the check box before the column and click
Remove.
This does not delete the column; it simply hides it from display on the sequence grid.
All hidden columns are displayed in the Available Columns list.
3. To display currently hidden columns, select the check box before the column and
click Add.
The column is added to the Displayed Columns list and is displayed on the sequence
grid.
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4. To change a column position:
a. Select the check box before the column name in the Displayed Columns list.
b. To move the column left in the grid, click Move Up.
c. To move the column right in the grid, click Move Down.
5. To change the display precision:
a. In the Places column of the Displayed Columns list, select the value you want to
change.
b. Type a new value for the number of decimal places to display in the column.
Note When the Values column is unavailable, your LCquan administrator has
specified decimal rounding for exported Excel reports. In this case, the number of
decimal places is fixed and cannot be edited.
6. To change a column width:
a. In the Width column of the Displayed Columns list, select the value you want to
change.
b. Type the new value.
Tip You can also resize a column width by dragging the column boundary in the
heading row of the sequence grid.
7. To change an item name:
a. In the Item column of the Displayed Columns list, select the item name you want to
change.
b. Type the new name.
8. To reset column values, click Factory Defaults.
There is no “undo” for this function.
Table 123. Column Arrangement dialog box parameters
Thermo Scientific
Parameter
Description
Available Columns
Lists parameters that are not currently selected for display.
Displayed Columns
Lists currently selected parameters, which appear in the data
grids.
Add / Remove
Displays / Hides selected columns.
Move Up / Move
Down
Move Up moves columns left in the grid.
Move Down moves columns right in the grid.
Factory Defaults
Resets original column values (as described in “Grid
parameters” on page 394 in Chapter 6, “Processing the Raw
Files and Reviewing the Analytical Results.” )
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Review Level Amounts
The Review Level Amounts dialog box displays the calibration or QC levels (depending on
the selected sample) and the component amounts in each level (Figure 189).
Figure 189. Review Level Amounts dialog box
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Editing a Processing Sequence
Using the Create Sequence (create) View
Use the Create Sequence (create) view (Figure 190) to build a processing sequence by
associating each raw file in the data set with a standard calibration level, a QC level, a blank
sample type, or an unknown sample type.
Figure 190. Associate raw files view
Step 1
Step 2b
Step 2b
Result
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 To build a new processing sequence
1. In the upper Available Files pane of the Create Sequence (create) view, search for and click
the folder containing the raw files to be quantitated.
The application displays the names of the raw files in the lower Available Files pane.
2. Associate the data files with the Standard sample type calibration levels:
a. Click the Standards tab in the Selected Files pane and select the appropriate
calibration level (Figure 191).
Figure 191. Date files associated with Standards sample type
b. To associate a data file with selected calibration level, click the raw file in the lower
Available Files pane and click Add.
The application adds the selected raw file to the selected calibration level.
c. To display the amount of standard sample associated with a calibration level,
right-click the calibration level and choose Show Level Amounts from the shortcut
menu.
3. Associate the data files with the QC sample type levels:
a. Click the QCs tab in the Selected Files pane and select the appropriate quality
control level.
b. To associate a data file with selected QC level, click the raw file in the lower
Available Files pane and click Add.
The application adds the selected raw file to the selected quality control level in the
Selected Files pane.
c. To display the amount of quality control sample associated with a quality control
level, right-click the quality control level and choose Show Level Amounts from the
shortcut menu.
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4. Associate the data files with the Blanks sample type:
a. Click the Blanks tab in the Selected Files pane.
b. To associate a data file with the Blanks sample type, click the raw file in the lower
Available Files pane and click Add.
The application adds the selected raw file to the Blanks sample type in the Selected
Files pane.
5. Associate the data files with the Unknowns sample type:
a. Click the Unknowns tab in the Selected Files pane.
b. To associate a data file with the Unknowns sample type, click the raw file in the lower
Available Files pane and click Add.
The application adds the selected raw file to the Unknowns sample type in the
Selected Files pane.
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 To watch an animation of these procedures
Click the play button.
Note To watch this animation, you must have Adobe Flash Player version 10 or later.
You can download the latest Adobe Flash Player from get2.adobe.com/flashplayer/.
 To select raw files by using other methods
• With the cursor, drag raw files to the Selected Files pane.
• Hold down SHIFT or CTRL to select multiple data files before dragging or clicking
Add.
Tip Use the sample type information in the file information pane at the bottom of the
window to identify the data files.
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Editing a Processing Sequence
Resolving Discrepancies in Level Names
When you add samples to a sequence, if the LCquan application detects a discrepancy in the
level names, one of these dialog boxes opens:
• The Standard or QC Level Names Association dialog box opens when the samples are
associated with calibration or QC level names that do not match the level names of the
workbook sequence. For more information, see “Resolving Mismatched Level Names.”
• Workbook Does Not Contain Levels dialog box opens when the samples are associated
with level names, but the workbook processing method has no calibration or QC levels
defined. For more information, see “Resolving Missing Calibration or QC Levels” on
page 329.
Resolving Mismatched Level Names
The Standard (or QC) Level Names Association dialog box warns you of a discrepancy in the
calibration level names or QC level names under the following conditions:
• Importing an acquisition sequence—The level names in the acquisition sequence do not
match the level names in the workbook.
• Importing a processing sequence—The level names in the imported processing sequence
do not match the level names in the workbook processing method.
• Adding sample files to a processing sequence—The level names associated with the added
samples do not match the level names in the workbook.
 To resolve the level names for an imported sequence
1. Verify that you imported the correct sequence.
2. To associate the level names, do one of the following (Figure 192):
• Select the level name in the Sequence Level Names pane and drag it to the
appropriate level name in the Method Level Names pane (processing method) or the
Workbook Level Names pane.
–or–
• Select the two level names and click Add.
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3. Click OK.
Figure 192. Standard (or QC) Level Names Association dialog box
If any discrepancy remains in the level names, the Level Name Association Not Complete
dialog box opens (Figure 193). Follow the instructions: To resolve incomplete level name
association.
Figure 193. Level Name Association Not Complete dialog box
 To resolve level names for added samples
1. In the Sample Level Names pane, do one of the following:
• Select the level name and drag it to the appropriate level name in the Workbook Level
Names pane.
–or–
• Select the two level names and click Add.
2. Click OK.
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Exporting a Processing Sequence
If any discrepancy remains in the level names, the Level Name Association Not Complete
dialog box opens (Figure 193 on page 328). Follow the instructions to resolve incomplete
level name association.
 To resolve incomplete level name association
When you add or import samples or sequences and associate the new level names with the
names in the current workbook, if any discrepancy remains in the level names, the
Level Name Association Not Complete dialog box opens (Figure 193 on page 324).
You have these options:
• To return to the Standard (or QC) Level Names Association dialog box and finish
associating the level names, click Complete.
• To assign the unknown sample type to the samples that have unassociated levels, click
Set to Unknown.
• To remove the samples that have unassociated levels from the sequence, click Discard.
Resolving Missing Calibration or QC Levels
The Workbook Does Not Contain Levels dialog box warns that the samples are associated
with level names, but the workbook processing method has no calibration or QC levels
defined.
You have these options:
• To set all samples in the sequence that have a specified QC or calibration level to sample
type unknown, click Set to Unknown.
• To remove all samples that have a specified calibration level from the sequence, click
Discard.
• To cancel the level names association process, click Cancel.
Make sure you are using the correct sequence and processing method for the workbook. To
modify the sequence, see “Editing a Processing Sequence” on page 308. To modify the
processing method, see Chapter 4, “Creating a Processing Method,”
Exporting a Processing Sequence
To save the current sequence to a file in the workbook Exports folder, choose File > Export >
Processing Sequence.
The application saves the file with the .sld file extension.
You can later import this file using a command such as File > Import > Processing Sequence >
From File.
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Processing the Raw Files and Reviewing the
Analytical Results
This chapter topic describes how to process raw data by using the processing method and the
processing sequence that you created in the previous chapters topics. It also explains how to
review the results for each component in each raw file and how to produce reports.
Contents
• Processing the Raw Files
• Reviewing the Calibration Curve and QCs
• Reviewing All Results
• Creating and Reviewing Reports
• Exporting Results
• Locking the Workbook
• Saving the Workbook and Exiting the LCquan Application
Processing the Raw Files
The LCquan application processes the raw files in the processing sequence when you open the
Survey view, the Review All Results view, or the Review Reports view of the Quantitate
window. It uses the peak detection and integration parameters in the processing method to
detect and integrate peaks for all components. Using the calibration parameters set in the
processing method, it builds a calibration curve to quantitate the QCs and unknowns.
Note You need to define a processing method and a processing sequence before you can
open the Survey view, the Review All Results view, or the Review Reports view.
You can review the results in any order.
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Reviewing the Calibration Curve and QCs
Reviewing the Calibration Curve and QCs
Use the Survey view in the Quantitate window to review and rework the calibration standards.
The process of reviewing and reworking the calibration standards involves these steps:
1. Opening the Survey View
2. Reviewing the Calibration Standards
3. Excluding a Calibration Standard from the Calibration Curve (optional)
4. Modifying the Peak Detection and Integration Settings (optional)
5. Manually Integrating Peaks (optional)
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Opening the Survey View
After creating the processing sequence, you are ready to review the calibration curves. To
process the raw files and open the Survey view (Figure 194), click the Survey icon in the
navigation pane.
Figure 194. Quantitate – Survey window
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The Survey view includes (clockwise from the top) the Result grid, the Component list, the
Calibration Curve pane, the ISTD Chromatogram pane, and the Chromatogram pane.
• The Result grid pane contains the peak integration results. It has three display tabs at the
bottom: All, Standards, and QCs. The Result grid also uses a system of color shading to
indicate the status of individual samples. For information about the Result grid shortcut
menu, see “Result grid shortcut menu.”
• The Component list pane contains the components that are defined in the current
processing method. When you select a component in the Component list, all the other
page elements are updated to display the results for that component.
Instead of a Component list on the right side of the view, you can display the components
on tabs above the grid. Choose View > Component Selector Bar from the window
menu. For information about the Component list shortcut menu, see “Component List
Shortcut Menu” on page 340.
• The Calibration Curve pane displays a plot of area ratio (or area) versus concentration (or
amount) for the selected component.
• The ISTD Chromatogram pane displays a plot of relative intensity versus retention time
of the internal standard in the current sample (if available).
• The Chromatogram pane displays a plot of relative intensity versus retention time of the
selected component in the current sample.
• Navigation Features
In the Chromatogram pane and in the ISTD Chromatogram pane, use the toolbar
buttons to zoom in and out along the x and y axes to show more detail (see Table 124).
Table 124. Zoom buttons (Sheet 1 of 2)
Icon
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Button
Description
Zoom In Y
Zooms in the traces along the y axis, vertically, to display more
detail and less range.
Zoom Out Y
Zooms out the traces along the y axis, vertically, to display
more range and less detail.
Normalize
Readjusts the display of all peaks in the trace based on the
largest peak height.
Zoom In X
Zooms in the traces along the x axis, horizontally, to display
more detail and less range.
Zoom Out X
Zooms out the traces along the x axis, horizontally, to display
more range and less detail.
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Table 124. Zoom buttons (Sheet 2 of 2)
Icon
Button
Description
Display All
Resets the display of the x axis to include the entire displayable
range.
Reset Scaling
Resets both x and y axes to display the maximum amount of
data.
You can also use the arrow keys on the keyboard to zoom. The left arrow key zooms in
along the x axis by a factor of two (2). The right arrow key zooms out along the x axis by
a factor of two (after you have zoomed in). Similarly, the up arrow zooms in along the y
axis by a factor of two and the down arrow zooms out.
Result Grid Shortcut Menu
The result grid shortcut menu is available from the Survey view and the Review All Results
view. Right-click the result grid to display the shortcut menu (Figure 195). Table 125 lists the
commands for the results grid shortcut menu.
Figure 195. Result grid shortcut menu
Table 125. Result grid shortcut menu commands (Sheet 1 of 2)
Thermo Scientific
Command
Description
Columns
Opens the Column Arrangement dialog box where you can
customize the column arrangement and display. See “Customizing
Column Arrangement” on page 337.
Delete Selected
Samples
Removes the selected samples (rows) from the Result grid.
Add Sample
Opens the Select Raw File dialog box where you can select samples
to add to the Result grid. The LCquan application obtains the
sample information from the selected files and adds the samples to
the sequence.
Duplicate Selected
Row
Copies the selected row and adds it to the Result grid. The new
row is added to the sequence according to the current sort criteria.
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Table 125. Result grid shortcut menu commands (Sheet 2 of 2)
Command
Description
Copy Selected Rows to Copies the selected rows to the Thermo LCquan TrackQC.
TrackQC
TrackQC provides calculations for intraday or interday QC-run
validation. The QC samples you copy to TrackQC can include
one or more QC levels for a single component and can be from
one or more LCquan workbooks. For details, refer to the
TrackQC online Help.
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Set Sorting Order
Opens the Quantitation Results Sorting Order dialog box where
you can change the sorting order of the rows in the sequence. See
“Customizing the Results Sorting Order” on page 339.
Color Coding Legend
Displays the color coding legend:
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Customizing Column Arrangement
 To customize the columns arrangement for the results grid.
1. From the results grid shortcut menu, select Columns.
The Column Arrangement dialog box opens (Figure 196). Table 126 lists the parameters
for the Column Arrangement dialog box.
Figure 196. Column Arrangement dialog box
2. To hide currently displayed columns, select the check box before the column and click
Remove.
This does not delete the column; it simply hides it from display on the sequence grid. All
hidden columns are displayed in the Available Columns list.
3. To display currently hidden columns, select the check box before the column and
click Add.
The column is added to the Displayed Columns list and is displayed on the sequence
grid.
4. To change a column position:
a. Select the check box before the column name in the Displayed Columns list.
b. To move the column left in the grid, click Move Up.
c. To move the column right in the grid, click Move Down.
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5. To change the display precision:
a. In the Places column of the Displayed Columns list, select the value you want to
change.
b. Type a new value for the number of decimal places to display in the column.
Note When the Values column is unavailable, your LCquan administrator has
specified decimal rounding for exported Excel reports. In this case, the number of
decimal places is fixed and cannot be edited.
6. To change a column width:
a. In the Width column of the Displayed Columns list, select the value you want to
change.
b. Type the new value.
Tip You can also resize a column width by dragging the column boundary in the
heading row of the sequence grid.
7. To change an item name:
a. In the Item column of the Displayed Columns list, select the item name you want to
change.
b. Type the new name.
8. To reset column values, click Factory Defaults.
There is no “undo” for this function.
Table 126. Column Arrangement dialog box parameters
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Parameter
Description
Available Columns
Lists parameters that are not currently selected for display.
Displayed Columns
Lists currently selected parameters, which appear in the data
grids.
Add / Remove
Displays / Hides selected columns.
Move Up /
Move Down
Move Up moves columns left in the grid.
Move Down moves columns right in the grid.
Factory Defaults
Resets original column values (as described in “Grid
parameters” on page 394 in Chapter 6, “Processing the Raw
Files and Reviewing the Analytical Results.” )
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Customizing the Results Sorting Order
From the Quantitation Results Sorting Order dialog box (Figure 197), change the sorting
order of the rows in the sequence. Table 127 lists the parameters for the Quantitation Results
Sorting Order dialog box.
Figure 197. Quantitation Results Sorting Order dialog box
Table 127. Quantitation Results Sorting Order dialog box parameters (Sheet 1 of 2)
Parameter
Description
First Order
Select a sorting topic as the first order of sorting.
Second Order
Select a sorting topic as the second order of sorting.
Third Order
Select a sorting topic as the third order of sorting.
Sort in Descending
Order
Select this check box to sort the list in descending (reverse) order.
% Difference
Increasing (negative to positive) percent difference. The percent
difference is defined as
100 × (calculated amount – specified amount) / specified amount
% RSD
Increasing percent relative standard deviation (RSD). The percent
RSD is the standard deviation of the difference of the calculated
amount and the specified amount, expressed as a percentage of the
average value.
Area/Height
Increasing peak area or height.
Sorts by peak area when you selected Response: Area in the
Create Method view in the Quantitate window or the dialog box.
Sorts by peak height when you selected Response: Height in the
Create Method view in the Quantitate window or the dialog box.
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Table 127. Quantitation Results Sorting Order dialog box parameters (Sheet 2 of 2)
Parameter
Description
Area/Height Ratio
Increasing ratio of the peak area or height of the selected
component to that of the internal standard.
Sorts by peak area ratio when you selected Response: Area in the
Create Method view in the Quantitate window or the dialog box.
Sorts by peak height ratio when you selected Response: Height in
the Create Method view in the Quantitate window or the dialog
box.
Exclude
Lists excluded samples first.
File Name
IDs are in alphabetical or numerical order.
Integration Type
Lists Method Settings integration type first, User Settings
integration type second, and Manual Integration integration
type last.
Level Name
Calibration standard and QC level names are in alphabetical
order.
Peak Status
Groups low responses, high response, excluded, and related status
markers by this tagging style.
Sample ID
IDs are in alphabetical or numerical order.
Sample Type
Type of sample: Standard, QC, Blank, and Unknown.
Sample RT
Displays retention time in chronological order.
Sample Original Order Displayed in original order.
Acquisition Time/Date Displayed in chronological order.
Component List Shortcut Menu
The Component list shortcut menu is available from the Survey view and the Review All
Results view. Right-click the Component list and choose one of the sort orders from the
shortcut menu (see Table 128).
Table 128. Component list shortcut menu commands
Sort Order
Description
Unsorted
Ascending order of times when components were added to the list.
By RT
Ascending order of Expected Retention Times for the
components.
Alphabetically
Alphabetical order of the components.
When you make a selection, the information is saved in the registry. All workbooks use the
current setting until the user changes it. The setting is independently saved for each user.
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Note To change the order of the Component tabs, set the sort order in the Component
list and choose View > Component Selector Bar to display the Component tabs.
Reviewing the Calibration Standards
Use the Survey view to confirm that the LCquan application properly detected and integrated
the peaks.
 To review the calibration standards for a target compound
1. In the Component list on the right side of the view, select the target compound.
The application automatically updates the Result list, the Chromatogram and ISTD
Chromatogram panes, and the Calibration Curve pane.
2. Ensure that the calibration standards are displayed in the Result list. If necessary, click the
Standards tab at the bottom of the Result list to display the calibration standards.
3. In the Calibration Curve pane, inspect the calibration curve at all concentrations.
Evaluate the calibration curve according to the criteria used in your laboratory.
4. To inspect the calibration curve at low concentrations (Figure 198):
a. With the mouse pointer, draw a rectangle around low concentration data points in
the calibration curve.
When you release the mouse button, the application displays only the selected low
concentration data points.
Figure 198. Calibration curve at low concentrations
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b. To reset the scaling of the x and y axes of the calibration curve to full scale, right-click
and choose Reset Scaling from the shortcut menu or click the Reset Scaling icon,
.
5. Inspect the Result list:
a. Check the entries in the Result list for peak detection and integration problems.
(Use the scroll bar at the bottom of the list to see all the columns.)
b. Ensure that the data files correspond to the correct levels and sample types.
6. Select a data file by clicking its row in the Result list.
7. Inspect the target compounds and internal standard peaks:
a. Inspect the component peak in the Chromatogram pane:
i.
Ensure that the LCquan application found the peak. It shades the peak it finds
gray and marks the starting and ending points of the peak with integration
markers.
ii. Ensure that the shaded area accurately represents the contribution of the
component to the chromatogram.
b. Inspect the internal standard peak in the ISTD Chromatogram pane:
i.
Ensure that the LCquan application found the peak. It shades the peak it finds
gray and marks the starting and ending points of the peak with integration
markers.
ii. Ensure that the shaded area accurately represents the contribution of the internal
standard to the chromatogram.
• To exclude a calibration standard from the calibration curve, go to the next topic:
Excluding a Calibration Standard from the Calibration Curve.
• To modify the peak detection and integration settings that you defined in the Create
Method view, go to the topic: “Modifying the Peak Detection and Integration Settings”
on page 353.
• You can manually change the integration starting and ending points and the baseline of
the peak. To manually integrate a peak, go to the topic: “Manually Integrating Peaks” on
page 371.
8. Repeat steps 1–7 for each of the remaining files in the Result list.
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Review and rework the internal standard results as you did for the target compound.
 To review the calibration standards for the internal standard
1. In the Component list, select the internal standard.
2. The LCquan application automatically updates the Result list and the Chromatogram
pane. It does not display a chromatogram in the ISTD Chromatogram pane for this
component but displays the response for each internal standard sample in the Calibration
Curve pane.
3. Check the entries in the Result list for peak detection and integration problems.
4. Inspect the chromatogram in the Chromatogram pane for each file:
a. Ensure that the LCquan application found the peak.
b. Ensure that the shaded area accurately represents the contribution of the component
to the chromatogram.
• To modify the peak detection and integration settings that you defined in the
Create Method view, go to the topic: “Modifying the Peak Detection and
Integration Settings” on page 353.
• You can manually change the integration starting and ending points and the
baseline of the peak. To manually integrate a peak, go to the topic: “Manually
Integrating Peaks” on page 371.
When you are satisfied that the LCquan application properly detected and integrated the
peaks, you are ready to review all the results.
• For additional information about reworking the data, see the following topics: “Excluding
a Calibration Standard from the Calibration Curve” on page 350, “Modifying the Peak
Detection and Integration Settings” on page 353, and “Manually Integrating Peaks” on
page 371.
• To review all the results, go to “Reviewing All Results” on page 373.
Modifying Calibration Settings
You can use the Calibration Settings dialog box to change the calibration curve parameters
that you specified on the Calibration page in the Create Method view of the Quantitate
window, including curve type and level information.
To open the Calibration Settings dialog box, right-click a Calibration Curve view in any of the
preview panes and choose Calibration Settings from the shortcut menu.
The Calibration Settings dialog box includes these tabs:
• Calibration Settings – Curve
• Calibration Settings – Isotope%
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• Calibration Settings – Levels
• Calibration Settings – Type
Calibration Settings – Curve
Use the Curve page to modify calibration curve settings (Figure 199). Table 129 lists the
parameters for the Calibration Settings – Compound dialog box.
Figure 199. Calibration Settings dialog box for Compound
Table 129. Calibration Settings – Compound dialog box parameters (Sheet 1 of 3)
Parameter
Description
Calibration Curve
Specifies a calibration curve type.
Linear
A linear curve that approximates experimental calibration data.
The LCquan application provides ignore/force/include origin
options for this calibration curve type.
Quadratic
A quadratic curve that approximates experimental calibration
data.
The LCquan application provides ignore/force/include origin
options for this calibration curve type.
Linear Log-Log
A linear polynomial curve.
Quadratic Log-Log
A quadratic log-log curve that approximates experimental
calibration data.
The LCquan application does not provide ignore/force/include
origin options for this calibration curve type.
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Table 129. Calibration Settings – Compound dialog box parameters (Sheet 2 of 3)
Parameter
Description
Average RF
The average response factor of all levels.
Point-to-Point
Data averages at each calibration level. Straight lines are drawn
between adjacent (averaged) calibration points.
This calibration curve can be used with one or more calibration
levels. The LCquan application provides ignore/force origin
options for this calibration curve type.
Cubic Spline
A cubic polynomial curve to fit between each pair of calibration
levels so that the slopes of the separate cubic polynomial curves
match at common calibration curve points.
The LCquan application provides ignore/force origin options for
this calibration curve type.
Locally Weighted
A calibration curve constructed from individual line segments.
At multiple points across the calibration region, a weighted linear
regression is performed. Lines are drawn between point slopes,
forming a continuous curve. At any point on the curve, the
calculated amount is based on the nearest weighted linear
regression.
The LCquan application does not provide ignore/force/include
origin options for this calibration curve type.
Origin
Origin Settings
Specifies how to use the origin in your calibration curve.
Ignore
Excludes the origin as a valid data point for calculation or
plotting.
Force
Forces the calibration curve plot to pass through the origin.
Include
Includes the origin as a single data point in the calculation of the
calibration curve, but the calibration curve is not required to pass
through the origin.
Weighting
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Weighting settings
Defines how the calibration data is weighted during the
least-squares regression calculation of the calibration curve.
Equal
Use to weight all calibration data points equally during the
least-squares regression calculation of the calibration curve.
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Table 129. Calibration Settings – Compound dialog box parameters (Sheet 3 of 3)
Parameter
Description
1/X
Specifies a weighting of 1/X for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants are weighted by the inverse of the square of their
quantity.
1/X^2
Specifies a weighting of 1/X^2 for all calibration data points
during the least-squares regression calculation of the calibration
curve. Calibrants are weighted by the inverse of their quantity.
1/Y
Specifies a weighting of 1/Y for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants are weighted by the inverse of their response (or
response ratio).
1/Y^2
Specifies a weighting of 1/Y^2 for all calibration data points
during the least-squares regression calculation of the calibration
curve. Calibrants are weighted by the inverse of the square of their
response (or response ratio).
1/s^2
Specifies a weighting of 1/s^2 for all calibration data points during
the least-squares regression calculation of the calibration curve.
Calibrants at a given level are weighted by the inverse of the
standard deviation of their responses (or response ratios). For this
weighting factor to be used, there must be two or more replicates
at each level. If only one calibrant is available for any level, then
1/s^2 weighting cannot be used.
Response
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Response settings
Specifies the area or the height of the target compound peak to
acquire the data used for the calibration response factor.
Area
Specifies the area of the target compound peak to acquire the data
used for the calibration.
Height
Specifies the height of the target compound peak to acquire the
data used for the calibration.
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Calibration Settings – Isotope%
Use the Isotope% page (Figure 200) to correct for an impurity in the internal standard
compound that elutes at the same time as the target compound, correct for an impurity in the
target compound that elutes at the same time as the internal standard, or correct for both (see
Table 130).
Figure 200. Calibration Settings dialog box showing the Isotope% page for Compound
Table 130. Calibration Settings dialog box, Isotope% page parameters
Parameter
Description
Contribution of
Specify the amount (as a percentage of the target compound) that
ISTD to
the internal standard contributes to the Target Compound’s peak.
Target Compound (%)
Contribution of
Target Compound to
ISTD (%)
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Specify the amount (as a percentage of the ISTD) that the Target
compound contributes to the ISTD’s peak.
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Calibration Settings – Levels
Use the Levels page (Figure 201) to view calibration levels and QC levels that you specified on
the Calibration page in the Create Method view of the Quantitate window (Table 131).
Figure 201. Calibration Settings dialog box showing the Levels page for Compound
Table 131. Calibration Settings dialog box, Levels page parameters
Parameter
Description
Cal Level
Displays the calibration levels for the selected component.
Amount
Displays the amounts of the target compound used for each
calibration level.
QC Level
Displays the QC (quality control) levels for the selected
component.
Amount
Displays the amounts of the target compound used for each QC
(quality control) level.
%Test
Displays a value for the acceptable difference (as a percentage)
between the known amount and calculated (measured) amount of
each QC level.
Note The Levels page of the Calibration Settings dialog box provides a read-only table.
Compare the measured quantity with a previously defined expected quantity and percent test.
If the calibration or QC levels must be changed, use the Calibration page in the Create
Method view of the Quantitate window.
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Calibration Settings – Type
Use the Type page (Figure 202) to view the component type settings that you specified on the
Calibration page in the Create Method view of the Quantitate window (Table 132).
Figure 202. Calibration Settings, Type page for Compound
Table 132. Calibration Settings – Compound dialog box, Type page parameters
Parameter
Description
Component Type
Target Compound
Displays the target compound or the internal standard you are
measuring. When you have selected a target compound on the
Calibration page in the Create Method view page, you can select
an ISTD using the drop down list.
ISTD
Select any available internal standard calibration to be associated
with the target compound.
Note This selection is not available when a target component is
selected.
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Excluding a Calibration Standard from the Calibration Curve
With the LCquan application, you can exclude specific calibration standards from the
calibration curve. Follow the procedures of your laboratory for proper treatment of calibration
data.
Use any of these options to exclude calibration data:
• The Exclude column of the Result list
• The Exclusion list
• The Calibration Curve pane
When you exclude a calibration standard using any of these methods, the LCquan application
highlights its row in the Result list in dark pink and displays the excluded data point as an
empty box in the Calibration Curve pane (Figure 203).
Figure 203. Excluding a calibration standard from the calibration curve
Excluded Samples
Excluded Data Points
 To use the Exclude column of the Result list
1. Select the Standards tab or the All tab at the bottom of the Result list.
2. For each standard that you want to exclude from the calibration curve, select the check
box in the Exclude column of its row (Figure 204).
Figure 204. Exclude column
3. To include the standard again, clear the check box.
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 To use the Exclusion list
1. Select the target compound in the Component list.
2. Right-click the Calibration Curve pane and choose Exclusion List from the shortcut
menu to display the Calibration Exclusion List dialog box.
The Cal Exclusion List dialog box displays a list of all the replicates (co-located data
points) used in creating the current calibration curve and their exclusion status
(Figure 205). Table 206 lists the parameters for the Cal Exclusion List dialog box.
Figure 205. Cal Exclusion List dialog box
• When points are co-located, they cannot be graphically individuated as plot points,
and the granularity of the cursor is not fine enough to manually change the
individual exclusion status.
• These points can be included or excluded in the Results grid if they are listed here.
Note When data is co-located, the plotted data appears to be mismatched to the
(text) entry lists.
3. For each standard that you want to exclude from the calibration curve, click the Exclude
column of its row.
The word Yes appears in the Exclude column.
4. Click Apply to incorporate the change.
To include the standard again, click the word Yes and click Apply.
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Figure 206. Cal Exclusion List dialog box parameters
Parameter
Description
Level
Displays calibration level names for the sample data points
displayed in the Calibration Curve pane.
Expected
Displays expected quantity values for the data points displayed
in the Calibration Curve pane.
%Diff
Displays percent difference values for the data points displayed
in the Calibration Curve pane. These values are the percentage
difference between the Calculated amount and the Expected
amount.
Exclude
• Yes: Replicate is excluded from the data points displayed
in the Calibration Curve pane.
• Blank: Replicate is included in the calibration curve plot.
 To use the Calibration Curve pane
1. In the Calibration Curve pane, click the data point that you want to exclude (Figure 207).
2. Right-click and choose Exclude from the shortcut menu.
3. To include the standard again, click the data point, right-click, and choose Include from
the shortcut menu.
Figure 207. Calibration curve showing excluded data points
Excluded data points
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Modifying the Peak Detection and Integration Settings
You can modify the peak detection and integration settings from the Survey or the Review All
Results views in the Quantitate window.
Note If you modify the user peak detection settings and if you have peak area or peak
height labeling enabled, the application labels the peak with AU, for area user (as opposed
to AA, for area automatic), or HU, for height user (as opposed to HA, for height
automatic).
 To modify the peak detection and integration settings
1. Select a sample by clicking its row in the Result list.
2. Right-click the Chromatogram pane and choose User Peak Detection Settings from the
shortcut menu.
The User Identification Settings dialog box opens. For details of user identification
settings, see Specifying Additional Peak Detection Criteria.
3. To modify the peak detection settings, click the Detection tab and change the settings as
necessary.
4. To modify the peak integration settings, click the Integration tab. Change the settings as
necessary to correct problems with noise in the peak, unresolved peaks, or peak tailing.
5. To modify the advanced peak detection parameters, click the Advanced tab. Adjust the
settings as necessary to improve peak detection and integration if baseline noise causes
interference.
6. Apply the changes:
• To apply the changes to the selected sample in the Result list, click Apply.
• To apply the changes to all the samples on the current page of the Result list (for
example, to all samples on the Standards page), click Apply To All.
7. When you are finished, click OK to close the dialog box.
If you changed any parameters since you last clicked Apply or Apply To All, clicking OK
applies the new changes to the sample selected in the Result list.
When you modify the peak detection and integration parameters, the application displays
User Integration in the Integration Type column of the Result list (Figure 208).
Figure 208. Integration Type column
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 To revert to the original parameters from the processing method
1. In the Integration Type column of the Result list, click the cell containing the words User
Integration for the sample that you want to change.
2. Click the down arrow and select Method Settings from the list.
The application reverts to the original peak detection and integration parameters from the
processing method.
Specifying Additional Peak Detection Criteria
Use the User Identification Setting dialog box to specify additional peak detection criteria
when the standard detection criteria do not provide the expected results.
Peak detection parameters are also available from the Quantitate window:
• The Peak Integration area on the Create page of the Explore view
• The Peak Integration area on the Identification page of the Create Method view
• The IRC Detection dialog box available from the ion ratio confirmation grid on the
Identification page of the Create Method view
To open the User Identification Settings dialog box, right-click a Chromatogram view in any
of the preview panes and choose User Peak Detection Settings from the shortcut menu.
The User Identification Settings dialog box includes these tabs:
• User Identification Settings – Identification
• User Identification Settings - Detection
• User Identification Settings – Genesis Integration
• User Identification Settings – Genesis Advanced
• User Identification Settings – ICIS Integration
• User Identification Settings – ICIS Advanced
• User Identification Settings – Avalon Integration
Note When you change user peak detection settings and click Apply to All, any samples
that have been manually integrated will be reintegrated using the new user settings. Their
Integration Type will be changed from Manual Integration to User Integration.
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User Identification Settings – Identification
Use this page (Figure 209) to set up advanced chromatographic parameters. The content of
the tabs varies according to the selected peak detection algorithm (ICIS, Genesis, or Avalon).
Table 133 lists the parameters for the Identification page of the User Identification Settings
dialog box.
Figure 209. User Identification Settings dialog box showing the Identification page
Table 133. User Identification Settings dialog box, Identification page parameters (Sheet 1 of 3)
Parameter
Description
Smoothing
Specifies the number of points to use for a moving mean filter to
smooth the chromatogram.
Format: integers
Range: 1 to 15, odd numbers only
Note Set the parameter to 1 to disable filtering.
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Table 133. User Identification Settings dialog box, Identification page parameters (Sheet 2 of 3)
Parameter
Description
Trace
Specifies the type of chromatogram:
• Mass Range: Specify up to 50 mass ranges. The masses are
added together to form the chromatogram.
• TIC: Full-scan acquisition resulting in a Total Ion Current
plot.
• Base Peak: In a differential chromatogram, the interpolation
of the baseline is derived from the distance between the
intersections of the tangents drawn to the peak sides and the
peak base.
• Summed: Uses ion summing to create a chromatogram that is
the sum of the chromatograms of related compounds. Ion
summing can increase sensitivity because it sums up to five
chromatograms of related masses, for example, water loss,
adducts, isotopes, or multiply charged peptides.
Note This definition set is the same for the second Trace box.
The second Trace box depends on which operators you select.
There is no second Trace box or trace operators for Trace:
Summed.
Trace: Mass Range, TIC, or Base Peak
+/-/“ “
Trace operator used to specify a trace operation.
This trace operation matrix shows the combinations used to set up
a method:
Mass Range+Mass Range
– Mass Range
TIC+ Mass Range
– Base Peak
Base Peak+Mass Range
– Mass Range
Mass1 (m/z)
Specifies the initial mass value.
Mass2 (m/z)
Specifies the second mass value to define the mass range when you
are using trace operator math.
Filter
Specifies an existing filter or a filter from a preloaded filter list
(obtained from the current raw file).
Note All filters are validated against the current set of filter
entry rules.
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Table 133. User Identification Settings dialog box, Identification page parameters (Sheet 3 of 3)
Parameter
Description
Trace: Summed
Summed Ions table
Displays the filters and mass-to-charge ratios of the ions you
specified for ion summing in the “Summing Ions Dialog Box” on
page 203.
Retention Time (of the component peak and the error window)
Expected (min)
The expected elution time of the component (peak apex).
Range: 0.0 to 999.0
Units: minutes
Window (sec)
The time boundaries for the expected peak apex occurrence.
Range: 1.0 to 999.0
Units: seconds
Use as RT Reference
Specifies that the active component peak is to be used as a
retention time reference. (This component’s actual retention time
is used to adjust the expected retention times of other components
automatically during processing.)
All RT References appear in the Adjust Using list.
View Width
The amount of time to display the Chromatogram pane.
Range: (Expected RT – [View Width/2]) through (Expected RT +
[View Width/2])
Range: 0.10 to 999.0
Units: minutes
Adjust Using
Specifies adjusting the retention time for this component based on
the actual RT of another component that has been designated an
RT Reference.
Retention time references are automatically created when you
select the Use as RT Reference option when the component is
active.
The processing method must have at least one retention time
reference for this box to be active.
All RT References appear in the Adjust Using list.
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
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User Identification Settings - Detection
Use this page (Figure 210) to specify advanced component detection criteria. Use these
additional criteria when the standard detection criteria do not provide the expected results.
Table 134 lists the parameters for the Detection page of the User Identification Settings dialog
box.
Figure 210. User Identification Settings dialog box showing the Detection page
Table 134. User Identification Settings dialog box, Detection page parameters (Sheet 1 of 2)
Parameter
Description
Peak Detection
Algorithm
Genesis, ICIS, or Avalon the peak integration parameters.
Highest Peak
The application searches for the highest peak within the search
window.
Nearest RT
The application searches for the peak nearest to the expected
retention time.
Ion Ratio Confirmation
Enable
When Ion ratio confirmation is enabled, the IRC grid is available.
Note When disabled, all entry areas within the Ion ratio
confirmation group are disabled.
Ion ratio using
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Displays area or height.
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Table 134. User Identification Settings dialog box, Detection page parameters (Sheet 2 of 2)
Parameter
Description
Mass
Specifies an ion mass value for the confirmation process.
Note You can enter up to five qualifier ions. New lines appear
for each new mass entry.
Target Ratio (%)
Displays the ratio of the Qualifier Ions response to the Quan Ions
response.
Range: 0 to 200%
Window (+/–%)
Specifies the window error value.
Window %
The acceptable range from the target window value that is still considered a confirmed ion.
Relative
Select the Relative option to use the target ratio tolerances in the
Window ± % column as relative percentages of the target ratio.
Absolute
Select the Absolute option to use the target ratio tolerances in the
Window ± % column as absolute percentages of the target ratio.
Qualifier Ion Coelution
Min
Specifies an acceptable drift from the expected retention time to
still be considered a confirmed ion.
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
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User Identification Settings – Genesis Integration
Use this page (Figure 211) to set up advanced chromatographic parameters. Table 135 lists
the parameters for the Genesis Integration page of the User Identification Settings dialog box.
Figure 211. User Identification Settings dialog box showing the Genesis Integration page
Table 135. User Identification Settings dialog box, Genesis Integration page parameters
(Sheet 1 of 3)
Parameter
Description
S/N Threshold
This multiplier specifies a signal-to-noise threshold for peak
integration. Only peaks with a signal-to-noise ratio greater than
this value are integrated.
Range: 0.0 to 999.0
Default multiplier: 0.5
Valley Detection
Enabled
Detects unresolved peaks with the valley detection approximation
method.
The application drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
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Table 135. User Identification Settings dialog box, Genesis Integration page parameters
(Sheet 2 of 3)
Parameter
Description
Expected Width (sec)
This multiplier specifies an expected peak width parameter that
controls the minimum width that a peak is expected to have when
valley detection is enabled.
With valley detection enabled, any valley points nearer than half
the expected width to the top of the peak are ignored. If a valley
point is found outside the expected peak width, the application
ends the peak at that point. It always ends a peak when the signal
reaches the baseline, independent of the value set for the expected
peak width.
Range: 0.0 to 999.0
Default multiplier: 0.0
Units: seconds
Note Valid only when you select Valley Detection Enabled.
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
Peak Height
Specifies a percentage of the total peak height. This is the
minimum that a signal must be above the baseline before
integration is turned on or off. This option is available only when
you select the Constrain Peak Width option.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
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Table 135. User Identification Settings dialog box, Genesis Integration page parameters
(Sheet 3 of 3)
Parameter
Description
Tailing Factor
Specifies a value for the factor that controls how the application
integrates the tail of a peak. This factor is the maximum ratio of
the trailing edge to the leading side of a constrained peak and
calculates the retention time of the maximum extent of the right
edge of the tailing peak. This option is available only when you
select the Constrain Peak Width option.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
User Identification Settings – Genesis Advanced
Use this page (Figure 212) to set up advanced chromatographic parameters. Table 136 lists
the parameters for the Genesis Advanced page of the User Identification Settings dialog box.
Figure 212. User Identification Settings dialog box showing the Genesis Advanced page
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Table 136. User Identification Settings dialog box, Genesis Advanced page parameters
Parameter
Description
Report Noise As
RMS or
Peak to Peak
Determines if the noise used in calculating S/N values is calculated
using an RMS calculation or peak-to-peak resolution threshold.
Rise Percentage
The percentage that the peak trace can rise above the baseline after
passing through a minimum (before or after the peak).
This method drops a vertical line from the apex of the valley
between unresolved peaks to the baseline. The intersection of the
vertical line and the baseline defines the end of the first peak and
the beginning of the second peak.
When the trace exceeds rise percentage, the application applies
valley detection peak integration criteria.
This test is applied to both the left and right edges of the peak.
The rise percentage criteria is useful for integrating peaks with
long tails.
Range: 0.1 to 500.0
Valley S/N
Specifies a value to evaluate the valley bottom. Using this
parameter ensures that the surrounding measurements are higher.
Range: 1.0 to 100.0
Default: 2.0
Peak S/N Cutoff
The peak edge is set to values below this defined S/N.
This test assumes an edge of a peak is found when the baseline
adjusted height of the edge is less than the ratio of the baseline
adjusted apex height and the peak S/N cutoff ratio.
When the S/N at the apex is 500 and the peak S/N cutoff value is
200, the application defines the right and left edges of the peak
when the S/N reaches a value less than 200.
Range: 50.0 to 10 000.0
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
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User Identification Settings – ICIS Integration
Use this page (Figure 213) to set up advanced chromatographic parameters. Table 137 lists
the parameters for the ICIS Integration page of the User Identification Settings dialog box.
Figure 213. User Identification Settings dialog box showing the ICIS Integration page
Table 137. User Identification Settings dialog box, ICIS Integration page parameters (Sheet 1 of 3)
Parameter
Description
Baseline Window
The number of scans used when searching for where the minima
are occurring. A local minimum becomes an anchor point,
making the entire curve locally reduced until these points are at
zero.
Range: 1 to 500
Default: 40
Area Noise Factor
The noise-level multiplier used to determine the peak edge after
the location of the possible peak, so that the peak can narrow or
broaden without affecting the baseline.
Range: 1 to 500
Default multiplier: 5
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Table 137. User Identification Settings dialog box, ICIS Integration page parameters (Sheet 2 of 3)
Parameter
Description
Peak Noise Factor
The noise level multiplier (a minimum S/N ratio) used to
determine the potential peak signal threshold.
Range: 1 to 1000
Default multiplier: 10
Constrain Peak Width
Constrains the peak width of a component during the peak
integration of a chromatogram. You can set values that control
when peak integration is turned on and off by specifying a peak
height threshold and a tailing factor.
Selecting this activates the Peak Ht (%) and the Tailing Factor
parameters.
Peak Height
A percent of the total peak height. This is the minimum that a
signal must be above the baseline before integration is turned on
or off.
Range: 0 to 100%
Default multiplier: 5.0%
The peak height percentage is defined as follows:
Note Valid only when you select Constrain Peak Width.
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Table 137. User Identification Settings dialog box, ICIS Integration page parameters (Sheet 3 of 3)
Parameter
Description
Tailing Factor
A peak integration multiplier that constrains the peak width of an
asymmetric chromatogram peak that has a tailing trace.
It is the maximum ratio of the trailing edge to the leading side of a
constrained peak and calculates the retention time of the
maximum extent of the right edge of the tailing peak.
Range: 0.5 to 9.0
Default multiplier: 1.0 (1.0 has no effect)
Note Valid only when you select the Constrain Peak Width
check box.
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
User Identification Settings – ICIS Advanced
Use this page (Figure 214) to set up advanced chromatographic parameters. Table 138 lists
the parameters for the ICIS Advanced page of the User Identification Settings dialog box.
Figure 214. User Identification Settings dialog box showing the ICIS Advanced page
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Table 138. User Identification Settings dialog box, ICIS Advanced page parameters
Parameter
Description
Noise Method
INCOS Noise
A single-pass algorithm is used to determine the noise level.
Repetitive Noise
A multiple-pass algorithm is used to determine the noise level. In
general, this algorithm is more accurate in analyzing the noise
than the INCOS Noise algorithm, but it takes longer.
RMS Noise
A root mean square calculation is used to determine
signal-to-noise values instead of the default ICIS noise method.
Min Peak Width
The minimum number of scans required in a peak.
Range: 0 to 100
Default: 3
Multiplet Resolution
The minimum separation in scans between the apexes of two
potential peaks. This is a criterion to determine if two peaks are
resolved. Use a larger number in a noisy environment when the
signal is bouncing around.
Range: 1 to 500
Default: 10 scans
Area Tail Extension
The number of scans past the peak endpoint to use in averaging
the intensity.
Range: 0 to 100
Default: 5 scans
Area Scan Window
The number of allowable scans on each side of the peak apex. A
zero value defines all scans (peak-start to peak-end) to be included
in the area integration.
Range: 0 to 100
Default: 0 scans
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
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User Identification Settings – Avalon Integration
Use this page (Figure 215) to specify advanced component detection criteria. Use these
additional criteria when the standard detection criteria do not provide the expected results.
Table 139 lists the parameters for the Identification page of the User Identification Settings
dialog box. Table 140 lists the parameters for initial and timed events.
Note To detect peaks, Avalon uses the settings for initial events and user-defined timed
events in the event list.
Figure 215. User Identification Settings dialog box showing the Avalon Integration page
Table 139. Avalon Integration page parameters (Sheet 1 of 2)
Parameter
Description
Auto Calculate Initial
Events
Estimates the initial values for the detection of peaks—based on
the data in the current raw file—to display initial values in the
event list and searches for the best values of initial events that
detect peaks in the data. Any timed event in the event list is
unchanged when you click Auto Calculate.
Determines initial values for only: Start Threshold, End
Threshold, Area Threshold, P-P [Resolution] Threshold, Bunch
Factor, Negative Peaks, and Tension.
Note Valid only if a raw file is open.
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Table 139. Avalon Integration page parameters (Sheet 2 of 2)
Parameter
Description
Time (Min)
Displays the initial time value in minutes.
Event
Displays descriptions of detection parameters for initial events and
timed events. For details, see Table 140.
Note Start Threshold, End Threshold, Area Threshold,
P-P [Resolution] Threshold, Bunch Factor, Negative Peaks, and
Tension are defined with initial values.
Value
Displays the values associated with initial events or timed events.
Range: Factors are specific to each event.
Add
Adds the Time, Event, and Value values to the Avalon Event List.
Delete
Deletes the selected row.
Change
Using the Time, Event, and Value values, updates the event list
and the chromatogram display.
Note You can test the results of the new criteria by clicking Apply or OK. You can apply
the new criteria to all files in the Result list by clicking Apply to All.
Table 140. Initial and Timed Events (Sheet 1 of 2)
Event
Description
Start/End Threshold
Half of the result is a good estimate for the Start Threshold. You
can modify the Avalon estimates by entering your own values and
clicking Add to save your Start or End Threshold.
The Start Threshold depends on the RMS noise in the
chromatogram. It is the fundamental control used for peak
detection, so picking the best Start Threshold is essential for
high-quality data collection.
Units: Absolute value of peak area (counts x seconds)
Bunch Factor
The number of points grouped together during peak detection.
This method groups several chromatographic points during
integration without affecting the final area calculation of the peak.
Range: 1 to 6
Note A high bunch factor groups peaks into clusters.
Area Threshold
Controls the area cutoff. Any peak with a final area less than the
area threshold is not recorded.
Format: units of area for the data
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Table 140. Initial and Timed Events (Sheet 2 of 2)
Event
Description
P-P Resolution
Defines how much peak overlap must be present before two or
more adjacent peaks create a peak cluster. Peak clusters have a
baseline drop instead of valley-to-valley baselines. This is specified
as a percent of peak height overlap.
Negative Peaks
Automatically resets after a negative peak has been found.
Tension
Controls how closely the baseline follows the overall shape of the
chromatogram.
A lower tension traces the baseline to follow changes in the
chromatogram more closely. A high baseline tension follows the
baseline less closely, over longer time intervals.
Units: minutes
Tangent Skim
Enables tangent skim on any peak clusters.
By default, the application selects the tallest peak in a cluster as the
parent (solvent) and detects peaks on either side (or both sides) of
the tallest peak. You can also identify which peak in the cluster is
the parent.
Tangent skim automatically resets at the end of the peak cluster.
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Integrate On/Off
Turns integration on or off at the set time.
Shoulders On
Turns on the detection of shoulders.
Shoulders Off
Turns off the detection of shoulders.
Force Cluster On
Turns on the grouping of peaks into a single peak.
Force Cluster Off
Turns off the grouping of peaks into a single peak.
Disable Cluster On
Enables the grouping effect in the specified time range.
Disable Cluster Off
Disables the grouping effect in the specified time range.
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Manually Integrating Peaks
You can manually change the baseline and the starting and ending points of a peak in either of
two ways:
• Drag the starting or ending points
• Use the Baseline dialog box
When you manually integrate a peak, the application displays Manual Integration in the
Integration Type column of the Result list (Figure 216). If you have peak area or peak height
labeling enabled, it labels the peak with AM, for area manual, or HM, for height manual.
Figure 216. Example of manually integrated peak
Moved Integration Markers
Manual Integration Type
 To drag a starting or ending point of a peak
1. Position the cursor over one of the integration markers.
The cursor turns into cross hairs (+).
2. Drag the integration marker to the new location.
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 To use the Baseline dialog box
1. Right-click the Chromatogram pane and choose Change Peak Baseline from the
shortcut menu.
The Baseline dialog box opens (Figure 217).
Figure 217. Baseline dialog box
2. Type the new coordinates for the starting and ending points in the appropriate boxes and
click OK.
Table 141 lists the parameters for the Baseline - Compound dialog box.
Table 141. Baseline dialog box parameters
Parameter
Description
Peak Baseline Endpoints
Left (min)
Type the left extreme of the integration baseline for the current
component, in minutes.
Right (min)
Type the right extreme of the integration baseline for the current
component, in minutes.
Left Height
Type the height of the current component peak at the left extreme
of the integration baseline, in units of counts.
Right Height
Type the height of the current component peak at the right
extreme of the integration baseline, in units of counts.
 To undo the manual integration
1. In the Integration Type column, click the cell containing the words Manual Integration
for the sample that you want to change.
2. Click the down arrow and select Method Settings from the list to return the integration
to its prior settings.
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Reviewing All Results
Use the Review All Results view in the Quantitate window to review and rework samples of all
types, including unknowns and blanks.
If necessary, rework the samples by modifying the peak detection and integration settings and
by manually integrating peaks.
For calibration standards and QCs, the Review All Results view functions exactly as the
Survey view does. (For more information, see “Reviewing the Calibration Curve and QCs” on
page 332.)
Opening the Review All Results View
To process the raw files and open the Review All Results view (Figure 218), click the Review
All icon in the navigation pane.
The Review All Results view includes (clockwise from the top) the Result list, the Component
list, the Calibration Curve pane, the ISTD Chromatogram pane, and the Chromatogram
pane. These elements function exactly as they do on the Survey view and have an additional
display tab in the Result list: the Unknowns tab, along with the All, Standards, QCs, and
Blanks tabs. Clicking the All tab displays the results for every sample in the sequence.
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Figure 218. Quantitate – Review All Results window
Reviewing the Unknowns
 To review and rework the results for the unknowns
1. Click the Unknowns tab at the bottom of the Result list to display the peak integration
results for the unknown samples.
2. In the Component list, select the internal standard.
3. Inspect each file in the Result list and check for peak detection and integration problems.
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4. Inspect the chromatogram in the Chromatogram pane for each file:
a. Ensure that the LCquan application found the peak.
b. Ensure that the shaded area accurately represents the contribution of the component
to the chromatogram.
• To modify the peak detection and integration settings, go to the topic:
“Modifying the Peak Detection and Integration Settings” on page 353.
• To integrate a peak manually, go to the topic: “Manually Integrating Peaks” on
page 371.
5. In the Component list, select a target compound.
6. Repeat step 3 and step 4 for each target compound.
7. When you are satisfied that the LCquan application has correctly detected and integrated
the peaks, inspect the Result list again:
a. The calculated amount of components in each unknown sample is displayed in the
Calculated Conc column of the list (Figure 219).
Figure 219. Calculated Concentration column
b. Right-click the Chromatogram pane and choose Show Peak Info from the shortcut
menu.
The Peak Information dialog box opens where you can review the peak properties for
the selected sample. For more information, see “User Identification Settings – ICIS
Integration” on page 364.
c. Leave the Peak Information dialog box open, select the other sample files in the
Result list, and view the peak properties for them.
Reviewing Peak Properties
To open the Peak Info dialog box, right-click a Chromatogram view in any of the preview
panes and choose Show Peak Info from the shortcut menu.
The Peak Information dialog box has these tabs:
• Peak Information – Info
• Peak Information – Flags
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• Peak Information – IRC Tests
• Peak Information – Spectrum
The IRC Tests tab is displayed only when showing peak information for an IRC.
Peak Information – Info
This page (Figure 220) provides information about the selected peak. Table 142 lists the
parameters for the Info page of the Peak Info dialog box.
Figure 220. Peak Info dialog box showing the Info page
Table 142. Peak Info dialog box, Info page parameters (Sheet 1 of 2)
Parameter
Description
Peak Properties (read-only)
Left (min)
Displays the left extreme of the integration baseline for the current
component.
Units: minutes
Apex (min)
Displays the apex point, in minutes, for the current component.
Right (min)
Displays the right extreme of the integration baseline for the
current component.
Units: minutes
Area (cts-sec)
Displays the area of the current component peak.
Units: count-seconds
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Table 142. Peak Info dialog box, Info page parameters (Sheet 2 of 2)
Parameter
Description
Baseline
Displays the baseline height directly below the apex of the current
component peak.
Units: counts
Expected RT (min)
Displays the expected retention time of the peak.
Units: minutes
Base Peak (m/z)
Displays the mass-to-charge ratio of the ion with the largest
response in the current component peak.
Left (height)
Displays the height (intensity) of the current component peak at
the left extreme of the integration baseline.
Units: counts
Peak Height
Displays the height (amplitude) of the current component peak
apex.
Units: counts
Right (height)
Displays the height (intensity) of the current component peak at
the right extreme of the integration baseline.
Units: counts.
ISTD Response
Displays the integrated area, in units of count-minutes, or the
height of the apex.
Units: counts.
Thermo Scientific
Response Ratio
Displays the ratio of the peak sample peak area or height to the
internal standard area or height.
Calculated Amount
Displays the amount in the sample as calculated with response
ratio and cal curve.
Signal To Noise
Displays the measured signal-to-noise ratio at the apex of the
current component peak.
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Peak Information – Flags
This page (Figure 221) provides information about how the peak was detected and integrated.
Table 143 lists the parameters for the Flags page of the Peak Info dialog box.
Figure 221. Peak Info dialog box showing the Flags page
Table 143. Peak Info dialog box, Flags page parameters (Sheet 1 of 4)
Parameter
Description
Integration Info (read-only)
Detected By
Displays the method the LCquan application uses to detect the
peak. It displays one of the following detection methods:
• Spectrum: the application uses the user-defined
mass/intensity pairs and applies a spectral-matching algorithm
to find the peak that contains the closest match to the
comparison spectrum. Up to 50 entries are allowed to define
the comparison spectrum.
• Highest Peak: the application searches for the highest peak
within the search window.
• Nearest RT: the application searches for the peak nearest to
the expected retention time.
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Table 143. Peak Info dialog box, Flags page parameters (Sheet 2 of 4)
Parameter
Description
Left Edge Type
Displays how the LCquan application detected the left baseline
edge of the current peak. It displays one of the following peak
baseline detection methods:
• Baseline (B) edge type: The edge of the peak is at baseline
level.
• Valley (V) edge type: The edge of the peak is in a peak valley.
• Manual (M) edge type: The edge of the peak has been
adjusted manually.
• Stripe (S) edge type: The edge of the peak reached the
Constrain Peak Height Percent specified in the method.
• Tail (T): The edge of the peak reached the Constrain Peak
Height Trailing Factor limit before the Height Percent.
• Tilt (-): An error occurred before the edge of the peak could
be determined.
• Unknown (?): An unknown error occurred.
Valid
Indicates whether the peak was successfully detected. The LCquan
application indicates the peak was detected by displaying the
check mark in the Valid check box.
Right Edge Type
The criteria that the LCquan application uses to detect the right
edge of a peak. The following edge types are defined:
• Baseline (B) edge type: The edge of the peak is at baseline
level.
• Valley (V) edge type: The edge of the peak is in a peak valley.
• Manual (M) edge type: The edge of the peak has been
adjusted manually.
• Stripe (S) edge type: The edge of the peak reached the
Constrain Peak Height Percent specified in the method.
• Tail (T): The edge of the peak reached the Constrain Peak
Height Trailing Factor limit before the Height Percent.
• Tilt (-): An error occurred before the edge of the peak could
be determined.
• Unknown (?): An unknown error occurred.
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Table 143. Peak Info dialog box, Flags page parameters (Sheet 3 of 4)
Parameter
Description
Flags (read-only)
Saturated
When selected, this indicates one or more saturated scans were
detected.
Calculated Amount
When selected, this indicates a quantitation calculation was
performed. The calculated value is displayed in the Result grid
view.
When cleared, this indicates that quantitation calculation was not
successful.
Valley Detect
When selected, this indicates valley detection is enabled in the
processing method.
QC Failed
When selected, this indicates that the sample type failed the QC
test.
If the calculated amount is greater than the specified percentage
difference from the expected amount, the sample fails the QC test.
For example, if the tolerance level is 10% and the expected
amount is 100, calculated amounts less than 90 or greater than
110 fail.
RT Ref OK
Indicates whether the retention time reference component was
found and whether it was used correctly by the processing
method.
When selected, this indicates the retention time reference peak
was found, or there is no correction at all because there is no
retention time reference.
When cleared, this indicates the peak was searched for and not
found.
Response OK
Indicates whether a response factor was calculated.
When selected, this indicates the peak was found, its internal
standard was found, and the response ratio was correctly
calculated.
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Table 143. Peak Info dialog box, Flags page parameters (Sheet 4 of 4)
Parameter
Description
Response Low
Indicates the calculated peak amount is < the lowest specified
standard amount of the component in the calibration curve.
When selected, this indicates the amount was calculated by
extrapolation.
Note Forcing or including the origin defines the lowest level to
be 0.0.
Response High
Indicates the calculated peak amount is > the highest specified
standard amount of the component in the calibration curve.
When selected, this indicates the amount was calculated by
extrapolation.
Peak Information – IRC Tests
This information is displayed only when showing peak information for an IRC (Table 144).
You can review the acceptable test levels to still be considered a confirmed ion.
Table 144. Peak Information – IRC Tests parameters
Parameter
Description
Ion Coelution Test
Passed
Indicates that the peak passed the coelution test.
If it did not pass, no further tests are performed and the Ion Ratio
Test section is empty.
Allowed Coelution
Delta
The allowed difference in retention time between the apex of the
target ion and the apex of the qualifier ion, as specified by the
Qualifier Ion Coelution parameter on the Identification page in
the Create Method view of the Quantitate window.
Measured Coelution
Delta
The measured difference in retention time between the apex of the
target ion and the apex of the qualifier ion. The Measured
Coelution Delta must fall within the range of ± the Allowed
Coelution Delta in order for the peak to pass the coelution test.
Ion Ratio Test
Thermo Scientific
Passed
Indicates the peak passed the ion ratio test.
Target Ratio
Indicates the peak passed the ratio test.
Allowed Target Range
The expected target ratio.
Measured Ratio
The measured ratio.
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Peak Information – Spectrum
This page (Figure 222) displays an unfiltered spectrum plot at the peak apex retention time.
This spectrum plot is display-only.
Figure 222. Peak Info dialog box showing the Spectrum page
Adding Comments to the Chromatogram Display
Use the Chromatogram Comment dialog box to add a comment to the header in the
Chromatogram view. Table 145 lists the parameters for the Chromatogram Comment dialog
box.
 To add a comment
1. Right-click the Chromatogram pane and choose Add or Change Peak Comment.
The Chromatogram Comment dialog box opens (Figure 223).
Figure 223. Chromatogram Comment dialog box
2. Type your comment and click OK or Apply.
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If Apply is used, the dialog box remains visible and you can select another sample,
component, or integration type. Figure 224 shows an example.
Figure 224. Example of chromatogram with comment
Comment Area
Table 145. Chromatogram Comment dialog box parameters
Parameter
Description
File Name
View only: Displays the name of the current chromatogram.
Integration Type
View only: Displays the peak integration types of the current
chromatogram.
• (Processing) Method Settings: The settings specified in the
processing method or LCquan method.
• User Settings: Settings specified in the User Identification
Settings dialog box.
• Manual Integration (on the selected peak): Manually adjust
the peak baseline and end points.
Comment
The text you enter as a chromatogram comment plots below the
header info.
Creating and Reviewing Reports
Use the Review Reports view (Figure 225 on page 385) of the Quantitate window to create
and review reports describing the quantitative analysis results for your data.
 To create and review reports for your data
1. To open the Review Reports view, click the Reports icon in the navigation pane.
2. To specify Excel reports, do the following:
a. In the Excel Report Selections table, select the Use check box in an empty row.
b. Click the Column Arrangement column and select a column arrangement from the
list.
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Three column arrangements are available by default: Quan Result Grid, Excel Long
Summary, and Excel Short Summary. For a description of each report type, see
“Report Options” on page 391.
When the Quan Result Grid option is selected, the report is generated using the
column arrangement of the current Quantitate results grid. Use the Column
Arrangement dialog box to create additional column arrangements.
c. To create additional Excel reports, repeat steps a and b.
d. To create sample style Excel reports with information on one sample per page, rather
than the default one component per page), select the Sample Style Excel Reports
check box.
3. To specify reports using the XReport templates, do the following:
a. In the XReport Report Selections table, select the Use check box in an empty row.
b. In the Save Type column, select the file format that you want to save the report in.
c. In the XReport Template column, type the name of an XReport template or click the
empty cell, and click the down arrow to browse for a template.
The standard report templates contain preselected methods and results summaries.
For more information, see “Report Options” on page 391.
Or, click Create Xreport Templates to create a custom report template.
Tip To preview reports with your data, open a template, and choose
Report > Simulate Report.
For information about XReport, refer to User Guide: Designing and Generating
Custom Reports with XReport.
d. To create additional reports with XReport, repeat steps a through c.
Note If your administrator has set up secure reporting, the Create XReport
Templates feature is unavailable, and you have access only to the templates in the
secure template folder. The only output option is Save Only, which saves the file
in PDF. The secure reports contain a serial number in the footer of each page, and
a watermark appears on the background of each page.
4. In the Select Report Options area, select the output option.
You can select Print Only, Save Only, or Print and Save.
5. To generate the specified reports, click Create Reports.
Note When you save a report using the Save Only or the Print and Save option, the
LCquan application places a copy of the report in the Exports folder of the workbook.
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Figure 225. Review Reports view
Generating Reports
Use the following options to generate reports in Excel or XReport:
• Excel Report Selections
• Manage Excel Column Arrangements
• XReport Report Selections
• Launch XReport Template Generator
• Select Report Options
• Function Buttons
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Excel Report Selections
Use the Excel Report Selections page to specify the Excel reports you want to create
(Table 146).
 To specify the Excel reports you want to create
1. Select the Use check box for each report that you want created in the Excel format
(Figure 226).
Figure 226. Excel report selection page
2. To create a new column arrangement, use the features in the Manage Excel Column
Arrangements area.
3. To add a row to the table, select the Use check box in the last row of the table, click in the
row, and select a report from the list.
4. To delete a row, select the entire row, right-click the selection, and choose Delete Selected
Rows from the shortcut menu.
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Table 146. Excel report selections page parameters
Parameter
Description
Use
Specifies which reports the LCquan application creates when you click Create Reports.
Select the check box of each report you want to generate.
Column Arrangement
Specifies the column arrangement to use for the Excel report.
The LCquan application comes with the following predefined column arrangements:
• Quan Result Grid—Generates an Excel report using the current Quan Results column
arrangement as specified on the Survey and Review All Results views of the Quantitate
window. You cannot modify this column arrangement from the Review Reports view.
• Excel Long Summary—Generates a detailed Excel report. You can use this column
arrangement to create your own column arrangement.
• Excel Short Summary—Generates a brief Excel report. You can use this column
arrangement to create your own column arrangement.
Sample Style Excel
Reports
Generates the Excel reports with one worksheet per sample and with information about all
components on each worksheet.
Specifies that the selected column arrangement is used to generate the reports, but the File
Name box is replaced by the Component Name box.
A header on each sheet of the Sample Style report displays the Sample File Name for each
sample. The row number of the sample in the processing sequence is displayed in
parentheses next to the file name.
When not selected, the LCquan application generates the Excel reports with one worksheet
per component and with information about all samples on each worksheet.
Manage Excel Column Arrangements
You can arrange columns in the Quan Result Grid or other Excel spreadsheet using these
instructions.
 To create a new arrangement
1. Select an arrangement from the Select an Arrangement list (Figure 227).
You cannot edit the predefined arrangements that ship with the LCquan application, but
you can use one of these standard arrangements as a template to create your own custom
arrangement.
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Figure 227. Manage Excel Column Arrangements page
2. Click Create/Edit/View an Arrangement.
The Column Arrangement dialog box for the selected arrangement opens. Table 147 lists
the parameters for the Column Arrangement dialog box.
3. In the Column Arrangement dialog box, change the Current Arrangement Name.
4. Edit the columns for the new arrangement and click OK.
Table 147. Column Arrangement dialog box parameters
Parameter
Description
Available Columns
Lists parameters that are not currently selected for display.
Displayed Columns
Lists currently selected parameters, which appear in the data
grids.
Add / Remove
Displays / Hides selected columns.
Move Up /
Move Down
Move Up moves columns left in the grid.
Move Down moves columns right in the grid.
Factory Defaults
Resets original column values (as described in “Grid
parameters” on page 394.)
 To delete an arrangement
1. Select an arrangement from the current list.
You cannot delete the Quan Result Grid, Excel Long Summary, or Excel Short Summary
column arrangements that ship with the LCquan application.
2. Click Delete Selected Arrangement.
The LCquan application confirms that you want to delete the arrangement.
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XReport Report Selections
Specify the XReports you want to create (Figure 228):
1. Select the Use check box of each report that you want to generate using an XReport
template.
2. To add a row to the table, select the Use check box in the last row of the table, click in the
row, and select a report from the list.
3. To delete a row, select the entire row, right-click the selection, and choose Delete Selected
Rows from the shortcut menu.
Figure 228. XReport report selections page
Table 148 lists the parameters for the XReport report selections page.
Table 148. XReport report selections page parameters
Parameter
Description
Use
Specifies which reports are created when you click Create Reports.
Select the check box of each report you want to generate.
Note If your administrator has set up secure reporting, you can
only access the templates in the secure templates folder.
Save Type
Specifies the report file type, which includes these options:
•
•
•
•
•
•
.txt (plain text)
.doc (Microsoft Word Document)
.html (HTML)
.pdf (PDF)
.rtf (Rich Text Format)
.xls (Microsoft Excel spreadsheet)
Note If your administrator has set up secure reporting, you can
only select the PDF option.
XReport Template
Specifies the XReport template to use in generating the report.
Click the empty cell, and click
to browse for the template file.
Note If your administrator has set up secure reporting, you can
only access the templates in the secure templates folder.
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Launch XReport Template Generator
To start the XReport template generation feature, click Create XReport Templates
(Figure 229). For more information about XReport, refer to the Help for XReport.
Note If your administrator has set up secure reporting, the Create XReport Templates
feature is unavailable.
Figure 229. Launch XReport Template Generator area
Select Report Options
Use the following options to save, print, and create reports (see Figure 230).
Parameter
Description
Print Only
Prints the report without saving.
Save Only
Saves the reports without printing.
Print and Save
Prints and saves the reports.
Figure 230. Select Report Options area
Note If your administrator has set up secure reporting, you can use only the Save Only
option.
Function Buttons
Create Reports: Creates the reports that are selected in the Use column check boxes. When
no Use check boxes are selected, the feature is unavailable.
Apply: Saves any changes to the Excel report or XReport grids on the Review Reports view.
When you do not click Apply and close the view, the grid reverts back to the last saved status.
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Review Reports Warning
The Review Reports dialog box warns that you selected report options in the Review Reports
view in the Quantitate window and exited the view before creating reports. Table 149 lists the
parameters for the Review Reports dialog box.
Table 149. Review Reports dialog box parameters
Parameter
Description
Save Data
Applies the changes you have made to the reports settings. Your
Automatically (default) changes are not saved until you save the workbook.
Discard Any Changes
Discards the changes you have made to the reports settings.
Don’t Tell Me About
This Again
Prevents this dialog box from appearing again.
Report Options
Table 150 lists the report options.
Table 150. Report Options (Sheet 1 of 3)
Report option
Description
Report Selectionsa
Acquisition Sequence Report
(LCquanAcqSequence.xrt)
Displays the sample information that is in the acquisition
sequence, for example, sample ID, raw file names, sample types,
and cal levels.
Component Calibration Report
(Avalon, Genesis, or ICIS algorithm)
(LCquanCompCalReport.xrt)
Provides the component identification and calibration parameters,
calibration curves, calibration and QC levels and amounts, and
Results list information (for example, peak areas and calculated
amounts) for all components in all samples.
Ion Ratio Confirmation Results Report
(LCquanIonRatioConfirmationGraphical.xrt)
Provides the chromatogram traces of the confirmation ion and
qualifier ions for each component. The report also lists sample
information, peak status, and calculated concentrations for each
sample.
Peak Integration Report
(LCquanPeakIntegration.xrt)
Provides the Results list information (for example, peak areas and
calculated amounts) for all components, the sample information,
and the instrument method name and processing method name if
applicable. The report includes plots of the chromatogram peaks
for all components.
Processing Method Report
(Avalon, Genesis, or ICIS algorithm)
(LCquanProcessingMethod.xrt)
Lists all the peak detection and integration parameters in the
processing method for each component. The report also lists level
amounts, IRC data, and the mass-to-charge ratios and intensities
of the peaks in the mass spectrum for each component.
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Table 150. Report Options (Sheet 2 of 3)
Report option
Description
Quan Components Peak Results Report
(LCquanQuanPeakResults_ESTD.xrt,
LCquanQuanPeakResults_ISTD.xrt)
Lists the sample information, acquisition conditions, and
quantitative analysis results for a single sample. The report also
displays the integrated chromatograms of each target compound
and the standard, and the calibration curves.
Quantify Component Report
(LCquanQuantifyComponentReport.xrt)
Provides a summary by component of the samples for each
component. The report includes sample information and
quantitative analysis results (for example, peak areas, response, and
calculated amount); and displays the integrated chromatogram
peaks.
Quantify Sample Report
(LCquanQuantifySampleReport.xrt)
Provides a summary by sample of the components for each
sample. The report includes sample information and quantitative
analysis results (for example, peak areas, response, and calculated
amount); and displays the integrated chromatogram peak.
Quan Results Report
(LCquanQuanResults.xrt)
Provides quantitative results for a single sample.
Excel Report Options
Quan Result Grid
Generates an Excel report using the current Quantitate Results
column arrangement as specified on the Survey and Review All
Results views of the Quantitate window.
This arrangement cannot be used as a template to create a new
arrangement from the Review Reports view.
For detailed descriptions of the displayed columns, see “Quan
Result Grid” on page 394.
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Table 150. Report Options (Sheet 3 of 3)
Report option
Description
Short Excel Summary
Displays the Result list of the Quantitate window in a Microsoft
Excel spreadsheet. Each component is placed on a separate
page/worksheet in the main workbook.
This arrangement can be used as a template to create a new
arrangement from the Review Reports view.
You can review, analyze, and graph the data by using all the
functions and features of Microsoft Excel. For more information,
see “Excel Short Summary” on page 402.
Long Excel Summary
Displays the Result list of the Quantitate window, processing
sequence, and component identification and calibration
information in a Microsoft Excel spreadsheet. Each component is
placed on a separate page/worksheet in the main workbook.
This arrangement can be used as a template to create a new
arrangement from the Review Reports view.
You can review, analyze, and graph the data by using all the
functions and features of Microsoft Excel. For more information,
see “Excel Long Summary” on page 403.
a
If your administrator has set up secure reporting, the Create XReport Templates feature is unavailable. You have access only to the templates in
the secure template folder. The only output option is Save Only, which saves the file as a PDF.
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Quan Result Grid
The Quantitate Results grid can contain any of the following column parameters. To select
which parameters to display in the grid (see Table 151), right-click the grid, choose Columns,
and use the Column Arrangement dialog box (Figure 231). The parameters displayed in the
Quantitate Results grid are used to create a Quan Result Grid Excel report.
Note Click Factory Default in the Column Arrangement dialog box to reset the columns
in the grid to the Displayed and Available categories as shown in the following table.
Figure 231. Column Arrangement dialog box
Table 151. Grid parameters (Sheet 1 of 9)
Parameter
Description
Displayed Column parameters (currently displayed in the grid)
FileName
Displays the name of the raw file that contains the sample data. The file name is a
combination of the base file name prefix assigned to the sequence and a sequential sequence
number. If the default sequence starting number 1 has not changed, the suffix number is the
same as the row number of the sequence: 001, 002, and so on. If the default sequence
starting number has changed to another number, the first sample will have the starting
number and subsequent rows in the sequence are incremented by 001. For example, if the
starting number is 100, the file name for the first sample will have the suffix 100, the second
sample will have the suffix 101, and so on.
To select a new file name, select from the file options in the FileName box.
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Table 151. Grid parameters (Sheet 2 of 9)
Parameter
Description
Sample Type
Displays the sample type defined in the sequence row. The sample type defines how the
LCquan application processes the sample data. Each sample must be classified as one of the
following sample types:
• Unknown—A sample type that is not a Calibration Sample, Calibration Blank, Quality
Control Sample, or Quality Control Blank. The application performs quantitative
analysis of unknown sample types by using internal or external standards.
• Blank—A sample type that contains no target components. You can add internal
standard components to calibration blanks. You can include blanks in the sequence to
assist in purging all residual components from the application prior to the analysis of
the next sample or sample sequence. Use an LCquan analysis of a blank sample to
confirm that there are no residual components in the solvent system that can cause
erroneous results. This is especially important during quantitation. You can expect
quantitative analysis of a blank sample to result in the detection of no target
compounds.
• QC (quality control)—A type of sample that contains known amounts of one or more
known components. QC samples are placed in the sequence so that quantitation results
can be compared with known component amounts or concentrations for quality
assurance purposes. The LCquan application performs quantitation on these samples
using the same calibration settings as it uses on Unknown sample types. It places
Quality Control Samples after Calibration Samples and before Unknown Samples in
the sequence.
• Standard—A sample with a known amount of calibration reference material.
To change the sample type, select from the list of sample type options. The new sample type
appears in the Sample Type box.
Sample Name
Displays the sample name that you specified when you created the sequence.
Integration Type
The type of integration used is displayed in the results grid but can be overridden. The three
types are Method, User, and Manual Integration. When you select Method, the LCquan
application uses the integration parameters embedded within the processing method. You
can enter new integration parameters by right clicking the chromatogram plot and selecting
User Peak Detection Settings. This sets the integration type to User. Dragging the
integration control handles on the integration baseline sets the integration type to Manual.
Response
Area or height of the detected peak. The value stored depends on the selection made in the
calibration section.
ISTD Response
Area or height of the detected, peak associated Internal Standard. The value stored depends
on the selection made in the calibration section.
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Table 151. Grid parameters (Sheet 3 of 9)
Parameter
Description
Response Ratio
The ratio of the analytes area to its associated internal standards area, or the ratio of the
analytes height to its associated internal standards height.
The numerical value of the ratio, Response/ISTD Response. The Xcalibur data system and
the LCquan application do not report the response ratio for an internal standard because the
ratio is exactly 1.0 by definition.
If the Response is Area in the Component Calibration window of the Processing Setup
window, the units of both Response and ISTD Response are counts-sec.
If the Response is Height in the Component Calibration window of the Processing Setup
window, units of both Response and ISTD Response are counts.
Specified Conc
The user entered amount of the component at the Cal or QC level.
Calculated Conc
Amount of component as determined by the response ratio and calibration curve.
% Diff
Percentage difference between the calculated amount and the specified amount. Undefined
for internal standards.
% RSD
Relative Standard Deviation, based on calculated amounts or response values (response
ratios when Internal standards are used).
% CV
Coefficient of Variation.
Peak Status
Displays peak status:
• If peak is excluded, display Excluded.
• If this peak is an unknown, display Peak Status.
• If this peak is from a QC and it fails, use QC Failed.
• If the peak is not found, use Not Found.
• For all others, use peak status. Peak Status is one of the following:
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ePeakNotFound:
–
eNotCalibrated:
–
eCalibExcluded:
–
ePeakFound:
–
eQCFailed:
–
eQCPassed:
–
eResponseHigh:
–
eResponseLow:
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Table 151. Grid parameters (Sheet 4 of 9)
Parameter
Description
Level
Indicates the level defined for a Calibration Sample or Quality Control Sample.
To change this level, click the grid cell and select another level.
Units
Displays the calibration or QC level of the sample. To change this value, click the grid cell
and select another level.
RT
Retention time in minutes at the peak maximum time when an analyte elutes after
injection. This is the total time that the analyte is retained on the chromatographic column.
If the maximum signal from an analyte is detected 5 minutes and 14 seconds after injection,
the analyte has a retention time of 5:14.
Sample ID
Displays the sample ID for each data file. The sample ID is an alphanumeric string of
characters that identifies a sample.
Exclude
Indicates if the sample point can be included or excluded from the calibration curve
(Standards) or %RSD (QCs). To exclude or include, click the grid cell and select or clear the
check box presented. (Selecting—checking—excludes the data.)
Available Column parameters (available for display)
Acq Date
Date when the data file was acquired.
Area
Integrated area under the detected peak (count secs). The area of the peak in units of
counts * seconds.
Barcode
Displays the barcode for this sample.
Barcode Status
Displays the status of the barcode reading.
Cal Eqn
The calibration curve equation for this component.
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Table 151. Grid parameters (Sheet 5 of 9)
Parameter
Description
Client
(User-defined) Displays information that is pertinent to the active sample row in the
Acquisition sequence. You can use this box to convey information about this sample to
others or as a reminder to yourself. The User Label 2 default name is Client.
To change definitions of User Labels and Values:
Right-click the grid on the Setup Sequence view of the Acquisition window and choose one
of the following:
Columns: Open the Column Arrangement dialog box. For more information, see “Using
the Acquisition Sequence Grid Shortcut Menu” on page 58 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
User Labels and Values to open the Change Sequence User Labels dialog box. For more
information, see “Parameters in the Change Sequence User Labels dialog box” on page 35 in
Chapter 2, “Preparing to Perform Quantitative Analysis.”
–or–
Right-click the sequence grid on any view of the Quantitate window and choose:
Columns: Open the Column Arrangement dialog box. For more information, see
“Customizing Column Arrangement” on page 320 in Chapter 5, “Creating a Processing
Sequence.”
Comment
Displays the comment entered for this sample.
Company
(User-defined) Displays information that is pertinent to the active sample row in the
Acquisition sequence. You can use this box to convey information about this sample to
others or as a reminder to yourself. The User Label 4 default name is Company.
To change definitions of User Labels and Values for any user-defined column, see the
instructions for the Client column.
Delta RT
The difference between the Expected RT and the Actual RT.
Dil Factor
Displays the dilution factor that was used to prepare the sample. The valid range is 0.000 to
10000.000. The application interprets a value of 0.000 as no dilution.
To change this factor, double-click the Dil Factor box. The cursor changes to the vertical bar
cursor. Type the correct factor.
If you have specified a processing method for the current sequence, the application
automatically enters the Dil Factor value from the processing method settings.
Duration
Length of the acquisition run, defined in the run header of the raw file.
Height
Integrated height under the detected peak (counts).
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Table 151. Grid parameters (Sheet 6 of 9)
Parameter
Description
Inj Vol
Displays the injection volume in microliters of sample to be injected.
To change the volume, type the new volume in the Injection Volume box. When you are
using an autosampler, you can set the default injection volume in the Autosampler dialog
box in the Instrument Setup window. The minimum and maximum injection volumes that
you can use depend on the autosampler you select. The usable range depends on the
injection mode and might be smaller than the range displayed in the status bar. For more
details, consult your autosampler manual.
Intg Code
Two-character code representing baseline status of the peak’s left edge and right edge
respectively. (B- Base, V-Valley, M-Manual, S-Stripe, T-Tail, _ - Tilt)
ISTD Area
Integrated area under the Internal Standard peak (count secs).
ISTD Base Amt
Internal Standard expected amount.
ISTD Calc Amt
Internal Standard calculated amount.
ISTD Height
Integrated height under the Internal Standard peak (counts).
Laboratory
(User-defined) Displays information that is pertinent to the active sample row in the
Acquisition sequence. You can use this box to convey information about this sample to
others or as a reminder to yourself. The User Label 3 default name is Laboratory.
To change definitions of User Labels and Values for any user-defined column, see the
instructions for the Client column.
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Table 151. Grid parameters (Sheet 7 of 9)
Parameter
Description
Left/Right Delta
Height
Left/Right Height
Left Delta Height is the vertical distance between the start of the chromatographic peak and
the starting point of the chromatographic peak integration.
Right Delta Height is the vertical distance between the end of the chromatographic peak
and the end point of the chromatographic peak integration.
Left Height is the vertical distance between the starting point of chromatographic peak
integration and the x axis of the chromatographic plot.
Right Height is the vertical distance between the end point of chromatographic peak
integration and the x axis of the chromatographic plot.
Left Time
The retention time corresponding to the start of peak integration.
Phone
(User-defined) Displays information that is pertinent to the active sample row in the
Acquisition sequence. You can use this box to convey information about this sample to
others or as a reminder to yourself. The User Label 5 default name is Phone.
To change definitions of User Labels and Values for any user-defined column, see the
instructions for the Client column.
Rel RT
Ratio of Actual RT to Expected RT.
Response Type
Area or height.
Right Delta Height,
Right Height
Refer to Left/Right Delta Height, described earlier.
Right Time
The retention time corresponding to the end of peak integration.
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Table 151. Grid parameters (Sheet 8 of 9)
Parameter
Description
S/N
The calculated signal-to-noise measured.
The ratio of the signal height (S) to the noise height (N). The signal height is the baseline
corrected peak height. The noise height is the peak-to-peak height of the baseline noise.
S/N Threshold
Threshold signal-to-noise (S/N) value for peak to be considered.
A user-specified chromatogram peak edge detection criterion used for peak integration. The
Xcalibur data system and the LCquan application determine the retention time when the
measured signal-to-noise (S/N) value first becomes less than the S/N threshold value.
The default value is 0.5. The Xcalibur data system and the LCquan application start at the
peak apex and test measured S/N values at successively lower retention times to determine
the left peak edge retention time (in minutes). They start at the peak apex and test measured
S/N values at successively higher retention times to determine the right peak edge retention
time (in minutes).
Sample Vol
Displays the volume of a component that has been placed in the sample. The unit for this
volume is specified in the Processing Setup window and is only included in LCquan reports.
The LCquan application does not convert units.
To change the sample volume: Double-click the Sample Volume box. The cursor changes to
the vertical bar cursor. Type the correct sample volume.
If you have specified a processing method for your sequence, the LCquan application
automatically enters the sample volume of the Calibration or Quality Control samples, or
both, from the processing method settings.
Sample Wt
Displays the amount of a component that has been placed in the sample. The unit for this
sample weight is specified in the Processing Setup window and is only included in LCquan
reports. The LCquan application does not convert units.
To change the sample weight: Double-click the Sample Weight box. The cursor changes to
the vertical bar cursor. Type the correct sample weight.
If you have specified a processing method for your sequence, the LCquan application
automatically enters the sample weights of the Calibration or Quality Control samples, or
both from the processing method settings.
Search Window
The retention time window over which the LCquan application searches the peak.
Smoothing
Number of smoothing points used in the chromatogram.
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Table 151. Grid parameters (Sheet 9 of 9)
Parameter
Description
Study
(User-defined) Displays information that is pertinent to the active sample row in the
Acquisition sequence. You can use this box to convey information about this sample to
others or as a reminder to yourself. The User Label 1 default name is Study.
To change definitions of User Labels and Values for any user-defined column, refer to the
instructions for the Client column.
Vial Pos
Displays the sample’s position number in the autosampler.
To change the position number: Type the new position number in the Vial Position box.
Excel Short Summary
The Excel Short Summary is a column arrangement for creating Microsoft Excel formatted
reports from the Reports view in the Quantitate window. You can use the Excel Short
Summary column arrangement as a template to create a new arrangement. Figure 232 shows
Excel Short Summary selected in the Column Arrangement dialog box.
Figure 232. Column Arrangement dialog box
The Excel Short Summary column arrangement displays the following parameters:
•
•
•
•
•
•
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FileName
Sample Type
Sample Name
Integration Type
Response
ISTD Response
•
•
•
•
•
•
Response Ratio
Response Type
Specified Conc
Calculated Conc
% Diff
% RSD
•
•
•
•
•
•
% CV
Peak Status
Level
Units
RT
Sample ID
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Excel Long Summary
The Excel long summary is a column arrangement for creating Microsoft Excel formatted
reports from the Reports view in the Quantitate window. You can use the Excel Long
Summary column arrangement as a template to create a new arrangement. Figure 233 shows
Excel Long Summary selected in the Column Arrangement dialog box.
Figure 233. Column Arrangement dialog box
These parameters are displayed in the Excel Long Summary column arrangement:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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FileName
Sample Type
Sample Name
Sample ID
Specified Conc
Calculated Conc
Units
% Diff
Level
% RSD
% CV
Peak Status
Response Ratio
Response Type
Cal Eqn
Area
Height
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
ISTD Area
ISTD Height
RT
Integration Type
Response
ISTD Response
Rel RT
Delta RT
S/N
Left Time
Right Time
Left Height
Right Height
Intg Code
Search Window
S/N Threshold
Smoothing
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Acq Date
Duration
Vial Pos
Inj Vol
Sample Wt
Sample Vol
ISTD Base Amt
ISTD Calc Amt
Dil Factor
Study
Client
Laboratory
Company
Phone
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Exporting Results
Exporting Results
From the Survey, Review All Results, or Review Reports views, you can export your results to
a file. Figure 234 shows the Results Export dialog box. Table 152 lists the parameters for the
Results Export dialog box.
Figure 234. Results Export dialog box
Table 152. Results Export dialog box parameters (Sheet 1 of 2)
Parameter
Description
File Selection
[FileName]
Specifies a name for the text file of the exported data you want to
save. When you use a name of an existing file, a warning message
prompts you to provide another name. The file extension .csv is
automatically appended to the file name.
Limit: 50 characters
Invalid characters: \ / : * ? “ < > |
One File for All
Components
Specifies that data for all components is to be saved in a single file.
One File for Each
Component
Specifies that the data for each component is to be saved in a
separate file. The files are named with the component name
appended to the end of the file name you provided.
For example, if two components are named C1 and C2 and you
provided the file name Export, the created file names became
Export_C1.csv and Export_C2.csv.
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Table 152. Results Export dialog box parameters (Sheet 2 of 2)
Parameter
Description
Format Options
Include Item Header
Specifies that column headers be exported as a line of data that
immediately precedes the results in the exported data file.
Tab Separation
Specifies that individual values in the file are to be separated by
tabs.
Comma Separation
Specifies that in the file, individual values are separated by
commas.
Select/Manage Export Column Arrangement
Select an Arrangement
Select a previously defined column arrangement from this list to
edit or delete.
Note You cannot delete the Quantitate Results Grid, Excel
Long Summary, and Excel Short Summary column
arrangements that ship with the LCquan application.
Create/Edit/View an
Arrangement
Opens the Column Arrangement dialog box to edit the currently
selected column arrangement. You can create a new column
arrangement by editing an existing arrangement and changing its
name.
Delete Selected
Arrangement
Deletes the selected arrangement.
Note You cannot delete the Quan Results grid, Excel Long
Summary, and Excel Short Summary column arrangements that
ship with the LCquan application.
Button
Export
Exports the data to the text file or files.
Locking the Workbook
You can create a locked version of a workbook at any time, except when you are acquiring
data, by using the File > Create Locked Version of Workbook command. This locked
workbook is essentially a copy of the workbook (and its associated files) that cannot be
overwritten. You cannot save any changes made to a locked workbook, and you cannot
acquire data in a locked workbook. You can create new reports, but the LCquan application
does not save the report selections.
Alternatively, you can have the LCquan application automatically lock the workbook (not a
copy of the workbook) after you create a report.
When you open a locked workbook, the LCquan application displays [Locked] in the title bar
next to the workbook name and in the status bar.
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Locking the Workbook
 To create a locked version of the current workbook
From any window, choose File > Create Locked Version of Workbook.
The LCquan application creates a copy of the workbook and its associated files under the
current study folder.
The locked workbook is renamed by appending “_locked_nnn” to the original workbook
name, where nnn is the number of the locked workbook. For example, the first time that
you create a locked workbook from the workbook Trial1, the LCquan application names
the locked workbook Trial1_locked_001. The second time that you lock the workbook
Trial1, it names the locked workbook Trial1_locked_002. You can create up to 999 locked
versions of a workbook. You cannot unlock a locked workbook.
 To automatically lock the workbook after you create a report
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager.
2. In the Authorization Manager, do the following:
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Quantitate Section folder.
e. Select Automatically Lock Workbook After Creating Reports.
The Permission Level options become available.
f.
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Select the Allowed option, and click OK (Figure 235).
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Locking the Workbook
Figure 235. Authorization Manager showing the Automatically Lock Workbook After Creating
Report permission set to Allowed
 To not automatically lock the workbook after you create a report
1. Choose Start > All Programs > Thermo Foundation > Authorization Manager to open
the Authorization Manager (Figure 236).
2. In the Authorization Manager, do the following:
a. Select a user group in the Secure Groups list.
b. Click Expand Tree to show the entire list of controlled features for the application.
c. From the list, click the plus sign before the LCquan folder.
d. Click the plus sign before the Quantitate Section folder.
e. Select Automatically Lock Workbook After Creating Reports.
The Permission Level options become available.
f.
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Select the Disallowed option, and click OK (Figure 236).
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Saving the Workbook and Exiting the LCquan Application
Figure 236. Automatically Lock Workbook After Creating Report permission set to Disallowed
Saving the Workbook and Exiting the LCquan Application
You can save the workbook at any step in the LCquan procedure. With this feature you can
exit the LCquan application and reenter at the same place at a later time. When you reopen a
workbook, the LCquan application displays the page and view that were open when you
exited the workbook.
 To save the workbook and exit the LCquan application
1. Choose File > Save to save the current workbook.
When you want to save the workbook with a different study or workbook name, choose
File > Save As. The Save As Wizard guides you through the procedure.
2. Choose File > Exit to exit the LCquan application.
Note When you acquire data, you cannot exit the program unless you save the
workbook.
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Quantitative Analysis Overview
This appendix describes some of the basic principles and terminology of quantitative analysis1
and contains the following topics:
Contents
• About Quantitative Analysis
• Considering the Variables of Quantitative Analysis by LC/MS/MS
• Quantitative Analysis Techniques
• Sample Types
About Quantitative Analysis
In some applications, such as a clinical trial, you might be seeking the maximum possible
accuracy from your measurements. Time and cost of analysis are less important than achieving
the highest possible standards in precision and accuracy. This process of measuring the
amount of a particular component in a sample is called quantitative analysis.
In other applications, such as in trace analysis, you might only want to estimate the quantity of
a component. It might be sufficient to know that the component is present at a level either
significantly higher or significantly lower than a defined threshold. For example, knowing
whether a patient has overdosed 15 or 20 times above a prescribed limit is generally not as
important as simply knowing that the limit has been exceeded. Such cases would require a
rapid measurement rather than a precise one. This form of measurement is generally called
semi-quantitative analysis.
Quantitative analysis consists of the following steps:
• Preparing samples
• Developing a suitable chromatographic method
1
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For further information about the principles of quantitative analysis, refer to Mass Spectrometry: Principles and
Applications; de Hoffman, E., Charette, J., Stroobant, V.; Wiley: New York, 1996; and Introduction to Mass
Spectrometry, 3rd ed.; Watson, J.T., Lippincott-Raven: Philadelphia, PA, 1997.
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Considering the Variables of Quantitative Analysis by LC/MS/MS
• Calibrating the mass spectrometer’s response
• Analyzing the samples
• Reviewing the results
This manual does not describe sample preparation and chromatographic method
development. This manual assumes that you have met these important prerequisites to
achieving high quality quantitative analysis. For guidance in these areas, refer to the getting
started and hardware manuals for your autosampler, LC pump or MS pump, and mass
spectrometer.
Considering the Variables of Quantitative Analysis by LC/MS/MS
The combination of liquid chromatography (LC) and mass spectroscopy (MS) sets up a
unique set of considerations. If you are familiar with quantitative analysis using one or the
other of these analytical tools, the information in the following topics will prove useful:
• Using LC for Analyte Separation
• Using MS/MS for Analyte Detection
Using LC for Analyte Separation
When working with LC systems, you become accustomed to developing methods for analytes
of interest. These methods take into account a variety of parameters. Consider the following
LC parameters for optimum separation of compounds:
• Composition of stationary phase
• Column diameter
• Column length
• Column usability over time
• Solvent(s) or composition of mobile phase
• Flow rates
• Isocratic or gradient (ramped) solvent compositions
Mass spectrometers can often successfully detect individual analytes even when two or more
compounds coelute as a single chromatographic peak. Coeluting compounds are ionized in
the mass spectrometer, and the parent or fragment ions specific to the analyte or analytes are
detected and measured for quantitative analysis. Because the mass spectrometer detection is so
specific, you can reduce the chromatographic resolution and shorten the run times.
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A Quantitative Analysis Overview
Considering the Variables of Quantitative Analysis by LC/MS/MS
Using MS/MS for Analyte Detection
To optimize detection of ions by MS/MS, consider the following variables when working with
a mass spectrometer interfaced to an LC:
• Solution chemistry and polarity of the analyte of interest
• Probe selection (H-ESI, ESI, APPI, or APCI)
• Collision energy to fragment parent ions inside the mass spectrometer (optimized by
experiment)
The LC provides a stream of analyte solution (eluate) into the mass spectrometer where the
analyte is detected. You must consider the content of modifiers, salts, and contaminants in the
eluate. Specifically, you must ensure that what goes into the inlet of the mass spectrometer
does not suppress ionization of the compound of interest. Salt concentrations above 10 mM
and strong acids and bases damage the LC column. Modifier concentrations greater than
10 mM are not usually necessary for chromatographic stability and can suppress ionization of
other compounds. For best results, whenever possible, use volatile modifiers.
Volatile modifiers include the following:
• Acetic acid
• Ammonium acetate
• Ammonium formate
• Ammonium hydroxide
• Formic acid
• Trifluoroacetic acid
Your analyte solution can contain neutral particles or ions. If the solution contains ions, the
ions can carry a single charge or multiple charges. The number of charges depends on the
structure of the analyte and the composition and pH of the mobile phase. Solvent systems
are generally composed of organic solvents, water, and volatile modifiers. The ionization
characteristics of your analyte influence your decisions about the optimum pH of your solvent
system and the type of probe to use at the interface of the LC and the mass spectrometer.
With the TSQ Quantum series, LTQ series, or LCQ series instruments, you can use either the
H-ESI probe, the ESI probe, the APCI probe, or the APCI/APPI probe at the interface of the
LC. The choice of probe depends on the class of compound that you want to analyze and, to
a small extent, on the flow rate of your experiment. In general, the APCI and the APCI/APPI
probes accommodate higher flow rates and molecules of a less polar nature than does the ESI
probe. Refer to the introduction in the getting started manual for your mass spectrometer for
what factors might influence your decision about flow rates and what probe to use for
optimum transfer of ions into the mass spectrometer.
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Quantitative Analysis Techniques
After the ions are inside the mass spectrometer and the parent ions are isolated, collision
energy is applied to dissociate the parent ions into product ions (MS/MS). The relative
collision energy for a particular analysis depends on the structure of the compound that you
are analyzing. For this reason, you optimize the collision energy on your analyte of interest in
a tuning experiment. Refer to the getting started manual for your mass spectrometer for the
tuning procedure that describes how to optimize the collision energy.
Quantitative Analysis Techniques
To carry out quantitative analysis, you must evaluate the instrument’s response to known
amounts of the target component. Response is based on either the height of the
chromatogram peak or, more commonly, the area under the peak’s profile (Figure 237). In
both cases, you must take into account the baseline of the detected peak.
Instrument response is generally measured with several samples commonly called standards,
or calibration standards. These standards must cover a suitably wide range of concentrations
or amounts and must bracket the range of expected concentrations in the unknown.
Responses to these standards are plotted in a graph called a calibration curve. Ideally, this
curve corresponds to the equation of a straight line to ensure the highest degree of precision.2
Fitting an equation to the calibration curve with a user-specified method (for example, a least
squares regression) provides a response factor—a comparative measure of the response of
the mass spectrometer to a component. It is based on the amount of sample injected and the
resulting peak area or peak height. The response factor gives an intuitive and quantitative
measure of how responsive or sensitive the mass spectrometer is to a certain component.
Relative Intensity
Figure 237. Integrated chromatographic peak
Time (min)
2
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Quantitative Analysis Techniques
To perform quantitative analysis of samples containing unknown amounts of the target
component, calculate the peak area or height and compute and apply the appropriate response
to the equation derived from the calibration curve. These steps provide an estimate of the
amount of the target component in the samples. The precision of the measurement depends
on the quality and, to a lesser extent, the quantity of the calibration data.
The detection limit of the quantitative analysis method is the lowest concentration of analyte
in a sample that can be detected but not necessarily quantitated as an exact value. The
lower and upper quantification limits are the lowest and highest concentrations of analytes in
a sample that can be measured with an acceptable level of accuracy and precision. In an
analytical method, the highest concentration calibration standard defines the upper
quantification limit.
The quantitative analysis technique you use determines the manner in which the response is
calculated, both for generating the calibration curves and for subsequent quantitative analysis.
The two basic methods are described in these topics:
• Using External Standards for Quantitative Analysis
• Using Internal Standards for Quantitative Analysis
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Quantitative Analysis Techniques
Using External Standards for Quantitative Analysis
An external standard is a separate sample that contains the compound of interest at a known
concentration in solution. In the quantitative analysis that uses external standards, a series of
standards are analyzed and a calibration curve is constructed by plotting the magnitude of the
detector response as a function of the external standard concentration (Figure 238). You
analyze the unknown sample and determine the concentration by matching the magnitude of
the detector response with the magnitude on the calibration curve.
Using external standards is advantageous when you are analyzing various components in a
sample and you can assay all compounds of interest by using a single set of external standards.
Although this approach offers time- and cost-effective quantitative analysis, it cannot achieve
the very highest precision and accuracy. Variations in analyte and solution stability, injection
reproducibility, and matrix interference lead to lower precision levels in the external standard
method than in the internal standard method.
Figure 238. Calibration curve generated by using an external standard
Response for
unknown sample
500000
Response for target compound
400000
300000
200000
Amount [A] in
unknown sample
100000
0
0
20
40
60
80
100
Amount of target compound [A]
Using Internal Standards for Quantitative Analysis
An internal standard (ISTD) is a component that is added to a sample to act as a response
reference for one or more non-ISTD components in the sample. The concentration or
amount of an ISTD in any standard or unknown sample remains constant.
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Quantitative Analysis Techniques
Because quantitative mass spectrometric analysis usually involves multiple steps, the total
error in the analysis results from the accumulation of the errors at each step. In general,
sample-handling errors account for a larger fraction of the total error than do
mass-spectrometer errors. Fortunately, the internal standard method can reduce both sources
of error. For example, internal standards can correct for variations in a component’s peak area
that are caused by the following:
• Injection irreproducibility
• Changes in analyte solution volume
• Matrix and coeluter interference (both suppression and enhancement)
• System instability
• Variations in the source conditions
For maximum precision, add the ISTD component as early as possible to the start of the
sample work-up, particularly in those quantitative methods that require sample manipulations
such as extraction, cleanup, and dilution. Because the ISTD and non-ISTD components are
analyzed together, the internal standard quantitative analysis approach has the advantage that
it corrects for injection and other sample handling errors. The ISTD must behave chemically
in an identical or similar manner to the target compound through the extraction, cleanup,
and analytical processes.
You can also add the ISTD component as the last step of sample preparation prior to the
sample’s use to compensate for fluctuations in the reproducibility of the sample injection.
Use ISTDs in a quantitative analysis experiment as follows:
1. Analyze a series of standard solutions containing known concentrations of the target
compound and ISTD, and plot the ratio of the target compound and the ISTD detector
responses as a function of the corresponding ratio for the two quantities present in the
solution.
2. Add a fixed amount of the ISTD to each sample prior to any manipulation, and, after
preparing and analyzing the samples, obtain the quantity of the target compound present
in an unknown sample from the calibration curve.
Ideally, an ISTD is closely related to the target component in terms of its physical and
chemical properties. It must be pure, not present in the sample, and inert toward the
components of the sample. ISTD components are typically analogs, homologs, or isomers of
the target non-ISTD component. An ideal ISTD is a structural or isotopically labeled analog
of one of the target components. Stable isotope-labeled ISTDs act almost identically to the
analyte throughout sample manipulation and with regard to ionization tendencies and
fragmentation. Internal standards labeled with two or more deuterium (D) atoms are
frequently used for LC/MS.
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Sample Types
There can be any number of ISTD components in a sample, but each non-ISTD component
can be calibrated against only one ISTD (Figure 239).
Response for target compound / response for ISTD
Figure 239. Calibration curve generated by using an internal standard
1.4
1.2
Response ratio for
unknown sample
1.0
0.8
0.6
0.4
0.2
0.0
0.0
Unknown [A]
0.5
1.0
1.5
Amount of target compound [A]
2.0
2.5
Sample Types
Each quantitative analysis consists of a number, or sequence, of samples. The sequence
represents the order of sample analysis. A quantification sequence contains:
• One or more standards
• One or more unknown samples
For more demanding applications, you can also use optional quality control (QC) samples
and blank samples.
Standards
A calibration standard is a sample containing known amounts of all target components. The
purpose of a standard is to measure the response of the instrument to the target components
so that the LCquan application can generate a calibration curve for each component.
Unknowns
An unknown sample is one containing unknown amounts of the target components. The
LCquan application performs quantitative analysis on any sample defined as an unknown
sample.
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Sample Types
QCs
A QC sample contains a known amount of one or more specific target compounds. The
LCquan application places QC samples in the sequence so that it can test quantitative analysis
results for quality assurance purposes. After the QC sample is analyzed, it compares the
measured quantity with the expected value and an acceptability range. The quantitative
analysis of a QC sample is classified as passed if the difference between the observed and
expected quantities is within the user-defined tolerance. A QC sample is classified as failed if
the difference between the observed and expected quantities is outside the defined tolerance.
Blanks
A blank sample contains no target components but might contain an ISTD when you use the
internal standard quantitative analysis technique. By analyzing a blank sample, you can
confirm that there are no residual components in the solvent system that can cause erroneous
results.
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LCquan Application Flow Diagrams
Use this set of LCquan application flow diagrams as a reference. The flow diagrams show
step-by-step progressions through the different LCquan application windows.
Contents
• LCquan Application Flow Diagram
• LCquan Application for Web Access Flow Diagram
• LCquan Application Acquisition Flow Diagram
• LCquan Application Quantitate Flow Diagram
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LCquan Application Flow Diagram
LCquan Application Flow Diagram
The LCquan application flow diagram shows the steps for creating a new study or workbook
and the four main windows of the interface.
Study and Workbook Names
page
Create new study or
workbook
Create new study or workbook
or open existing workbook
Open existing or
last used workbook
LCquan
opens last used view
Click Next
Import Raw Files
page
Click Open
and Next
Import from legacy files
Import Instrument Method,
Acquisition Sequence,
and Processing Parameters
page
Do not import
prior data
Select Legacy Files page
Click Next
Import from existing workbook
Click Next
Click Next
and Finish
Select Workbook
page
Click Next
and Finish
Click Next
and Finish
Basic instrument method
created for configured
instruments
No
Instrument
Method
imported?
Yes
Instrument method updated
for configured instruments
Startup Method page
Instrument Setup
view
Instrument Method page
Shutdown Method page
Acquisition view
(See Acquisition flow diagram)
Click Setup
Setup Sequence page
Click Acquire
Run Sequence dialog box
Click OK
Status page
Explore
view
Click Method
Create Explore Method page
Click Review
Review the
Explore Results page
Quantitate view
(See Quantitate flow diagram)
Click Method
Create Method page
Click Sequence
Create Sequence page
Survey page
Click Survey
Review All Results page
Click Review
Review Reports page
Click Reports
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LCquan Application for Web Access Flow Diagram
LCquan Application for Web Access Flow Diagram
The LCquan application for Web Access flow diagram shows the steps for creating a new
study or workbook and the two main windows of the interface.
Study and Workbook Names
page
Create new study or
workbook
Create new study or workbook
or open existing workbook
Open existing or
last used workbook
LCquan
opens last used view
Click Next
Import Raw Files
page
Click Open
and Next
Import Instrument Method,
Acquisition Sequence,
and Processing Parameters
page
Do not import
prior data
Click Next
and Finish
Import from legacy files
Select Legacy Files page
Click Next
Import from existing workbook
Click Next
Select Instrument Method (optional),
Acquisition/Processing Sequence,
and Processing Method
Select Workbook
page
Click Next and Finish
Click Next
and Finish
Quantitate view
Explore
view
(See Quantitate flow diagram)
Click Method
Click Method
Create Method page
Create Explore Method page
Click Review
Click Sequence
Create Sequence page
Review the
Explore Results page
Survey page
Click Survey
Review All Results page
Click Review
Review Reports page
Click Reports
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LCquan Application Acquisition Flow Diagram
LCquan Application Acquisition Flow Diagram
Import Sequence File
dialog box
Click Next
and Finish
Base acquisition on a
previously saved file
in
New Acquisition
wizard
Create new
acquisition sequence
Create
new method
in
New Acquisition
wizard
Generate Sample Names
page
Click Next
Sample Information page
Click Next
Vial Positions page
Click Next
Add Standards page
Click Next
Add QCs page
Click Next
Component Name page
Click Next
Acquisition view Setup Sequence page
Define
levels
Click Acquire
in viewbar
Click Next
and Finish
User Label page
Acquisition view Run Sequence dialog box
Click OK
Acquisition view Status page
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Automatically enter
Processing view if
Process After Acquisition
was selected in the
Run Sequence dialog box
Quantitate
view
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LCquan Application Quantitate Flow Diagram
LCquan Application Quantitate Flow Diagram
Select
Import Existing Method
option
Import Quantitation Method
dialog box
in
New Method wizard,
Click Next
then click Next
Create or import
method
Select
Create New Method
option
in
New Method wizard,
then click Next
Calibration Options
page
Click Next
Select Raw File
dialog box
Click Next
and Finish
Create Method - Identify
Components page
Click on
Calibrate tab
Create Method - Define
Calibration Settings page
Click Sequence
in viewbar
Import Sequence
dialog box
Click Next
Select
Import Existing Sequence
option
in
New Processing
Sequence wizard,
then click Next
Create or import
sequence
Select
Create New Sequence
option
in
New Processing
Sequence wizard,
then click Next
Create Sequence Select Files page
Click Next
Select
Create New Sequence option in
New Processing Sequence wizard,
then click Next
Create Sequence Review and Edit page
Survey standards
and QCs
Click
Review All
in viewbar
Click Survey
in viewbar
Survey
page
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Review
all results
Review All Results
page
Review
Reports
Click Reports
in viewbar
Review Reports
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LCquan Application Menu and Toolbar Reference
This appendix provides a reference to the LCquan menus, icon bars, and toolbars.
Contents
• Using the Menus
• Actions Menu for Acquisition Window Only
• Apps Menu
• Change Menu for Acquisition Window Only
• File Menu
• Help Menu
• Options Menu
• View Menu
• Zoom Menu
• Icon Bars
• Toolbar
Using the Menus
 To use the keyboard to activate a command
1. Press the ALT or F10 key to activate the menu bar.
2. Type the character underlined in the menu title, such as F in File.
3. Type the character underlined in the command name, such as N in New.
If you do not select a command, you can close the menu by pressing the ESC key.
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Actions Menu for Acquisition Window Only
Actions Menu for Acquisition Window Only
Use this menu to check disk space and start, stop, and pause data acquisition (see Table 153).
Table 153. Actions menu commands of the Acquisition window
Command
Description
Keyboard shortcut
Check Disk Space
Opens the Disk Space dialog box where you can determine how
much disk space is available on your disk drives (see “Verifying
Disk Space” on page 109).
ALT+A > D
Restart Acquisition
Restarts an acquisition that has been paused.
ALT+A > R
Stop Acquisition
Stops the acquisition of the current sample and pauses.
ALT+A > T
Pause Acquisition
Pauses the acquisition after the current sample has been completely ALT+A > P
acquired.
Devices On
Puts all devices in the On state.
ALT+A > O
Devices Standby
Puts all devices in the Standby state.
ALT+A > A
Devices Off
Puts all devices in the Off state. The Off state indicates that all
power to the instrument that can be controlled by the LCquan
application is turned off.
ALT+A > F
CAUTION The Off state does not guarantee that all voltages are
turned off, nor does it indicate that all heated components are at
room temperature. To perform maintenance on an instrument,
refer to the hardware maintenance manual.
Automatic Devices On
Use this option to automatically turn on all devices controlled by
the LCquan application prior to starting a data acquisition.
ALT+A > U
If this command has a check mark to its left, the LCquan
application automatically turns on all devices that are in the Off or
Standby states.
If this command does not have a check mark to its left, the LCquan
application posts the following message when you have one or
more devices in the Standby or Off states:
One or More devices to be used by this sequence are not ‘On’. The
sequence will not start until all the requested devices are ready. Do
you want all the devices to be switched ‘On’? Press ‘Yes’ to switch
devices On, or ‘No’ to continue with devices in the ‘Off ’ or in
‘Standby’ state. When you select ‘No’, you must select the Devices
On command from the Actions menu before the sequence will
proceed.
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Apps Menu
Apps Menu
Use this menu to add external applications to the Apps menu for quick access and to select
those applications (see Table 154).
Table 154. Apps menu commands
Command
Description
Keyboard shortcut
Add Apps
Displays the App Selection dialog box where you can add external
applications to the Apps menu for quick access. For additional
information, see “App Selection dialog box parameters” on page 9
in Chapter 1, “Introduction.”
ALT+A > A
Change Menu for Acquisition Window Only
Use this menu to modify user labels and values and select the autosampler tray type (see
Table 155).
Table 155. Change menu commands of the Acquisition window
Command
Description
User Labels
Opens the Change Sequence User Labels dialog box where you can ALT+C > U
modify the user labels associated with a sequence. For more
information, see “Parameters in the Change Sequence User Labels
dialog box” on page 35 in Chapter 2, “Preparing to Perform
Quantitative Analysis.”
Tray Name
Opens the Tray Selection dialog box where you can select the
autosampler tray type to be used in the current session. For more
information, see “Tray Selection” on page 75 in Chapter 2,
“Preparing to Perform Quantitative Analysis.”
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Keyboard shortcut
ALT+C > T
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File Menu
File Menu
You can use the mouse or keyboard to activate File menu commands (see Table 156). A few of
the most commonly used commands can also be activated by clicking a Toolbar button.
Commands Common to All LCquan Application Windows
Table 156. File menu commands common to all LCquan application windows (Sheet 1 of 2)
Keyboard shortcut/
toolbar icon
Command
Description
New
Opens the New Study or Workbook Wizard that you use to create
a new study or workbook. For more information, see “Creating a
New Study and Workbook” on page 13 in Chapter 2, “Preparing
to Perform Quantitative Analysis.”
Open
Opens the LCquan Welcome page that you use to open an existing ALT+F > O or
workbook or to create a new study or workbook. For more
information, see “Creating a New Study and Workbook” on
page 13 in Chapter 2, “Preparing to Perform Quantitative
Analysis.”
Save
Saves the currently open workbook.
Save As
Opens the Save As Wizard that you use to name a workbook and to ALT+F > A
select the storage location (folder). For more information, see
“Saving a Workbook” on page 21 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
Layout Configuration >
Restore Factory Layout
Configuration
Applies the factory-defined view layouts and column arrangement
information to all windows.
ALT+F > L >
RIGHT ARROW
Layout Configuration >
Import Layout
Configuration
Loads a view layout and column arrangement configuration file
and applies it to the current workbook.
ALT+F > L >
RIGHT ARROW >
I
Layout Configuration >
Export Layout
Configuration
Saves the view layout and column arrangement configuration
information to a file in the Export folder with a user-supplied
name. This data is file-tracked, and an event is made stating that
the file was exported.
ALT+F > L >
RIGHT ARROW >
E
Summary Info
Opens the Workbook Summary Information dialog box that you
can use to obtain information and provide reference information
about the current workbook. For more information, see
“Workbook Summary Info dialog box parameters” on page 26 in
Chapter 2, “Preparing to Perform Quantitative Analysis.”
ALT+F > U
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File Menu
Table 156. File menu commands common to all LCquan application windows (Sheet 2 of 2)
Keyboard shortcut/
toolbar icon
Command
Description
Audit Trail
Opens the Audit Viewer utility, which is shared by other
ALT+F > T
Xcalibur-based applications. Audit Viewer provides a chronological
listing of user-initiated events. When you start Audit Viewer from
within the LCquan application, Audit Viewer displays only the
items associated with the current workbook, including
uncommitted items.
You can print the audit trail for an LCquan workbook if the page
displays only saved entries. For more information, refer to the Help
within Audit Viewer or refer to the Foundation Administrator
Guide.
Create Locked Version of Opens the Create Locked Workbook dialog box that you use to
Workbook
save a copy of the current workbook as a locked workbook.
ALT+F > L > L
Recently opened files
Displays a list of recently opened files. To open a recently opened
workbook, select the workbook file from this list.
Exit
Exit
Quits the LCquan application.
ALT+F > X
Commands Specific to Instrument Setup Window
Table 157. Commands specific to the Instrument Setup window
Command
Description
Import Instrument
Method
Opens the Import Instrument Method File dialog box that you use ALT+F > I
to import an instrument method file.
Print Current
Instrument Method
Opens a Print dialog box that you use to print the instrument
method (.meth).
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Keyboard shortcut
ALT+F > P
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File Menu
Commands Specific to Acquisition Window
Table 158. Commands specific to the Acquisition window
Command
Description
Keyboard shortcut
Import Acquisition
Sequence > From File
Opens the Load Sequence File dialog box that you use to import an ALT+F > I > F
acquisition sequence.
Import Acquisition
Sequence >
Copy from Processing
Sequence
Makes the acquisition sequence identical to the processing
sequence.
ALT+F > I > P
Export Acquisition
Sequence
Exports the current acquisition sequence to a sequence file.
ALT+F > E
Print Sequence Info
Opens a Print dialog box that you use to print a copy of the current ALT+F > P
sequence in a spreadsheet format.
Commands Specific to Explore Window
Table 159. Commands specific to the Explore window
Command
Description
Keyboard shortcut
Import Peak Name List
Opens a file selection dialog box where you can import the naming ALT+F > I
list to a text file (.txt or .csv). A copy of the file is created in the
Import folder, and both an event record and a file tracking record
are created. After the file is accepted, any peak list or
chromatogram is relabeled as required.
Export Peak Name List
Opens a file selection dialog box where you can import the naming ALT+F > E
list to a text file (.txt or .csv).
A copy of the file is created in the Import folder, and both an event
record and a file tracking record are created. After the file is
accepted, any peak list or chromatogram is relabeled as required.
Commands Specific to Both Explore and Quantitate Windows
Table 160. Commands specific to both the Explore and Quantitative windows
Command
Description
Open Raw File
Opens the Select Raw File dialog box, where you can open an
existing data file of extension raw.
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toolbar icon
ALT+F > F or
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File Menu
Commands Specific to Quantitate Window
Table 161. File menu commands specific to the Quantitate window
Command
Description
Import >
Processing Method
Opens the Import Quantitation Method dialog box, where you
ALT+F > I
import a sequence from an existing file on disk. If an acquisition
sequence exists, the Initialize with Acquisition Component Names
box is selected, and default method components are created with
the names in the acquisition component list. These components
use the acquisition component level tables.
Import >
Processing Sequence >
From File
Opens the Load Sequence File dialog box, where you can import a
sequence from a file on disk. A copy of the imported file is
maintained in the import folder, and an audit log entry is created
for this event. The entire sequence is replaced with the imported
sequence.
ALT+F > I >
DOWN ARROW >
RIGHT ARROW >
ENTER
Import >
Processing Sequence >
Copy from Last
Acquired Sequence
Replaces the defined processing sequence with a shortened
sequence that is based on the data already acquired.
–
Import >
Processing Sequence >
Copy from Acquisition
Sequence
Replaces the processing sequence with a copy of the acquisition
sequence.
ALT+F > I >
DOWN ARROW >
RIGHT ARROW >
DOWN ARROW >
ENTER
Export >
Processing Sequence
Saves the current processing sequence in the Export folder with a
ALT+F > E >
name you supply. An export event is logged and the exported file is ENTER
tracked in the audit trail for the workbook.
Export > Results
Opens the Results Export dialog box where you can save the
current results information to a .csv file in the Export folder. This
data is file-tracked, and an event is made stating that the file was
exported. For more information, see “Results Export dialog box
parameters” on page 404 in Chapter 6, “Processing the Raw Files
and Reviewing the Analytical Results.”
Export >
QuickCalc Data
Saves QuickCalc versions of the current LCquan processing
–
sequence (.sld) and processing method (.pmd) in the Export folder,
using the file names that you supply. An export event is logged and
the exported QuickCalc files are tracked in the audit trail for the
workbook.
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Keyboard shortcut
ALT+F > E >
DOWN ARROW >
ENTER
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Help Menu
Help Menu
Use this menu to access Help topics for LCquan (see Table 162).
Table 162. Help menu commands.
Command
Description
Keyboard shortcut
LCquan Help
Opens the LCquan Help system at the first Help topic.
–
Current View Help
Opens the LCquan Help system and displays the topic for the
currently displayed LCquan view.
F1
Glossary
Opens the glossary.
–
How to use Online Help Opens an HTML Help system that describes how to use the Help
viewer.
–
About LCquan
–
Opens the About LCquan dialog box where you can check the
version of each installed Xcalibur application, including LCquan,
and view a list of the configured instruments.
Options Menu
The LCquan application groups commands that deal with identification, calibration, and
calibration levels, and graphic display control commands in the Options menu (see
Table 163).
Options Commands Common to All LCquan Windows
Table 163. Options menu commands common to all LCquan windows (Sheet 1 of 2)
Command
Description
Enable Warnings
Enables the display of warning messages. You can disable warnings, ALT+O > E
for example, by selecting the Don’t Tell Me About This Again box
in the Save Settings Options dialog box. For more information, see
“Save Settings Options” on page 110 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
Wizards > Show the New
Acquisition Sequence
Wizard when no
sequence is defined
Opens the New Acquisition Wizard if there is no acquisition
sequence defined when you enter the Acquisition window. The
New Acquisition Wizard steps you through a procedure for
creating a new acquisition sequence or importing an existing
acquisition sequence. For more information, see “Creating an
Acquisition Sequence” on page 39 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
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ALT+O >W > A
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Options Menu
Table 163. Options menu commands common to all LCquan windows (Sheet 2 of 2)
Command
Description
Keyboard shortcut
Wizards > Show the New
Processing Method
Wizard when no method
is defined
Opens the New Method Wizard if there is no processing method ALT+O >W > M
defined when you enter the Quantitate window. The New Method
Wizard steps you through a procedure for creating a new
processing method or importing an existing processing method.
Wizards > Show the New
Processing Sequence
Wizard when no
sequence is defined
Opens the New Processing Sequence Wizard if there is no
processing sequence defined when you display the Sequence view
of the Quantitate window. The New Processing Sequence Wizard
steps you through a procedure for creating a new processing
sequence. For more information, see “Defining a Processing
Sequence” on page 302 in Chapter 5, “Creating a Processing
Sequence.”
Acquisition Sequence
Info
Opens the Acquisition Sequence dialog box where you can specify ALT+O >A
that the LCquan application update the processing sequence with
acquisition sequence information whenever a sample is run. In the
Acquisition Sequence dialog box, you can also specify the
maximum number of rows in the acquisition sequence. For more
information, see “Acquisition Sequence dialog box parameters” on
page 107 in Chapter 2, “Preparing to Perform Quantitative
Analysis.”
ALT+O >W > P
Options Commands Specific to Quantitate Window
Table 164. Option menu commands specific to the Quantitate window (Sheet 1 of 2)
Command
Description
Identification
Opens the Identification Options dialog box where you can select a ALT+O > I
baseline, noise window, and void time for peak identification
purposes. For more information, see “Identification Options
parameters” on page 239 in Chapter 4, “Creating a Processing
Method,”
Calibration
Opens the Calibration Options dialog box where you can select
internal or external calibration for the current processing method.
For more information, see “Calibration Options dialog box
parameters” on page 254 in Chapter 4, “Creating a Processing
Method,”
Delete Component
Removes the selected component from the processing method. For ALT+O > D
more information, see “Specifying Method Identification” on
page 193 in Chapter 4, “Creating a Processing Method,”
Delete All Components
Removes all components from the processing method. For more
information, see “Specifying Method Identification” on page 193
in Chapter 4, “Creating a Processing Method,”
Thermo Scientific
Keyboard shortcut
ALT+O > C
–
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Options Menu
Table 164. Option menu commands specific to the Quantitate window (Sheet 2 of 2)
Command
Description
Keyboard shortcut
New Processing Method
Wizard
Opens the New Method Wizard that steps you through a
procedure for creating a new processing method or importing an
existing processing method.
ALT+O > N
Display Options –
Chromatogram
Opens the Chromatogram Display Options dialog box—where
you can label peaks and enter the peak width displayed at both
ends of a chromatogram peak. For more information, see
“Chromatogram Display Options” on page 268 in Chapter 4,
“Creating a Processing Method,”
–
Display Options –
Spectrum
Opens the Spectrum Display Options dialog box where you can
–
modify the appearance of spectrum plots. For more information,
see “Spectrum Display Options dialog box parameters” on page 95
in Chapter 2, “Preparing to Perform Quantitative Analysis.”
Display Options –
Ion Ratio Chro
Opens the Ion Ratio Chromatogram Display Options dialog box –
where you can label peaks and enter the peak width displayed at
both ends of a chromatogram peak. For more information, see “Ion
Ratio Chromatogram Display Options” on page 279 in Chapter 4,
“Creating a Processing Method,”
Save Chromatograms in
file
Saves chromatogram peak integration information. This speeds up ALT+O > S
data processing done after the information is saved because existing
chromatograms are not integrated again.
Commands Specific to Both Explore and Quantitate Windows
Table 165. Commands specific to both the Explore and Quantitate windows
Command
Description
Masses
Opens the Masses dialog box where you can specify tolerance and ALT+O > M
precision settings for the mass data displayed in the Chromatogram
view. For more information, see “Masses dialog box parameters” on
page 197 in Chapter 4, “Creating a Processing Method,”
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Keyboard shortcut
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View Menu
Commands Specific to Acquisition Window
Table 166. Commands specific to the Acquisition window
Command
Description
Keyboard shortcut
Realtime Display
Settings
Opens the Realtime Display Settings dialog box where you can
specify the properties of the real-time chromatograms that the
LCquan application displays in the Chromatogram and Spectrum
panes of the Acquisition window. For more information, see
“Realtime Display Settings dialog box parameters” on page 89 in
Chapter 2, “Preparing to Perform Quantitative Analysis.”
ALT+O > R
View Menu
The View menu has group commands that you can use to display or hide the toolbar or status
bar in the View menu. You can also change the visual display of the toolbar using the View
menu commands.
Commands Common to All LCquan Windows
Table 167. Commands common to all LCquan windows (Sheet 1 of 2)
Command
Description
Keyboard shortcut
Toolbar
Displays or hides the LCquan window toolbar. The toolbar appears ALT+V > T
if it was previously hidden or hides if it is currently displayed.
Status Bar
Displays or hides the status bar. (The status bar is the horizontal
box at the bottom of the LCquan window.)
ALT+V > S
The status bar appears if it was previously hidden or hides if it is
currently displayed.
Icon Bar
Displays or hides the Icon Bars. For more information, see “Icon
Bars” on page 439.
ALT+V > I >
ENTER
Section Indicator
Displays or hides the view title banner. For example: Explore –
Review the explore results.
ALT+V >
DOWN ARROW >
ENTER
Show Large Toolbar
Increases the size of the Toolbar. For more information, see
“Toolbar” on page 440.
ALT+V > L
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View Menu
Table 167. Commands common to all LCquan windows (Sheet 2 of 2)
Command
Description
Keyboard shortcut
Show Large Icons in Bar
Increases the size of the icons in the Icon Bars. For more
information, see “Icon Bars” on page 439.
ALT+V > I > I >
ENTER
Section Selection
Choose this command to select a window:
ALT+V >
DOWN ARROW >
RIGHT ARROW >
ENTER
•
•
•
•
Instruments
Acquisition
Explore
Quantitate
–or–
DOWN ARROW >
ENTER
Commands Specific to Instruments Window
Table 168. Commands specific to the Instruments window
Command
Description
Keyboard shortcut
Instrument Selector
Selects the instrument to be edited.
ALT+V >
DOWN ARROW >
RIGHT ARROW >
ENTER
–or–
DOWN ARROW >
ENTER
Commands Specific to Acquisition Window
Table 169. Commands specific to acquisition window
Command
Description
Keyboard shortcut
Step Selector
Switches to the selected Acquisition view:
–
• Acquisition Setup
• Acquisition Acquire
• Acquisition Status
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View Menu
Commands Specific to Explore Window
Table 170. Commands specific to the Explore window
Command
Description
Keyboard Shortcut
Select Review Display
Selects a review layout for the current display:
ALT+V >
DOWN ARROW >
RIGHT ARROW >
ENTER
•
•
•
•
•
Multi Peak View
Comparison View
Peak List View
Large Chro View
Sample Info View
–or–
DOWN ARROW >
ENTER
Commands Specific to Quantitate Window
Table 171. Commands specific to Quantitate window
Command
Description
Keyboard shortcut
Component Selector Bar Only in Survey and Review All Results views: Displays or hides the –
Component list at the far right of the screen. When this option is
cleared, the components are listed as tabs above the Results grid.
Step Selector
Switches to the selected Quantitate view:
•
•
•
•
•
Select Review Display
–
Quantitate Method
Quantitate Sequence
Quantitate Survey
Quantitate Review All
Quantitate Reports
Selects a review layout for the current display:
• Triple Pane
• Dual Pane
• Single Pane
ALT+V >
DOWN ARROW >
RIGHT ARROW >
ENTER
–or–
DOWN ARROW >
ENTER
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Zoom Menu
Zoom Menu
Use this menu to adjust the visual display of your view (see Table 172). You can increase the
size of the view and reset the display to the original state.
Table 172. Zoom menu commands
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Command
Description
Keyboard Shortcut
Zoom In Y
Zooms in on y axis to display more detail
and less range.
ALT+Z > Z
Zoom Out Y
Zooms out on y axis to display less detail but ALT+Z > O
more range.
Normalize
Zooms in on y axis to largest peak height.
ALT+Z > N
Zoom In X
Zooms in on x axis to display more detail
and less range.
ALT+Z > X
Zoom Out X
Zooms out on x axis to display less detail but ALT+Z > m
more range.
Display All
Sets x axis to display entire displayable range. ALT+Z > D
Reset Scaling
Resets both x and y axes to display maximum ALT+Z > R
amount of data.
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Icon Bars
Icon Bars
Use the left navigation panes to navigate between LCquan windows.
Figure 240. Icon bars
Instruments icon bar
Thermo Scientific
Acquisition icon bar
Explore icon bar
Quantitate icon bar
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Toolbar
Toolbar
Use the toolbar buttons to quickly select their corresponding commands (see Table 173). The
available toolbar buttons vary depending on the LCquan window: Instruments, Acquisition,
Explore, or Quantitate.
 To display the LCquan toolbar
Choose View > Toolbar.
Table 173. Toolbar buttons (Sheet 1 of 4)
Icon
Button
Description
New
Opens the New Study or Workbook Wizard. The New Study or Workbook Wizard
prompts you for information that the LCquan application requires to create a new
study or workbook. For more information, see “Creating a New Study and
Workbook” on page 13 in Chapter 2, “Preparing to Perform Quantitative
Analysis.”
Open Workbook
Opens the LCquan Welcome page that you use to open an existing workbook or to
create a new study or workbook. For more information, see “Create a New
Workbook” on page 14 in Chapter 2, “Preparing to Perform Quantitative
Analysis.”
Save
Saves the current workbook.
Open Raw
Opens the Select Raw File dialog box, where you can open an existing data file of
extension raw.
Note This feature is not available in the Instruments window.
Icon Bar
Displays or hides the Icon Bars. Use the left navigation panes to navigate between
the LCquan windows and the windows within each window. For more
information, see “Icon Bars” on page 439.
Component Bar
Displays or hides the Component bar.
Note This feature is available only for the Quantitate window.
Status Information
View
Displays or hides the Status pane on the Status view. For more information, see
“Using the Status View” on page 83 in Chapter 2, “Preparing to Perform
Quantitative Analysis.”
Note This feature is available only for the Acquisition window.
Realtime Plot View
Displays the Status view. For more information, see “Using the Status View” on
page 83 in Chapter 2, “Preparing to Perform Quantitative Analysis.”
Note This feature is available only for the Acquisition window.
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Toolbar
Table 173. Toolbar buttons (Sheet 2 of 4)
Icon
Button
Description
Run Sample
Displays the Run Sequence dialog box where you can run a single sample. For more
information, see “Run Sequence dialog box parameters” on page 78 in Chapter 2,
“Preparing to Perform Quantitative Analysis.”
Note This feature is available only for the Acquisition window.
Run Sequence
Displays the Run Sequence dialog box where you can run a sequence of samples.
For more information, see “Run Sequence dialog box parameters” on page 78 in
Chapter 2, “Preparing to Perform Quantitative Analysis.” .
Note This feature is available only for the Acquisition window.
Method View
When you are in the Quantitate window, displays the Create Method view in the
Quantitate window. For more information, see “Specifying Method Calibration”
on page 242 in Chapter 4, “Creating a Processing Method,”
When you are in the Explore window, displays the Explore – Create view. For more
information, see “Creating Explore Methods” on page 118 in Chapter 3,
“Exploring the Data.”
Note This feature is available only for the Quantitate and Explore windows.
Sequence View
When you are in the Acquisition window, displays the Acquisition – Setup
Sequence view. For more information, see “Using the Setup Sequence View” on
page 32 in Chapter 2, “Preparing to Perform Quantitative Analysis.”
When you are in the Quantitate window, displays the Create Sequence view in the
Quantitate window. For more information, see “Defining a Processing Sequence”
on page 302 in Chapter 5, “Creating a Processing Sequence.”
Note This feature is available only for the Acquisition and Quantitate windows.
Results View
When you are in the Quantitate window, displays the Review All Results view in
the Quantitate window. For more information, see “Reviewing All Results” on
page 373 in Chapter 6, “Processing the Raw Files and Reviewing the Analytical
Results.”
When you are in the Explore window, displays the Explore – Review view. For
more information, see “Exploring the Results” on page 138 in Chapter 3,
“Exploring the Data.”
Note This feature is available only for the Quantitate and Explore windows.
Zoom In Y
Zooms in the traces along the y axis, vertically, to display more detail and less range.
Note This feature is not available in the Instruments window.
Zoom Out Y
Zooms out the traces along the y axis, vertically, to display more range and less
detail.
Note This feature is not available in the Instruments window.
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Toolbar
Table 173. Toolbar buttons (Sheet 3 of 4)
Icon
Button
Description
Normalize
Readjusts the display of all peaks in the trace based on the largest peak height.
Note This feature is not available in the Instruments window.
Zoom In X
Zooms in the traces along the x axis, horizontally, to display more detail and less
range.
Note This feature is not available in the Instruments window.
Zoom Out X
Zooms out the traces along the x axis, horizontally, to display more range and less
detail.
Note This feature is not available in the Instruments window.
Display All
Resets the display of the x axis to include the entire displayable range.
Note This feature is not available in the Instruments window.
Reset Scaling
Resets both x and y axes to display the maximum amount of data.
Note This feature is not available in the Instruments window.
Add a Peak
Manually defines a peak in a chromatogram displayed on the Survey or Review All
Results views in the Quantitate window. The feature is available when no peak is
detected.
 To add a peak
1. Select the component, which is either listed in the pane to the right of the
window or on a tab at the top of the Results grid.
2. In the Item Selector list, select Selected.
, on the LCquan toolbar.
3. Click the Add a Peak icon,
The pointer changes to
.
4. Drag the peak baseline, defining the start and end of the peak. You can
manually adjust the peak baseline and endpoints by grabbing the square blue
handles and dragging them.
Note This feature is available only for the Survey or Review All Results views in
the Quantitate window with the Item Selector set to Selected.
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Update Raw File
[Explore]
Only when you are in Explore while acquiring data: Updates the raw file with a
partial sequence created from the acquired samples.
Update Sequence
[Quantitate]
Only when you are in Quantitate while acquiring data: Updates the current
processing sequence with a partial sequence created from the acquired samples.
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Toolbar
Table 173. Toolbar buttons (Sheet 4 of 4)
Icon
Button
Description
Shut Down Instrument Displays the Emergency Shutdown dialog box where you can shut down all devices
and stop the acquisition of the current sample and pause, stop the acquisition of the
current sequence and pause, or stop the acquisition of all sequences. For more
information, see “Emergency Shutdown” on page 111 in Chapter 2, “Preparing to
Perform Quantitative Analysis.”
Help
Thermo Scientific
Displays the Help topic for the current view or displays the Help system.
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I
Index
A
acquiring data
acquisition sequence 32
flow diagrams 422
overview 10
procedure 76
remote acquisition 112
time-stamping raw files during remote acquisition
always time-stamp 112
never time-stamp 112
Acquisition Levels parameters 66
acquisition queue, navigation 100
acquisition sequence
copying to processing sequence 306
definition 33
exporting 56
grid parameter definitions 70
printing 56
Acquisition Sequence History
sample selector 139
viewing 104
Acquisition Sequence History parameters
Explore 136
Status 105
Acquisition Sequence History shortcut menu commands
Acquisition 38
Explore 137
Status 106
Acquisition Sequence parameters 107
Acquisition window
overview 32
Run Sequence dialog box 75
Run Status page 97
Status page 83
algorithms, peak detection
Avalon
baseline 239
integration 234
Genesis
Thermo Scientific
advanced 230
baseline 239
integration 227
ICIS
advanced 234
baseline 239
integration 232
user identification settings
Avalon, integration 368
Genesis
advanced 362
integration 371
ICIS
advanced 371
integration 364
analyte detection using mass spectrometry 411
animations
create method 257
create sequence 326
APCI probe 411
APCI/APPI probe 411
App Selection parameters 9
Apps menu commands 427
associating raw sample files with sample types 323
audit trail, opening the utility 429
Avalon peak detection
baseline 239
integration 234
user identification settings, integration 368
Avalon Peak Integration parameters
Explore 132
Quantitate 222
B
Baseline parameters 372
Blank samples
acquisition setup 32
defined 417
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Index: C
C
Cal Exclusion List parameters 352
calibration curve
described 412
excluding standards 350
inspecting at low concentrations 341
using external standard 414
using internal standard (illustrated) 416
weighting 6
Calibration Curve pane, Survey page 334
Calibration Curve parameters 264
Calibration Curve shortcut menu commands 264
Calibration Curve Type area parameters 247
calibration levels, matching names 55
Calibration Options parameters 254
Calibration page shortcut menu commands 250
Calibration Settings
Curve parameters 345
Isotope parameters 347
Levels parameters 348
Type parameters 349
calibration standards, defined 416
CE Quan, import processing method data for Q Exactive 188
Change Instruments In Use parameters 82
Change menu commands, Acquisition window 427
Change Sequence User Labels parameters 35
Chromatogram Comment parameters 383
Chromatogram Definition area parameters
Explore 120
Quantitate 195
Chromatogram Display Options parameters
Explore 157
Quantitate 269
Chromatogram List parameters
Explore 159
Quantitate 281
Chromatogram List shortcut menu commands 160
chromatogram normalization
with respect to detected peak 205
with respect to highest peak 205
Chromatogram pane
Review All Results page 375
Survey page 334
Chromatogram pane shortcut menu commands 91
Chromatogram parameters
Explore 156
Quantitate 267
Review 271
Chromatogram shortcut menu commands
Quantitate 267
Review 271
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Column Arrangement parameters
Acquisition 63
Quantitate 321
Review All Results 338
comparing plots 142
Component list shortcut menu commands
Quantitate 249
Review 340
Component Type area parameters 244
components
Component List pane 249
component types, specifying 244
Survey page component list 334
contacting us xi
copying, acquisition sequence to processing sequence 306
Correction for Isotope Contribution parameters 253
Create page 118
Create Sequence (create) page 323
Create Sequence (edit) page 309
Current Review Display view layouts 143
D
detection limit 413
detection, peak
See algorithms, peak detection
Disk Space parameters 109
documentation survey xi
E
Emergency Shutdown parameters 111
Error Report parameters
Explore 161
Quantitate 282
Error Report shortcut menu commands 283
ESI probe 411
Excel long summary report 403
Excel short summary report 402
Explore Sequence, sample selector 139
Explore window
about 4
Create page 118
introduction 117
locks 142
Review page 138
status plots 174
status reports 176
export layout configuration 428
exporting an acquisition sequence 56
external standards defined 414
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Index: F
F
file and folder structure 7
File menu commands 428
File Tracking Results parameters 25
Fill Down parameters
Acquisition 60
Quantitate 316
Filter List parameters
Explore 162
Quantitate 284
Filter List shortcut menu commands 284
flow diagrams
acquiring data 422
creating study or workbook 420
creating study or workbook (Web Access) 421
processing data 423
G
General Parameters Plot parameters
Explore 163
Quantitate 285
General Parameters Plot shortcut menu commands
Explore 164
Quantitate 286
Genesis Advanced Component Options parameters
Explore 125
Quantitate 215
Genesis peak detection
advanced 230
baseline 239
integration 227
user identification settings
advanced 362
integration 360
Genesis Peak Integration parameters
Explore 123
Quantitate 213
H
Help menu commands 432
H-ESI probe 411
history, viewing acquisition 104
I
ICIS Advanced parameters
Explore 129
Quantitate 219
ICIS peak detection
advanced 234
integration 232
Thermo Scientific
user identification settings
advanced 371
integration 364
ICIS Peak Integration parameters
Explore 128
Quantitate 218
importing
layout configuration 428
processing method 258
processing sequence 306
raw files 17
Initial and Timed Events
Explore 133
IRC detection 237
Quantitate 223
Instrument Method List parameters 287
Instrument Method parameters 165
instrument methods
creating 29
defined 27
Instrument Setup window 27
Instrument Setup window overview 27
integrating peaks manually 371
internal standards (ISTDs)
defined 414
identifying 254
using for quantitation 415
Ion Ratio Chromatogram Display Options parameters 279
ion ratio confirmation (IRC)
Avalon, integration 236
description 241
example chromatogram 241
Genesis
advanced 230
integration 227
hydrocortisone example 241
ICIS
advanced 234
integration 232
Ion Ratio Confirmation area parameters 201
Ion Ratio Confirmation area shortcut menu commands 202
ion summing
Summing Ions dialog box 203
trace type 195, 356
IRC Chromatogram parameters 277
IRC Chromatogram shortcut menu commands 277
IRC Detection Method
Avalon Integration parameters 236
Genesis Advanced parameters 230
Genesis Integration parameters 228
ICIS Advanced parameters 234
ICIS Integration parameters 232
LCquan User Guide
447
Index: K
Identification parameters 226
isotope %, calibration settings 347
ISTD Chromatogram pane 334
K
keyboard shortcuts
Apps menu commands 427
File menu commands 428
Options menu commands 432
toolbar commands 440
View menu commands 435
L
levels
in processing method 312
resolving names 327
show amounts 322
Limit Peaks parameters 135
liquid chromatography (LC), analyte separation 410
lock 406
locking plots for comparison 142
locking the workbook 405
locking workbook automatically after creating report 406
locks against raw file change 142
lower quantitation limit 413
M
Mass List parameters
Explore 166
Quantitate 288
Mass List shortcut menu commands
Explore 167
Quantitate 288
mass range 257
mass spectrometry, analyte detection 411
Masses parameters 197
method level names 329
modifiers, volatile 411
Multi Peak Plot parameters
Explore 181
Quantitate 299
Multi Peak Plot shortcut menu commands
Explore 181
Quantitate 299
Multi-Peak Options parameters 182
448
LCquan User Guide
N
New Acquisition Sequence Wizard 40
New Method Wizard 184
New Processing Sequence Wizard 304
New Study or Workbook Wizard 14
normalization, chromatogram
with respect to detected peak 205
with respect to highest peak 205
O
Options menu commands 432
overview of the LCquan application 1–11
P
parameter tables
Acquisition Levels 66
Acquisition Sequence 107
Acquisition Sequence History
Explore 136
Status 105
Acquisition Sequence History shortcut menu
Acquisition 38
Explore 137
Status 106
App Selection 9
Avalon Peak Integration
Explore 132
Quantitate 222
Baseline 372
Cal Exclusion List 352
Calibration Curve 264
Calibration Curve shortcut menu 264
Calibration Curve Type area 247
Calibration Options 254
Calibration page shortcut menu 250
Calibration Settings
Curve 345
Isotope 347
Levels 348
Type 349
Change Instruments In Use 82
Change Sequence User Labels 35
Chromatogram
Explore 156
Quantitate 267
Review 271
Chromatogram Comment 383
Chromatogram Definition area
Explore 120
Quantitate 195
Thermo Scientific
Index: P
Chromatogram Display Options
Explore 157
Quantitate 269
Chromatogram List
Explore 159
Quantitate 281
Chromatogram pane shortcut menu 91
Chromatogram shortcut menu
Quantitate 267
Review 271
Column Arrangement
Acquisition 63
Quantitate 321
Review All Results 338
Component list shortcut menu
Quantitate 249
Review 340
Component Type area 244
Correction for Isotope Contribution 253
Current Review Display 143
Disk Space 109
Emergency Shutdown 111
Error Report
Explore 161
Quantitate 282
Error Report shortcut menu 283
File Tracking Results 25
Fill Down
Acquisition 60
Quantitate 316
Filter List
Explore 162
Quantitate 284
Filter List shortcut menu 284
General Parameters Plot
Explore 163
Quantitate 285
General Parameters Plot shortcut menu
Explore 164
Quantitate 286
Genesis Advanced Component Options
Explore 125
Quantitate 215
Genesis Peak Integration
Explore 123
Quantitate 213
ICIS Advanced
Explore 129
Quantitate 219
ICIS Peak Integration
Explore 128
Quantitate 218
Initial and Timed Events
Explore 133
Thermo Scientific
IRC detection 237
Quantitate 223
Instrument Method 165
Instrument Method List 287
Ion Ratio Chromatogram Display Options 279
Ion Ratio Confirmation area 201
Ion Ratio Confirmation area shortcut menu 202
IRC Chromatogram 277
IRC Chromatogram shortcut menu 277
IRC Detection Method
Avalon Integration 236
Genesis Advanced 230
Genesis Integration 228
ICIS Advanced 234
ICIS Integration 232
Identification 226
Limit Peaks 135
Mass List
Explore 166
Quantitate 288
Mass List shortcut menu
Explore 167
Quantitate 288
Masses 197
Multi Peak Plot
Explore 181
Quantitate 299
Multi Peak Plot shortcut menu
Explore 181
Quantitate 299
Multi-Peak Options 182
Peak Identification area 200
Peak Information
Flags 378
Info parameters 376
IRC Tests 381
Peak List
Explore 168
Quantitate 289
Peak List shortcut menu
Explore 168
Review 290
Peak Name List Editor 149
processing sequence grid columns 316
processing sequence grid shortcut menu 314
Quantitation Results Sorting Order 339
Realtime Display Settings 89
result grid shortcut menu 335
Results Export 404
Retention Time area 198
Review Reports 391
Run Sequence 78
Run Status shortcut menu 99
LCquan User Guide
449
Index: P
Sample Info
Explore 172
Review 291
Sample Info shortcut menu
Explore 172
Review 291
Sample Information 102
Sample Selector 141
Sample Selector shortcut menu 141
Select Component 251
Select Directory 110
Sequence Sorting Order 319
Sort Sequence 61
Spectrum
Explore 173
Review 276
Spectrum Display Options 95
Spectrum pane shortcut menu 94
Spectrum shortcut menu
Explore 173
Review 276
Status Plot
Explore 174
Review 293
Status Plot shortcut menu
Explore 175
Review 294
Status Report
Explore 176
Review 295
Status Report shortcut menu
Explore 177
Review 296
Switching to Processing during Acquisition 108
Target Compound area 246
Tune Method
Explore 178
Review 297
Tune Method shortcut menu
Explore 179
Review 297
User Identification Settings
Avalon Integration 368
Detection 358
Genesis Advanced 363
ICIS Advanced 367
ICIS Integration 364
Identification 355
Workbook Summary Information 26
peak detection
See algorithms, peak detection
peak detection and integration settings, editing 353
peak detection type
450
LCquan User Guide
Avalon 121
Genesis 121
ICIS 121
Peak Identification area parameters 200
Peak Information
Flags parameters 378
Info parameters 376
IRC Tests parameters 381
peak integration 362
Peak List parameters
Explore 168
Quantitate 289
Peak List shortcut menu commands
Explore 168
Review 290
peak lists, generating 146
Peak Name List Editor parameters 149
peak parameters 239
peaks
integrated (illustrated) 412
integrating manually 371
modifying integration parameters 353
undoing manual integration of 372
peaks, limiting 135
printing, acquisition sequence 56
probes, choosing 411
processing
overview 10
while acquiring data 107
processing method
creating 183
import data from CE Quan
Q Exactive, import processing method data from CE
Quan 188
importing 258
saving 258
processing raw files 331
processing sequence
copying acquisition sequence 306
creating 301
defined 301
editing 309
grid parameter definitions 316
importing 306
reviewing 309
switching to processing during acquisition 108
processing sequence grid column parameters 316
processing sequence grid shortcut menu commands 314
Thermo Scientific
Index: Q
Q
QC levels, matching names 55
Qual Browser, starting from Explore window 151
quality control (QC) samples
acquisition setup 32
overview 417
Quantitate result grid parameters 394
Quantitate Sequence, sample selector 139
Quantitate window 183
description 5
quantitation flow diagram 423
quantitation limits 413
Quantitation Results Sorting Order parameters 339
quantitative analysis
described 409–417
internal standards and target compounds 254
LCquan overview 10
sources of error 415
steps of 409
techniques 412
using external standards 414
using internal standards 414
R
raw files
associating with sample types 323
displaying in Chromatogram pane 86
importing into new workbook 17
processing 331
time-stamping during remote acquisition
always time-stamp 112
never time-stamp 112
raw files, locked and unlocked 142
Realtime Display Settings parameters 89
remote acquisition
always time-stamp raw files 112
never time-stamp raw files 112
reports
do not lock workbook after creating report 407
lock workbook after creating report 406
response factor 412
restore factory layout configuration 428
result grid shortcut menu commands 335
result grid, description 334
Results Export parameters 404
Retention Time area parameters 198
Review All Results page 373
review mode 13
Review page 138
Review Reports page 383
Thermo Scientific
Review Reports parameters 391
reviewing all results 373
reviewing calibration standards 341
Run Sequence dialog box 75
Run Sequence parameters 78
Run Status page 97
Run Status shortcut menu commands 99
S
Sample Info parameters
Explore 172
Review 291
Sample Info shortcut menu commands
Explore 172
Review 291
Sample Information parameters 102
Sample Selector parameters 141
Sample Selector shortcut menu commands 141
sample types
blanks 417
quality controls (QCs) 417
standards 416
unknowns 416
Save As Wizard 21
saving workbook 408
scan filters, matching with components 208
Select Component parameters 251
Select Directory parameters 110
semi-quantitative analysis, definition 409
sequence
See acquisition sequence, processing sequence
sequence grid function buttons 36
Sequence Sorting Order parameters 319
shortcut menus
Acquisition Sequence History
Acquisition 38
Explore 137
Status 106
Calibration Curve 264
Calibration page 250
Chromatogram
Quantitate 267
Review 271
Chromatogram List 160
Chromatogram pane 91
Component list
Quantitate 249
Review 340
Error Report 283
Filter List 284
LCquan User Guide
451
Index: T
General Parameters Plot
Explore 164
Quantitate 286
Ion Ratio Confirmation area 202
IRC Chromatogram 277
Mass List
Explore 167
Quantitate 288
Multi Peak Plot
Explore 181
Quantitate 299
Peak List
Explore 168
Review 290
processing sequence grid 314
result grid 335
Run Status 99
Sample Info
Explore 172
Review 291
Sample Selector 141
Spectrum
Explore 173
Review 276
Spectrum pane 94
Status Plot
Explore 175
Review 294
Status Report
Explore 177
Review 296
Tune Method
Explore 179
Review 297
shortcuts, keyboard
Apps menu commands 427
File menu commands 428
Options menu commands 432
toolbar commands 440
View menu commands 435
shutdown methods 27
Sort Sequence parameters 61
Spectrum Display Options parameters 95
Spectrum pane shortcut menu commands 94
Spectrum pane, Status page 93
Spectrum parameters
Explore 173
Review 276
Spectrum shortcut menu commands
Explore 173
Review 276
standard samples, acquisition setup 32
452
LCquan User Guide
standards
described 412
external standards 414
internal standards
creating 254
overview 414
sample types 416
starting LCquan 13
startup methods, defined 27
Status page 83
Status Plot parameters
Explore 174
Review 293
Status Plot shortcut menu commands
Explore 175
Review 294
status plots, Explore window 174
Status Report parameters
Explore 176
Review 295
Status Report shortcut menu commands
Explore 177
Review 296
status reports, Explore window 176
study
creating 13
description 7
Summing Ions dialog box 203
survey link xi
Survey page 333
Switching to Processing during Acquisition parameters 108
T
Target Compound area 245
Target Compound area parameters 246
time stamps
always time-stamp raw files during remote acquisition
112
never time-stamp raw files during remote acquisition
112
toolbar buttons 440
toolbar buttons for zooming 334
trace type
base peak 195, 356
mass range 195, 356
summed 195, 356
TIC 195, 356
Tune Method parameters
Explore 178
Review 297
Thermo Scientific
Index: U
Tune Method shortcut menu commands
Explore 179
Review 297
U
unknowns
acquisition setup 32
overview 416
unknowns, reviewing 374
upper quantitation limit 413
User Identification Settings
Avalon Integration parameters 368
Detection parameters 358
Genesis Advanced parameters 363
ICIS Advanced parameters 367
ICIS Integration parameters 364
Identification parameters 355
user identification settings
advanced parameters 355
Avalon, integration 368
detection 358
Genesis
advanced parameters 362
integration 371
ICIS
advanced parameters 371
integration 364
user labels, setting 104
W
Web Access
flow diagram 421
LCquan for 11
Wizards
New Acquisition Sequence 40
New Method 184
New Processing Sequence 304
New Study or Workbook 14
Save As 21
Workbook Summary Information parameters 26
workbooks
creating 13
description 7
locking 405
locking automatically after creating reports 406
not locking automatically after creating reports 407
saving 408
Z
Zoom menu commands 438
zooming
in Chromatogram pane 86
in Spectrum pane 94
toolbar buttons 334
V
validation, Web Access 11
variables
quantitation with internal standards 415
separation by LC 410
View menu commands 435
Thermo Scientific
LCquan User Guide
453
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