Xcalibur 2.2 Qualitative Analysis User Guide Version D

Xcalibur 2.2 Qualitative Analysis User Guide Version D
Thermo Xcalibur
Qualitative Analysis
Version 2.2
User Guide
XCALI-97211 Revision D
May 2011
© 2011 Thermo Fisher Scientific Inc. All rights reserved.
Xcalibur, Surveyor, and Accela are registered trademarks and LCQ and LCquan are trademarks of Thermo
Fisher Scientific Inc. in the United States.
Microsoft, Windows, Windows Vista, and Excel are registered trademarks of Microsoft Corporation in the
United States and other countries. Adobe, Acrobat, and Reader are registered trademarks of Adobe Systems
Incorporated in the United States and other countries.
The following are registered trademarks in the United States and possibly other countries:
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, January 2009; Revision B, September 2010; Revision C, January 2011 (to reflect
Microsoft Windows 7 compatibility); Revision D, May 2011
Software version: Thermo Xcalibur version 2.2
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
About This Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Understanding Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Ionization Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Adduct Formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Effect of Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Analysis Modes of the Xcalibur Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Full Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Selected Ion Monitoring (SIM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
MS/MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 2
Using the Qual Browser Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Using the Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Displaying Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Customizing the Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Using the Info Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Working with Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Using the Cursor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Viewing Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Opening Single Raw Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Viewing Sequence File Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Viewing Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Working with Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Making a Cell View Active . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Creating and Deleting Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Adjusting Cell Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Amplifying Regions of a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Adding Text to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Adding Graphics to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Removing Text and Graphics from a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Opening or Changing Views in Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
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Scaling a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Managing Layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Creating and Saving a Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Opening a Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Applying a Layout to the Active Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Displaying Layout Summary Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Using the Cell Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Chromatogram Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Spectrum Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
iv
Chapter 3
Using Views Interactively . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Selecting a Point on a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Selecting a One-Dimensional Range on a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . 43
Selecting a Two-Dimensional Range on a Plot . . . . . . . . . . . . . . . . . . . . . . . . . 47
Using Scan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Scan Filter Format. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Applying a Scan Filter to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Expanding Regions in the Same Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Chapter 4
Using a Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Using Chromatogram Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Setting Up Chromatogram Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Setting Chromatogram Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Setting Automatic Processing Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Using the AutoFilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Setting Chromatogram Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Setting the Chromatogram Axis Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Setting the Chromatogram Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Setting the Chromatogram Label Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Setting the Chromatogram Normalization Options. . . . . . . . . . . . . . . . . . . . 69
Setting the Chromatogram Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Detecting Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Automatic Detection of One Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Automatic Detection of All Plots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Manual Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Changing Peak Detection Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Chapter 5
Using a Map View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Setting Map Ranges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Setting Map Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Setting the Map Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Setting the Map Axis Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Setting the Map Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Setting the Map Normalization Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Qualitative Analysis User Guide
Thermo Scientific
Contents
Setting the Band Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 6
Setting Spectrum Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Setting Spectrum Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Setting the Spectrum Axis Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Setting the Spectrum Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Setting the Spectrum Label Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Setting the Spectrum Normalization Options . . . . . . . . . . . . . . . . . . . . . . . . 89
Setting the Spectrum Style Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Setting Spectrum List Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Setting the Spectrum List Normalization Options . . . . . . . . . . . . . . . . . . . . . 92
Setting the Spectrum List Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Setting Up Spectrum Plot Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Setting Spectrum Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Setting Spectrum Automatic Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Specifying Spectrum Composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Subtracting Background Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Appendix A Qual Browser Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101
Qual Browser Menus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Actions Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Display Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Grid Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Window Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Qual Browser Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Qual Browser Amplify Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Qual Browser Main Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Qual Browser Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Error Log View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Instrument Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Ion Map View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Map View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Result File Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Sample Information View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Scan Filter View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Scan Header View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Spectrum List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
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Status Log View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Tune Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Qual Browser Info Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Cell Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Elemental Composition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
MSn Browser Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Avalon Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
ICIS Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Genesis Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Result File Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Sequence Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Spectrum Simulation Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Qual Browser Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Add Graphics Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Add Programs To Tool Menu Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . 200
Add Text Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Add Tool Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Amplify by Other Factor Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Average Filter Selection Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Cell Size Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
Choose Centroiding Algorithm Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . 210
Color Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Copy to Clipboard Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Display Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Global Mass Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
Heading Editor Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
Library Search Constraints Page (Qual View) . . . . . . . . . . . . . . . . . . . . . . . 244
Peak Purity Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Print Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Ranges Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Select Isotopes Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Specify Mixture for Simulation Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 278
Subtract Background Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Toolbars Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .281
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Qualitative Analysis User Guide
Thermo Scientific
P
Preface
This user guide for qualitative analysis describes how to use the Thermo™ Xcalibur™ mass
spectrometry data system to identify unknown compounds or carry out a trace analysis.
Before reading this manual, read the Getting Started manual for the Xcalibur data system and
the Getting Started manual for the instrument so that you are familiar with the basic features
of the Xcalibur application, such as the Home Page and Instrument Setup.
Contents
• About This Guide
• Related Documentation
• Safety and Special Notices
• Contacting Us
To provide us with comments about this document, click the link below. Thank you in
advance for your help.
About This Guide
This guide describes how to do the following:
• Set up a method for automatic qualitative processing.
• Create a sequence or batch of samples for analysis and processing under full software
control.
• Get the best out of the data using qualitative reviewing utilities in the Xcalibur data
system.
• Submit spectra to library searches.
For information about setting up personal user libraries of reference spectra, refer to the
Creating and Using Libraries User Guide.
Thermo Scientific
Qualitative Analysis User Guide
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Preface
Related Documentation
Thermo Fisher Scientific provides these documents for the Xcalibur data system:
• Xcalibur Getting Started (Quantitative Analysis)
• Acquisition and Processing User Guide
• Quantitative Analysis User Guide
• Qualitative Analysis User Guide
• Creating and Searching Libraries User Guide
• XReport User Guide
• Help from within the software
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.
Safety and special notices include the following:
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
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Preface
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Introduction
This introduction provides a basic understanding of mass spectra and explains how to use
Thermo™ Xcalibur™, the Thermo Scientific mass spectrometry data system, for qualitative
analysis. Qualitative analysis is concerned with solving two analysis problems:
• The identification of unknown compounds
• Trace analysis and the confirmation of target compounds
Contents
• Understanding Spectra
• Analysis Modes of the Xcalibur Data System
Understanding Spectra
There are many different types of mass spectrometry (MS) detectors but the basic principles
are the same in all cases: the MS ionizes the sample, separates the ions according to their
mass1, and moves the separated ions towards a detector where they are counted. The data
system compiles a spectrum showing the mass distribution of the ions produced from the
sample—a snapshot of ion intensities plotted against their mass1.
Ionization initially produces molecular ions, but complex secondary processes can cause the
molecular ions to fragment. Together with molecular ions, these fragment ions make up the
mass spectrum. For individual substances, a mass spectrum can be a characteristic molecular
fingerprint.
In standard practice, the most abundant ion, called the base peak, is given an arbitrary
abundance or intensity of 100. The Xcalibur data system reports all other peaks as a
percentage of the size of the base peak. After this normalization, the Xcalibur application can
compare spectra directly.
1
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Strictly, this should be mass-to-charge ratio (m/z), but in the majority of cases z=1 and the X-axis becomes
equivalent to mass, m.
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Introduction
Understanding Spectra
Figure 1 is an example of a simple library spectrum showing the fragmentation of acetone
C3H6O (molecular weight = 58 u) in an EI ion source. The most abundant ions have been
labeled with their mass-to-charge ratios. In this example, the molecular ion (58 u) is not the
most abundant. The base peak is actually 43 u because of the acetyl ion.
Figure 1.
70 eV electron ionization (EI) mass spectrum of acetone
You can use fragmentation patterns like the pattern in the figure above to determine
molecular structure. For example, the neutral loss of 15 u from the molecular ion of acetone
indicates the presence of a methyl group in the original molecule. A subsequent loss of 28 u
corresponds to the loss of CO. Commonly observed neutral losses, measured by the molecular
weight of the compound, are listed in Table 1. Assign such losses to help deduce the structure
of an unknown compound. A full structural analysis generally relies on the presence of a
molecular ion and the measurement of the molecular weight of the compound.
Table 1. Common neutral losses (Sheet 1 of 2)
2
Loss
Fragment
15
CH3
18
H2O
19
F
28
CO
29
C2H5 or CHO
35
Cl
46
NO2
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1 Introduction
Understanding Spectra
Table 1. Common neutral losses (Sheet 2 of 2)
Loss
Fragment
59
C3H7O, COOCH3 or CH2COOH
77
C6H5
In some cases, fragmentation is extensive, leaving little or no trace of a molecular ion. With no
molecular ion, determining either the molecular weight or the structure is difficult.
Ionization Modes
Select an ionization mode that supports the type of instrument used: liquid chromatography
mass spectrometers (LC/MS) or gas chromatography mass spectrometers (GC/MS). This
mode can affect the spectrum characteristics of a compound.
This section contains the following sections:
• Ionization Modes for LC/MS Instruments
• Ionization Modes for GC/MS Instruments
Ionization Modes for LC/MS Instruments
LC/MS instruments use a variety of techniques, collectively called atmospheric pressure
ionization (API). Detectors of this type can be configured to detect positive or negative ions.
API techniques offer soft ionization, usually with little or no fragmentation. An API spectrum
typically contains only the protonated or deprotonated molecular ion. Compounds with basic
sites (such as amines) can form protonated molecules. These can be analyzed in positive ion
detection modes, giving a quasi-molecular ion peak at m/z M+1 (where M represents the
molecular weight of the compound).
Compounds with acidic sites (sulphonic acids, for example) can form deprotonated molecules
[M-H]-. These can be analyzed in negative ion modes as quasi-molecular ion peaks at
m/z M-1.
Ionization Modes for GC/MS Instruments
GC/MS instruments offer two techniques: electron ionization (EI) and chemical
ionization (CI).
EI is very commonly used because it is simple and reproducible. The fragmentation pattern is
effectively determined by the energy of the impacting electrons alone (electron energy,
measured in eV). Very different types of mass spectrometers with EI can produce virtually
identical spectra as long as the electron energy is the same.
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Introduction
Understanding Spectra
This reproducibility has led to an extensive library compilation for 70 eV EI spectra. With the
Xcalibur Library Browser, you can access the optional NIST/EPA/NIH Mass Spectral Library
with over 108000 reference EI spectra. You can use library data to select confirmatory ions for
your target compounds.
Chemical ionization (CI) offers a softer method of forming ions. In CI, a controlled flow of a
reagent gas, commonly ammonia, methane, or isobutane, is introduced into the area where
ionization occurs (the ion source). Energetic electrons that pass through the source ionize the
reagent gas, as in EI. These ions can then collide with neutral molecules, causing hydrogen
transfer. This process is repeated when the reagent gas ions collide with analyte molecules.
CI usually produces protonated molecules, generally at a mass one unit greater than the
molecular mass of the compound. Significantly less fragmentation occurs than in comparable
EI spectra. Depending on the choice of reagent gas, adduct ions can form. For example,
M+NH4 is a typical adduct ion when ammonia is used as the reagent gas.
Under certain conditions, CI produces negative molecular ions formed by electron capture.
The sensitivity of negative ion CI for certain classes of compounds (those containing double
bonds, sulfur, phosphorus, chlorine, or bromine) can be orders of magnitude greater than
positive CI or EI modes for those compounds.
For more information about the ionization modes available on your instrument, read the
hardware manual and the instrument manual on how to get started.
Adduct Formation
If ionization takes place in the presence of contaminants or additives such as ammonium or
sodium ions, some compounds are susceptible to adduct formation. These spectra show other
ions in addition to, or instead of, the molecular ion (see Figure 2). Here are two common
adducts:
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Qualitative Analysis User Guide
[M+18]+ NH4+
[M+23]+ Na+
[M+39]+K+
[M+42]+ ACN+H+
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1 Introduction
Analysis Modes of the Xcalibur Data System
Figure 2.
Mass spectrum showing sodium and acetonitrile adducts
Take care when determining molecular weights to account for possible adduct ions.
Effect of Isotopes
In some cases, the effect of less abundant isotopes might cause you to use an average molecular
weight rather than one based on the most abundant isotopes. When the molecular structure
of the target compound contains large numbers of certain elements, the less abundant
isotopes become significant. This situation might result in a shift in the mass peaks from their
expected m/z values.
For example, the most abundant isotope of chlorine is Cl35. However, Cl37 occurs with a
natural abundance of 24.47 percent. If a compound contains four chlorine atoms, its
molecular ion is two mass units greater than that expected from a calculation based solely on
Cl35. Using chlorine’s average atomic weight (35.453), the molecular ion is correctly
identified. Also, you observe a distribution of molecular ions across eight mass units from
molecules containing between zero and four Cl37 atoms.
Analysis Modes of the Xcalibur Data System
The Xcalibur application has these analysis modes:
• Full Scan
• Selected Ion Monitoring (SIM)
• MS/MS
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Analysis Modes of the Xcalibur Data System
Full Scan
In full-scan operation, the MS detector scans repetitively over a wide mass range and records
successive full spectra throughout the analysis.
Display full-scan information in several ways:
• A Total Ion Current (TIC) chromatogram represents the summed intensities of all the
ions in each spectrum plotted against chromatographic retention time. Each peak in the
TIC represents an eluting compound, which can be identified from the mass scans
recorded during its elution.
• Mass chromatograms show the ion intensities of selected mass-to-charge ratios (m/z). the
Xcalibur system extracts these from each stored scan and plots them against retention
time. Use this technique to increase selectivity by displaying an m/z value characteristic of
the compound of interest but not present in other sample components.
Full-scan mode is suited to the identification of unknowns and can also be used for trace
analysis when sensitivity is not important.
Selected Ion Monitoring (SIM)
In SIM mode, configure the MS detector to monitor a limited number of m/z values,
characteristic of a targeted compound or compounds. The mass analyzer switches between the
selected m/z values, each value being monitored repeatedly for a programmed dwell time
before averaging and moving on to the next.
SIM generates mass chromatograms only of the monitored m/z values, not complete mass
spectra as in full-scan operation. Without a complete spectrum, you cannot perform a library
search to identify an unknown.
Selected ion monitoring (SIM) is ideally suited to trace analysis and offers reduced file sizes
compared to full-scan operation because SIM records only the information of interest.
MS/MS
Depending on your instrument, you might also be able to do additional stages of mass
analysis called MS/MS.
In MS/MS, an ion from the mass spectrum is selected for fragmentation while all other masses
are discarded. The selected ion, called a parent ion, is then collided with a neutral background
gas. As a result of the collisions, the parent ion is broken into fragments called product ions.
The product ions with either full-scan or SIM analysis. MS/MS with SIM is called SRM or
selective reaction monitoring. In an ion trap, additional stages of MS (called MSn) can be
performed, up to MS10.
You can create your own libraries of full-scan MSMS data to use for matching.
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Using the Qual Browser Window
Thermo Xcalibur Qual Browser is a powerful and versatile utility for viewing chromatograms
and spectra from raw files or qualitative processing results. Use Qual Browser to view and
manipulate data from single or multiple files in any number of separate data windows (see
Figure 3). The MSn tab is not displayed with all instruments. You can open a raw or result file,
display chromatograms, spectra, and maps of the data, choose spectra from chromatograms,
average scans, subtract background data, create and save layouts, add text and graphics, apply
filters, amplify regions, and print the resulting graphic.
Figure 3.
Qual Browser window
Info
buttons
Pin
Info
pages
Previews
Cell
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Using the Qual Browser Window
In Qual Browser you can do any of these tasks:
• Generate a variety of chromatogram plots and determine suitable peak detection
parameters for subsequent automated analysis using a processing method.
• Optimize a chromatogram peak’s spectrum by averaging scans across its apex and
subtracting other scans averaged from the baseline on either side of the peak.
• Determine the elemental composition of the peaks in the spectrum.
• Simulate the isotopic distribution mass spectrum of a single compound or mixture of
compounds.
• Export a spectrum to the Library Browser to create and maintain user libraries.
• Submit the spectrum of an unknown compound to a library search (if a suitable reference
library is present).
• Print a report showing data analysis and library results.
To open Qual Browser, click Qual Browser on the Home Page Road Map view. In other
Xcalibur programs, access Qual Browser by choosing the relevant View menu command.
Contents
• Using the Toolbar
• Using the Info Bar
• Working with Windows
• Using the Cursor
• Viewing Data Files
• Working with Cells
• Managing Layouts
• Using the Cell Information Page
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Using the Qual Browser Window
Using the Toolbar
Using the Toolbar
Use the buttons on the toolbar to rescale a chromatogram or spectrum preview. The Zoom
menu contains equivalent commands. You can also access these commands in a shortcut
menu by right-clicking the appropriate preview. To rescale the chromatogram, use the cursor
(see Table 2).
The buttons on the toolbar are divided into two groups:
Main
Provides tools for loading, saving or printing files, scaling plots,
manipulating cells, peak detection, changing views, and arranging data
windows.
Amplify
Provides tools for adjusting the normalization in specific sections of a
chromatogram, spectrum, or map plot.
By default these two toolbar groups are positioned along the top of the Qual Browser window,
just beneath the menu bar. Drag them anywhere within the window or dock them along any
of the other window edges.
Qual Browser is equipped with a large number of tools. You can view or hide toolbars in the
Toolbars dialog box (see Figure 4). Choose View > Toolbars and select tool groups as
required. Also, use the Toolbars dialog box for these tasks:
• Viewing or hiding the display of ToolTips
• Choosing between large or small buttons on the toolbar
Figure 4.
Thermo Scientific
Toolbars dialog box
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Using the Qual Browser Window
Using the Toolbar
Displaying Toolbars
 To display or hide the toolbars
1. Choose View > Toolbars. The Toolbars Dialog Box opens.
2. To display a toolbar, select its check box. To hide the toolbar, clear its check box.
3. To display ToolTips, select the Show ToolTips check box. To hide ToolTips, clear the
ToolTips check box.
4. Select a button size option.
• To display large buttons on the toolbar, select the Large Buttons check box.
• To display small buttons on the toolbar, clear the Large Buttons check box.
5. To save the settings and close the dialog box, click OK.
Customizing the Toolbar
You can add application programs to and remove application programs from the Tools menu.
Application programs have an .exe extension. You can then launch any added program by
double-clicking the added Tool menu command.
• Adding a Tool Button
• Removing or Repositioning a Tool Button
 To add or remove buttons on the toolbar on the Main toolbar
Choose View > Customize Toolbars. The Customize Toolbar dialog box opens
(Figure 5).
Figure 5.
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Customize Toolbar dialog box
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Using the Qual Browser Window
Using the Toolbar
Adding a Tool Button
 To add a button to the tool menu
1. Choose Tools > Add Tools from the Qual Browser window or Home Page window. The
Add Programs to Tool Menu dialog box opens.
2. Click Add. The Add Tool Dialog Box opens.
3. To specify the tool to add, click Browse to select the path and filename of the tool, or
type the path and filename of the tool you want to add in the Locate Programs to be
Added dialog box.
4. To store the path and filename of the tool and close the Add Tool dialog box, click OK.
The Add Programs to Tool Menu dialog box stays open.
The Xcalibur data system adds the filename without the extension at the bottom of the
Menu Contents box and the Menu Text box.
The Xcalibur data system also adds the path and filename in the Programs box and the
directory path in the Initial Directory box.
The Menu Contents box displays the tool commands exactly as the Xcalibur application
displays them in the Tools menu.
5. To edit tool menu entries, select one of these options:
• To change the command name of a tool listed in the Menu Contents box, select the
tool and edit the text in the Menu Text box.
• To change the tool sequence in the Tools menu, select the tool in the Menu Contents
box and click Move Up or Move Down.
6. When the tools in the Menu Contents box are correct, click Close to save settings and
close the dialog box. The data system displays the current selection of added tools at the
bottom of the Tools menu.
Removing or Repositioning a Tool Button
 To remove a button from the Tool menu
1. Choose Tools > Add Tools from the Qual Browser window or Home Page window. The
Add Programs To Tool Menu Dialog Box opens.
2. To select a tool to remove, click the tool in the Menu Contents box. The Xcalibur data
system highlights your selection.
3. Click Remove.
4. To store your changes, click Close. The Add Programs to Tool Menu dialog box closes.
The data system displays the current selection of added tools at the bottom of the Tools
menu.
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Using the Qual Browser Window
Using the Info Bar
 To reposition a button on the toolbar in the Main toolbar
1. Open the Customize Toolbar dialog box.
2. Drag the button in the Main toolbar to its new position.
The button moves to its new position.
Note Use this technique to group buttons together and to put a space between
groups: to close up a space, drag a button to the left; to open up a space, drag to the
right.
Using the Info Bar
The Info Bar initially is located on the left side of the Qual Browser window. See Figure 3.
To show or hide the Info Bar, click
on the main toolbar or choose View > Info Bar.
The Info Bar has seven tabs. Each tab displays a separate function on a separate page:
12
Cell Information
View details of the plots contained in the active cell.
Sequence Information
View the raw files available from an open sequence.
Result File Information
View peak data from a result file.
Elemental Composition
Calculate the best matching chemical formula for a mass or a list of masses
from a spectrum.
Spectrum Simulation
Create a simulated isotopic distribution spectrum of a chemical formula.
Detection Tab
Set peak parameters and advanced noise methods. The letter in the upper
left corner of the tab indicates which algorithm (ICIS, Avalon, or Genesis) is
currently selected. This button appears when you turn on peak detection.
MSn Browser Information
View MSn experimental data for analysis. This button appears when you
open a raw file.
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Using the Qual Browser Window
Working with Windows
Working with Windows
Qual Browser’s main window displays raw files, interactive library search results, and
qualitative processing. View raw files in the same or separate windows. Use these Window
commands to arrange data windows within Qual Browser:
Cascade
Arrange windows diagonally so they overlap.
Tile
Arrange windows as non-overlapping tiles.
Each window can be subdivided into a grid of cells, each cell displaying a view. A view can be
a chromatogram, spectrum, mass map, spectrum list, scan header, scan filter list, tune
method, experiment method, sample information, status log, or error log. Chromatogram and
spectrum views can contain up to eight plots.
The arrangement of cells within a window is termed a layout. Save layouts to disk for
future use. For more information, see “Managing Layouts” on page 32.
You can apply various automatic processing options as follows:
In a chromatogram view
In a spectrum view
Smoothing to all plots in the cell
Smoothing
Peak detection to the active plot in the
current cell or all plots in the current cell
Refine enhancement
When you pin a cell, you designate it as the target for operations performed in other cells. For
operations involving the use of menu commands or buttons on the toolbar, pinning is not
necessary, but the target cell must be active. If no cell is pinned, the active cell is the last cell
acted on by a mouse action and is identified by a gray border.
If you have not pinned a cell, the last selected cell is active. The Xcalibur application shades its
unpinned icon and places a gray border around the cell to indicate the active status. To place a
cell in the active state, click its pin icon:
Pin icon for an unpinned cell: not active
Pin icon for a pinned cell: active status
With chromatogram or spectrum views containing more than one plot, any menu operations
target the active plot, indicated by a shaded background. To select an individual plot in a
multi-plot cell, click it.
For more information about cells, views, and pinning, see “Using Views Interactively” on
page 39.
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Using the Qual Browser Window
Using the Cursor
Using the Cursor
Within the Chromatogram and Spectrum previews, use the cursor in three ways:
• To select a point on the preview, click the point.
• To select a range, drag a line parallel to any axis.
• To select an area, drag a line in any diagonal direction.
The effect of these actions depends on the state of the preview:
• Active and pinned
(each preview has a pin icon in its top right corner)
• Active and unpinned
• Inactive (another preview is active)
Only one of the previews can be active at any one time. The Xcalibur system highlights the
active preview with a gray border. You can have an active view that is not pinned, but clicking
the cursor in a different view changes the active view. Pin the view to make it permanently
active until you pin a new view. If no other preview is pinned, click the preview to make it
active.
 To make a preview active
1. Make sure the current preview is not pinned. If it is, click the pin icon to unpin it.
2. Click anywhere in the preview that you want to make active. The data system highlights
it with a gray border. Click its pin icon to fix it as the active preview.
Cursor actions in an active preview cause the preview to be scaled according to the dimensions
of the dragged line or area (see Table 2).
Table 2. Cursor action in unpinned preview when no views are active (pinned)
Cursor action in active preview
Effect
Drag parallel to X-axis
Rescale graph showing selected X range only, same Y range.
Drag parallel to Y-axis
Rescale graph showing selected Y range only, same X range.
Drag diagonally over X- and Y-axes
Rescale graph showing both the selected X and Y ranges.
The same actions in the unpinned or inactive preview have a very different effect when there is
an active preview available. In this case, the cursor actions affect the active preview.
Within the graphic region of a chromatogram, spectrum or map view, the cursor becomes a
cross hair. The status bar at the bottom of the Qual Browser window shows the coordinates of
the cursor in appropriate units for the view. In a spectrum view, for example, the status bar
shows the cursor position in terms of mass (m/z) and intensity.
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Using the Qual Browser Window
Using the Cursor
The effect of these actions depends on the state of the cell. If it is pinned, the actions cause the
graph to be rescaled according to the dimensions of the dragged line or area (see Table 3).
Table 3. Cursor action in a pinned cell
Cursor action
Effect on view in pinned preview
Click
Makes the view active.
Drag parallel to X-axis
Rescales the graph showing selected X range only. The Y range might rescale depending
on the selected Normalization display options.
Drag parallel to Y-axis
Rescales the graph, showing selected Y range only, same X range.
Dragged area
Rescales the graph, showing selected ranges only.
The same actions in an unpinned cell have a very different effect. In this case, the action
affects the pinned cell (see Table 4). Qual Browser displays the pinned cell using data
appropriate to the selected point, range, or ranges.
Table 4. Cursor action in an unpinned cell
Pinned cell
View acted on
by the cursor
Spectrum
Chromatogram
Click retention time (RT) = 1.98 min Cell displays mass scan that occurs at
in the chromatogram view.
retention time = 1.98 min.
Status Log
Chromatogram
Click retention time (RT) = 3.16 min Cell displays status log at retention
in the chromatogram view.
time = 3.16 min.
Scan Filter
Chromatogram
Click retention time (RT) = 1.36 min Cell displays the scan filter used for
in the chromatogram view.
the scan that occurs at retention time
= 1.36 min.
Spectrum
Chromatogram
Drag the cursor across a peak of
interest.
Cell displays a spectrum that is the
average of all the scans recorded across
the peak within the selected range of
retention times.
Chromatogram
Spectrum
Drag the cursor from m/z 198.4
through 299.7.
Cell displays a mass chromatogram
consisting of masses 198.4 through
299.7.
Chromatogram
Map
Drag the cursor over an area enclosing Cell displays a mass chromatogram
the ranges 0.5 to 1.0 min and
consisting of masses 100 through 200
m/z 100 to 200.
with a time range of 0.5 to 1 min.
Cursor action
Effect on active view in the pinned cell
*No action occurs in the unpinned cell.
The preceding table illustrates only a few of the possible effects of Qual Browser’s interactivity.
To get expected results, remember these actions:
• Pin the target view to make it active.
• Within a pinned cell, use the cursor to rescale the view.
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Using the Qual Browser Window
Viewing Data Files
• Use the coordinates in the Status bar to select ranges precisely.
• To correct mistakes, choose Edit > Undo.
Viewing Data Files
View data files in Qual Browser by doing any of these procedures:
• Opening Single Raw Files. Raw files have a .raw file extension.
• Viewing Sequence File Information. Select one or more raw files from the Sequence
Information page of the Info Bar. Sequence files have an .sld file extension.
• Viewing Result File Information. Result files are the product of processing raw data files
with a processing method. Result files have an .rst file extension.
Opening Single Raw Files
 To open a single raw data file
1. Choose File > Open or click
opens (Figure 6).
Figure 6.
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in the toolbar. The Open Raw File dialog box
Open Raw File dialog box
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Using the Qual Browser Window
Viewing Data Files
2. Find the file.
3. Select a Replace option:
• To replace all the plots in the current window (in all cells) with plots of an equivalent
type from the selected raw file, select Window.
• To replace all plots in the current cell with plots of an equivalent type from the
selected file, select Cell.
• To replace the current plot with a plot of an equivalent type from the selected file,
select Plot.
4. Select an Add option:
• To open the selected raw file in a new window using the layout of the currently active
window, select Window. If no layout is available, Qual Browser applies the most
recently saved layout file or, if this is invalid, the default layout.
• To add the file as a plot in the active cell of the current window, select Plot.This
option is not available if the cell already contains the maximum number (8) of plots.
5. If you select the Add Window option, choose the layout to be applied to the new
window.
• To apply the most recently saved default layout, select Default Layout.
• To apply the layout of the currently active window to the new window, select
Current Layout. If no layout is available, Qual Browser applies the default layout.
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Using the Qual Browser Window
Viewing Data Files
Viewing Sequence File Information
 To open and view sequence file information
1. Choose File > Open Sequence or click
on the toolbar.
2. Click Browse to select a sequence file (.sld). The Xcalibur data system displays the
sequence on the Sequence Information page of the Info Bar (see Figure 7).
Figure 7.
Sequence Information page showing the shortcut menu
Sequence
Information
page
• Choose Open - Replace and select an option:
–
To open the selected file in the active window, replacing the plots in all cells with
equivalent spectra or chromatograms, select All in Current Window (or
double-click the file).
–
To replace all plots in the active cell with equivalent plots from the selected file,
select All in Current Cell.
–
To replace the current plot in the active window with an equivalent from the
selected file, select Current Plot.
• Choose Open - Add, and select an option:
–
To open the selected raw file in a new window, select New Window.
–
To open the selected file as a plot in the active cell, select New Plot.
• To open a result file associated with the selected raw file, select Open Result File.
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Viewing Data Files
• Select Properties. The Sample Properties dialog box opens (Figure 8), showing basic
information about the selected sample. This information includes the row, filename,
sample ID, name, sample type, and result filename.
Figure 8.
Sample Properties dialog box
The Sample Properties dialog box displays this information: the row, file name,
sample ID, sample name, and sample type of the current file and the name of the
result file.
The Sample Properties dialog box closes if you click outside of it. Click the pin icon to
keep the Sample Properties dialog box open. Click the close box icon to close the dialog
box or unpin the dialog box by clicking the pin icon again. Click anywhere outside the
dialog box to close it.
3. To change the view, select from these options:
• To replace the data in the current window, double-click the name of the file on the
Sequence List page of the Info Bar or right-click the name of the file and choose
Open - Replace > All In Current Window from the shortcut menu.
• To replace the data in the active cell, right-click the name of the file and choose
Open - Replace > All In Current Cell from the shortcut menu.
• To replace data in the active plot, right-click the name of the file and choose
Open - Replace > Current Plot from the shortcut menu.
• To open the file in a new window using the current layout, right-click the name of
the file and choose Open - Add > New Window from the shortcut menu.
• To open the file as a new plot in the active cell, right-click the name of the file and
choose Open - Add > New Plot from the shortcut menu.
Using the Sequence Information Page
 To view sequence information
1. Double-click any sample file in the sequence to open it in the active window and replace
the plots in all cells with equivalent spectra, chromatograms, or maps.
2. Right-click any file within the sequence. The Sequence shortcut menu opens.
3. In the shortcut menu, select an option.
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Using the Qual Browser Window
Viewing Data Files
Viewing Results
The Xcalibur data reviewing component is called Results Review (see Figure 9). This is
organized into three core browsers:
Figure 9.
Results Review section of the Xcalibur Home Page
Qual Browser
Displays and manipulates chromatograms and spectra, activates library
searches, and produces reports.
Quan Browser
Displays a peak list or calibration curve to be manipulated. For more
information about performing quantitative analysis, go to the
Quantitative Analysis User Guide.
Library Browser
Activates the NIST Mass Spectral Search Program to match spectra to
library entries. Also used to generate user libraries. For more
information about using libraries to search for spectra, go to the
Creating and Searching Libraries User Guide.
Viewing Result File Information
A result file contains the list of detected peaks from the chromatogram and the qualitative
processing results associated with each peak. Qual Browser displays the result file in a fixed,
two-cell arrangement (see Figure 10). This dialog shows a chromatogram plot in the upper
cell, with the detected peaks highlighted and the spectrum associated with the currently
selected chromatogram peak in the lower cell. For more information about using
chromatogram and spectrum views, see “Using a Chromatogram View” on page 57 and
“Setting Spectrum Options” on page 85, respectively.
 To view result file information
on the toolbar or choose File > Open Result File. The Open Result file dialog
1. Click
box opens.
2. To select a result file (.rst), click Browse.
3. Click Open.
To open a result file for a file in an opened sequence, right-click the filename on the
Sequence List page of the Info Bar and choose Open Result File from the shortcut menu.
Note If no result file exists for the selected file, the Xcalibur application grays the
menu command.
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Using the Qual Browser Window
Viewing Data Files
Figure 10. Result File view showing the Result File Information page in the Info Bar
Chromatogram
view
Spectrum
view
Information page
The Xcalibur data system displays library search results for the displayed spectrum in a
separate library search results window. For more information about searching libraries and
interpreting library search results, refer to the Creating and Searching Libraries User Guide.
It is not possible to submit the spectrum from the results display to a library search. If a
library search has been carried out during processing (when the result file was created),
search results are stored in the result file and displayed for each detected peak. To submit
a spectrum to a library search or to export a spectrum to the Library Browser, open the
raw file.
Note Many of the features in Qual Browser are not available for use with a result file
because the raw file is not directly available for processing.
4. To view Result File information, see the Result File Information page in the Info Bar.
This page shows basic information about all detected peaks in the result file, including:
• Retention times at the peak start (left), peak apex, and peak end (right)
• The peak area and height
For more detailed information about the peak, including flags, open the Peak Properties
dialog box.
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Using the Qual Browser Window
Working with Cells
 To open the Peak Properties dialog box
1. Right-click the peak identifier in the Peak List.
2. Choose Peak Properties from the shortcut menu. The Peak Properties dialog box
opens (Figure 11).
Figure 11. Peak Properties dialog box
The Peak Properties dialog box closes if you click outside of it. Click the pin icon to keep
the Properties dialog box open. Click the Close box icon to close the dialog box or unpin
the dialog box (by clicking the pin icon again) and click anywhere outside the dialog box.
Working with Cells
Qual Browser displays chromatograms and spectra in a grid of cells. This section describes the
commands used to manipulate cells and contains these topics:
• Making a Cell View Active
• Creating and Deleting Cells
• Adjusting Cell Size
• Amplifying Regions of a Plot
• Adding Text to a Plot
• Adding Graphics to a Plot
• Removing Text and Graphics from a Plot
• Opening or Changing Views in Cells
• Scaling a Plot
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Working with Cells
Making a Cell View Active
The active cell contains the active view. There can only be one active view at a time.
 To select the current view
1. To make a view active, click the pin icon of the cell containing the view.
The Xcalibur application changes the pin icon from
active cell and therefore the active view.
to
to indicate that it is the
All other cells contain inactive cells, as indicated by their pin icons
.
2. To make a plot active, click the plot within the view.
To show the plot is active, the data system shades the background of the plot.
Creating and Deleting Cells
When a raw file is open, Qual Browser displays one or more cells according to the selected
layout.
 To create a new cell
1. To select the active cell, click the pin of the cell adjacent to the cell or cells you want to
create.
• The Xcalibur application changes the cell pin icon from
active cell.
to
in the single
• The application displays all of the other inactive cells with this icon:
.
2. To add additional cells, select from these options:
on the toolbar or
• To insert a duplicate cell to the left of the active cell, click
choose Grid > Insert Cells > Left. If the active cell is in a column of cells, the
application inserts a duplicate column of cells to the left of the column containing the
active cell.
• To insert a duplicate cell to the right of the active cell, click
on the toolbar or
choose Grid > Insert Cells > Right. If the active cell is in a column of cells, the
application inserts a duplicate column of cells to the right of the column containing
the active cell.
• To insert a duplicate row of cells above the row containing the active cell, click
on the toolbar or choose Grid > Insert Cells > Above. If the active cell is in a row of
cells, the application inserts a duplicate row of cells above the row containing the
active cell.
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Working with Cells
• To insert a duplicate row of cells below the row containing the active cell, click
on the toolbar or choose Grid > Insert Cells > Below. If the active cell is in a row of
cells, the application inserts a duplicate row of cells below the row containing the
active cell.
Note When you add cells, the Xcalibur data system creates duplicate cells that
contain the same view as the active cell. As you add additional cells, the cell size of all
cells becomes smaller. the data system might not be able to include all header
information in views that are opened in small cells.
 To delete one or more cells
1. Click the pin icon of the cell in the same row or column of the cell or cells you want to
delete to make it active. To delete all of the cells but one, click the pin icon of the cell that
you want to keep.
2. Select from these options:
• To delete the row of cells that includes the active cell, click
choose Grid > Delete > Row.
• To delete the column of cells that includes the active cell, click
choose Grid > Delete > Column.
• To delete all cells except the active cell, click
Grid > Delete > All Cells.
on the toolbar or
on the toolbar or
on the toolbar or choose
Note As you delete excess cells, the cell size of the remaining cells becomes larger.
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Working with Cells
Adjusting Cell Size
 To adjust the cell size
1. To activate a cell in the Qual Browser window so that you can adjust its size, click the pin
in the upper right corner of the cell.
2. Choose Grid > Cell Size. The Cell Size Dialog Box opens (Figure 12). You must have at
least two cells in the grid.
Figure 12. Cell Size dialog box
3. To specify the column width, drag the Column width scroll box or click the scroll box left
and right arrows until you reach the desired width within the range 5 to 300%. The
current width is displayed below the scroll box.
Note The Cell Size dialog box is not available if the grid contains a single cell. The
Column control has no effect if the view contains a single column. Similarly, the Row
Height control has no effect in a grid containing a single row.
4. To specify the row height, drag the Row height scroll box or click the scroll box left and
right arrows until you reach the desired height within the range of 5 to 300%. The
current height is displayed below the scroll box.
5. To save the settings and close the dialog box, click OK.
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Using the Qual Browser Window
Working with Cells
Amplifying Regions of a Plot
You can use Qual Browser to open a raw file and display chromatograms, spectra, and maps.
Then, you can use the Xcalibur toolbar buttons or menu commands to amplify selected
regions.
 To amplify regions of a graph
1. To specify the amplification factor required, select from the following options:
• Select an amplify factor from the Amplify Factor combo box on the Amplify toolbar.
If the value you want is not in the list, type your required factor into the combo box.
Click
in the toolbar. The data system changes the cursor to
.
• Choose Display > Amplify > Other Factor to open the Other Factor dialog box.
Enter a value in the Amplification Factor text box and click OK. The Xcalibur
application changes the cursor to
.
2. To specify the region to amplify, drag the cursor horizontally over the region that you
want to amplify. the Xcalibur application amplifies the region, places a label above the
amplified region like the following: ------x5------, and displays the original cursor.
Adding Text to a Plot
You can add text to your chromatogram, spectrum or map plots. Text orientation options are
horizontal or vertical. Multiple lines can be aligned to the left, center, or right.
Your annotation text can be placed anywhere on the plot using the
marked position.
cursor to point to the
To change the style, color, label, axis, or normalization of a plot, use the Display Options
Dialog Box.
 To add text to a spectrum, chromatogram, or map plot
1. Determine what annotation text needs to be added and how you want it to be positioned
on the plot.
2. To open the Add Text Dialog Box, choose Display > Annotate > Add Text or click
on the toolbar.
3. Type one or more lines of annotation text in the Annotation Text text box.
Use the <Enter> key to enter multiple lines.
4. Use one of the following options in the Multiple Lines Aligned group box to determine
the multiple line alignment of text when it appears on the plot:
• To align lines to the left (left justification), choose the Left option button.
• To align lines in the center (center justification), choose the Center option button.
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Working with Cells
• To align lines to the right (right justification), choose the Right option button.
The application does not display the text alignment in the Annotation Text text box.
5. Use one of the following options in the Height Drawn group box to determine the
vertical alignment of text when it appears on the plot:
• To place the text slightly above a peak, choose the Just Above Graph option button.
• To place the text above where you position the cursor pointer on the plot, choose the
Above Marked Position option button.
• To place the text below where you position the cursor pointer on the plot, choose the
Below Marked Position option button.
6. Use one of the following options in the Marked Position Is group box to determine the
left/center/right alignment where the text is placed relative to the marked position:
• To place the text to the left of the cursor pointer position on the graph, choose the
Left option button.
• To place the text in the center of the cursor pointer position on the graph, choose the
Center option button.
• To place the text to the right of the cursor pointer position on the graph, choose the
Right option button.
7. To save settings and close the Add Text dialog box, click OK.
The data system closes the Add Text dialog box and changes the cursor.
8. Place the cursor at the position of the plot where you want your annotation text to appear
and click. The data system adds your text and changes the cursor back to your default
cursor.
Note You cannot move the text after it is placed.
If the text is not where you want it, immediately choose Edit > Undo or click
to
remove the text. Then, repeat step 8 of the procedure. The Xcalibur application saves
your previous text and settings.
Adding Graphics to a Plot
You can add graphics to a plot. Graphics include horizontal lines, vertical lines, diagonal lines,
boxes, and filled boxes. You can also select the color of all added lines and fills. Filled boxes
can either appear behind a plot or in front of a plot.
To change the style, color, label, axis, or normalization of a plot, use the Display Options
Dialog Box.
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Working with Cells
 To add graphics to a view
1. Determine what annotation graphic needs to be added and how you want the graphic to
be positioned on the plot.
2. Click
on the toolbar or choose Display > Annotate > Add Graphics. The Add
Graphics Dialog Box opens.
3. To specify the style of the graphic to be added, select one of the following options:
• To add a horizontal line, choose the Horizontal Line option. Go to step 4.
• To add a vertical line, choose the Vertical Line option. Go to step 4.
• To add a diagonal line, choose the Diagonal Line option. Go to step 4.
• To add a rectangular box, choose the Box option. Go to step 4.
• To add a filled box, choose the Filled Box option button. If the filled box is to be
displayed behind a plot, select the Behind Graph check box. If the filled box is to be
displayed in front of (on top of ) a graph, clear the Behind Graph check box. The
following filled boxes use a black line color for the box outline and a brown fill and
demonstrate the use of the Behind Graph check box feature. Go to step 5.
Behind graph
Not behind graph
4. To specify the line color, click Line and select a different color. Go to step 6. The current
line color is displayed to the right of the Line button in the Colors group box.
5. To specify the fill color, click Fill and select a different color. Go to step 6. The current fill
color is displayed to the right of the Fill button in the Colors group box.
6. To close the Add Graphics dialog box, click OK so that you can draw the graphic on the
plot.
7. Select one of the following graphic options:
• To draw a horizontal line, drag the cursor on the plot. You can drag from right-to-left
or from left-to-right.
• To draw a vertical line, drag the cursor on the plot. You can drag from bottom-to-top
or from top-to-bottom.
• To draw a diagonal line, drag the cursor on the plot. You can drag from left-to-right
or from right-to-left. You can move the cursor before you release the mouse button to
position the angle of the line.
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Working with Cells
• To draw a box, start at any corner of the box and then drag the cursor to the opposite
corner. The data system draws a box similar to the following:
• To draw a filled box, select a fill color. Start at any corner of the box and then drag
any cursor to the opposite corner. The system draws a box similar to the following:
You cannot move the graphic after it is placed.
If the graphic is not where you want it, immediately click
or choose Edit > Undo to
remove the graphic. Then, repeat this step. The system saves your previous text and
settings.
Removing Text and Graphics from a Plot
You can easily remove all or selected annotation text and graphics from a plot. Header text
cannot be edited or removed.
To change the style, color, label, axis, or normalization of a plot, use the Display Options
Dialog Box.
 To remove text and graphics from a plot
1. Specify the text or graphics item to remove by clicking the pin of the cell containing the
text or graphics.
2. Select one of these options:
• To select and remove previously added annotation text or graphics, go to step 2.
• To remove all previously added annotation text and graphics from a plot, go to step 3.
3. To select and remove text/graphics, click
Annotate > Clear.
in the toolbar or choose Display >
Repeat this step, as required, to remove text and graphics in other locations of the plot.
4. To remove all annotation text and graphics from the active cell, click
Display > Annotate > Clear All.
If you change your mind, click
Thermo Scientific
or choose
in the toolbar or choose Edit > Undo.
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Using the Qual Browser Window
Working with Cells
Opening or Changing Views in Cells
 To open views in cells
1. To choose a cell to hold the view, click the pin icon of the cell.
The Xcalibur application changes the cell pin icon from
the active cell.
to
to indicate that it is
Because there can only be one active cell, all other cells are inactive.
2. To choose the view that you want to open in the active cell, select from options in
Table 5.
 To change the view displayed in a cell
1. Click the cell where you want to change the view.
2. Select the required view from the main toolbar or choose a view from the View menu or
the shortcut menu (right-click the active cell). The Xcalibur data system replaces the view
in the active cell with the view that you select (see Table 5 for options).
Table 5. Opening views in cells (Sheet 1 of 2)
View
Select one of these options to open the view
Chromatogram View
• Choose View > Chromatogram.
• Right-click the cell and choose View > Chromatogram from the shortcut menu.
• Click
Spectrum View
on the toolbar.
• Choose View > Spectrum.
• Right-click the cell and choose View > Spectrum from the shortcut menu.
• Click
Map View
on the toolbar.
• Choose View > Map.
• Right-click the cell and choose View > Map from the shortcut menu.
• Click
Spectrum List View
on the toolbar.
• Choose View > Spectrum List.
• Right-click the cell and choose View > Spectrum List from the shortcut menu.
• Click
Scan Header View
on the toolbar.
• Choose View > Scan Header.
• Right-click the cell and choose View > Scan Header from the shortcut menu.
• Click
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Working with Cells
Table 5. Opening views in cells (Sheet 2 of 2)
View
Scan Filter View
Select one of these options to open the view
• Choose View > Scan Filters.
• Right-click the cell and choose View > Scan Filters from the shortcut menu.
• Click
Tune Method View
on the toolbar.
• Choose View > Report > Tune Method.
• Right-click the cell and choose View > Report > Tune Method from the shortcut
menu.
• Click
Instrument Method View
on the toolbar.
• Choose View > Report > Instrument Method.
• Right-click the cell and choose View > Report > Instrument Method from the
shortcut menu.
• Click
Sample Information View
on the toolbar.
• Choose View > Report > Sample Information.
• Right-click the cell and choose View > Report > Sample Information from the
shortcut menu.
• Click
Status Log View
on the toolbar.
• Choose View > Report > Status Log.
• Right-click the cell and choose View > Report > Status Log from the shortcut
menu.
• Click
Error Log View
on the toolbar.
• Choose View > Report > Error Log.
• Right-click the cell and choose View > Report > Error Log from the shortcut
menu.
• Click
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Managing Layouts
Scaling a Plot
The chromatogram, spectrum, and map views show plots. Use the Zoom and Pan menu
commands to adjust the display of the active plot.
Zoom In Y
Zoom in on the Y-axis by a factor of two (2) from the current baseline to show more
detail. For example, you can change the Y-axis range from 0 to 100 to 0 to 50.
Zoom Out Y
Open out on the Y-axis by a factor of two (2) to show more data. For example, you can
change the Y-axis range from 0 to 25 to 0 to 50.
Auto Range
Display the chromatogram, which is normalized from the minimum to the maximum
signal. Auto Range is useful for PDA and UV data.
Normalize
Normalize the intensity scale of the data display to a fixed range on the Y-axis, for
example, from 0 to 25% to 0 to 100%.
Zoom In X
Make the X-axis larger by a factor of two (2) to show more detail. For example, change
the X-axis range from 0 to 20 to 5 to 15.
Zoom Out X
Make the X-axis smaller by a factor of two (2) from the center to show more data. For
example, change the X-axis range from 7.5 to 12.5 to 5 to 15.
Display All
Display all data on the X-axis or all text in a report. For example, you can change the
X-axis range from 7.5 to 12.5 to 0 to 20.
Reset
Restore the data display to the full range of the X-axis and Y-axis.
Pan graph
Use the Pan Graph button on the toolbar to pan across a zoomed plot by dragging it to
the left or right with the mouse.
Managing Layouts
A layout consists of any arrangement of cells, views, and plots within a data window. Use the
Xcalibur data system to create, save, and open layouts. When you open the Qual Browser
window, the data system uses the last layout file to display data from a raw file in the
predefined arrangement and with predetermined option settings. Open a previously created
layout or create a new layout at any time.
See these topics for more information:
• Creating and Saving a Layout
• Opening a Layout
• Applying a Layout to the Active Window
• Displaying Layout Summary Information
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Managing Layouts
Creating and Saving a Layout
 To create and save a layout
1. To create the desired arrangement of cells for the data displays, choose Grid > Insert
Cells and Grid > Delete commands.
2. To create the desired arrangement of views, choose View menu commands.
3. To make a cell active, click the cell pin icon. Choose View > Add Plot commands to
insert the required number of plots in the cell. Repeat for each cell to create the desired
arrangement of plots.
4. To select display options, choose Display > Display Options menu commands.
5. To save the layout, select one of these options:
• To save a modified layout with the current name, click the Save Layout button on
the toolbar or choose File > Layout > Save.
• To assign a filename and save a new layout, choose
File > Layout > Save As.
or choose
• To save the current layout as the new default layout (default.lyt), click
File > Layout > Save As Default.
or choose
For additional information, see “Using Views Interactively” on page 39.
Opening a Layout
 To open a layout
1. To review and select a previously saved layout file, choose File > Layout > Apply.
2. Click the arrow in the List Files of Type list and select Layout Files (*.lyt). The Xcalibur
application displays all available layout files in the File Name list.
3. Select a layout file and click OK.
The application opens the current raw file using the data display arrangement and options
defined in the layout file. The application also writes the current layout file in the Qual
Browser Window title bar. Example: Qual Browser - Layout File Name.lyt.
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Managing Layouts
Applying a Layout to the Active Window
 To apply a layout
Select one of these options:
• To select a previously saved layout, click
• To display the current default layout, click
Default.
or choose File > Layout > Apply.
or choose File > Layout > Apply
Displaying Layout Summary Information
Choose File > Layout > Summary Info to display this file’s information.
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User
The name of the user currently logged in to the Xcalibur data system and
Qual Browser.
Header
Basic details about the layout: the File ID, the date the layout was created,
and the User ID of the originator of the layout.
Description
Any additional details about the layout such as modifications.
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Using the Qual Browser Window
Using the Cell Information Page
Using the Cell Information Page
The cell information page of the Info Bar displays information about the active cell (see
Figure 13). Its contents depends on whether the plot is a chromatogram or a spectrum.
Figure 13. Cell Information page showing Spectrum cell information
 To view cell information
1. Right-click a plot. The Cell Information page shortcut menu opens.
2. Choose Ranges. The Ranges dialog box opens. See “Setting Up Chromatogram Display
Options” on page 58 and “Setting Up Spectrum Plot Ranges” on page 94 for more
information. This dialog box shows the properties of all the plots in the active cell.
3. View or change any of these:
• Time and mass ranges
• Background subtraction
• Smoothing parameters
4. To remove the selected plot from the cell, choose Delete.
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Using the Qual Browser Window
Using the Cell Information Page
Chromatogram Information
For a chromatogram plot (see Figure 14), the Cell Information page shows these icons:
The plot type and filename
The pathname of the raw file
The scan filter (if applied)
The fixed scale upper limit (if applied)
The chromatogram delay (if applied)
The mass range (for mass range plot type only)
The chromatogram time range or ranges used for background subtraction (if
applied)
Figure 14. Cell Information for a chromatogram plot
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Using the Cell Information Page
Spectrum Information
For a spectrum plot, the Cell Information page (see Figure 15) shows these icons:
The filename
The pathname of the raw file
The scan filter (if applied)
The fixed scale upper limit (if applied)
The chromatogram time range or ranges used for background subtraction (if
applied)
Figure 15. Cell Information for a spectrum plot
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Using Views Interactively
Use the Qual Browser window to open a raw file, a sequence, or a results file. With raw files,
opened individually or from a sequence, you can create a grid of interactive cells and display
information from the raw file in any of the cells. From this display, you can use menu
commands to select display options or use the cursor to select regions of interest.
Contents
• Selecting a Point on a Plot
• Selecting a One-Dimensional Range on a Plot
• Selecting a Two-Dimensional Range on a Plot
• Using Scan Filters
• Applying a Scan Filter to a Plot
• Expanding Regions in the Same Plot
You can view a chromatogram, spectrum, map, spectrum list, scan header, scan filter, tune
method, processing method sample information, status log, or error log from the current raw
file in any of the cells that appear in the Qual Browser window. With chromatogram,
spectrum, and map views, you can display up to eight plots in each cell. You can use the
cursor and mouse to select points, ranges, or filters within a view. Cursor actions are always
directed toward the active cell.
A results file contains the list of detected peaks from the chromatogram and the qualitative
processing results associated with each peak. Qual Browser displays the results file in a fixed,
two-cell arrangement. Many of Qual Browser's features are not available for use with a results
file because the raw file is not available for processing.
You can use Qual Browser to do the following:
• Use a chromatogram to generate a mass spectrum (incorporating single or averaged scans,
with background subtraction if required) or maps with specific time ranges.
• Use maps to generate a single or averaged spectrum or mass chromatograms with specific
mass or time ranges.
• Use a spectrum to generate mass chromatograms.
• Apply scan filters to chromatograms using the drag-and-drop method.
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Using Views Interactively
Selecting a Point on a Plot
Selecting a Point on a Plot
 To select a point on a plot
1. To activate the cross-hair cursor and status bar, move the cursor to the graphic region of a
plot. This is the region above the X-axis and to the right of the Y-axis.
The Xcalibur data system displays a cross-hair cursor (+) and the coordinates in
appropriate units for the display in the status bar at the bottom of the Qual Browser
window.
For example, this information appears in the status bar:
• Chromatogram view: Time, Intensity
• Spectrum view: Mass (m/z), Intensity
• Map view: Time, Mass (m/z)
The data system only displays the cross-hair and status bar when a view can be used to
pick a point, range, or scan filter for application to a plot in the active view.
2. To use the cursor to determine the coordinates of a peak, position the cross-hair cursor on
the point on the plot. The application provides the X-axis and Y-axis coordinate values.
3. To select a point in an inactive view to apply to the active plot, click a point in one of the
inactive views to apply the point to the active view.
The application displays a red vertical marker to indicate the point selected:
When you click any other cell, the Xcalibur application removes the red vertical marker.
You can apply these coordinate values from an inactive chromatogram view to the
following active views:
• Spectrum: Scan Number and Retention Time
• Map: Retention Time and Mass Range
• Spectrum List: Scan Number and Retention Time
• Scan Header: Scan Number and Retention Time
• Scan Filter: Scan Number
• Tune Method: Segment Number
• Instrument Method: No effect
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Using Views Interactively
Selecting a Point on a Plot
• Sample Information: No effect
• Status Log: Scan Number and Status Log Time (RT)
• Error Log: No effect
See these examples for responses to cursor actions.
Active View: Spectrum
Inactive View: Chromatogram
Cursor/Mouse: Click retention time (RT) = 1.98 minutes in the chromatogram view.
Result: The Xcalibur data system displays the spectrum of scan number = 168 that occurs
at retention time = 1.98 minutes.
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Using Views Interactively
Selecting a Point on a Plot
Active View: Status Log
Inactive View: Chromatogram
Cursor/Mouse: Click retention time (RT) = 3.16 minutes in the chromatogram view.
Result: The Xcalibur data system displays the status log at retention time 3.16 minutes.
Active View: Scan Filter
Inactive View: Chromatogram
Cursor/Mouse: Click retention time (RT) = 1.36 minutes in the chromatogram view.
Result: The Xcalibur data system displays the scan filter used for the scan that occurs at
retention time = 1.36 minutes.
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Selecting a One-Dimensional Range on a Plot
Selecting a One-Dimensional Range on a Plot
 To select a one-dimensional plot range
1. To activate the cross-hair cursor and status bar, move the cursor to the graphic region of a
plot. This is the region above the X-axis and to the right of the Y-axis.
The data system displays a cross-hair cursor and the coordinates in the appropriate units
for the view in the status bar at the bottom of the Qual Browser window.
This information appears in the status bar of these views:
• Chromatogram view: Time, Intensity, Filter
• Spectrum view: Mass (m/z), Intensity
• Map view: Time, Mass (m/z)
The data system only displays the cross-hair and status bar when a view can be used to
pick a point, range, or scan filter for application to the active view.
2. To use the cursor to redraw the active plot using the selected range of axis values, place the
cross-hair cursor at the beginning of the desired range in the active plot. Drag the cursor
to the end of the range.
The data system displays a red horizontal marker (
selection.
) to define the range of the
When you click any other cell, the application removes the red vertical marker.
The application replots the active plot using the new range.
Use this procedure with the X-axis or Y-axis of the chromatogram, spectrum, and map
views.
Figure 16. Position the cross-hair
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Figure 17. Drag the cursor
Figure 18. Xcalibur system redraws the active plot
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Selecting a One-Dimensional Range on a Plot
3. To use the cursor to apply a different range of values for the active plot, drag the cursor
across an axis of a plot in an inactive view to apply the selected range to the active plot.
See these examples for responses to cursor actions.
Active Plot: Spectrum
Inactive View: Chromatogram
Cursor/Mouse: Drag across a peak of interest.
Result: The Xcalibur data system displays a spectrum that is the average of the 52 scans
from scan 150 through 201. These correspond to the scans at retention times (RT) 1.78
through 2.35.
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Active Plot: Chromatogram
Inactive View: Spectrum
Cursor/Mouse: Select the Add/Replace Plots button (
m/z 198.4 through 299.7.
) in the toolbar. Drag from
Result: The Xcalibur data system displays chromatograms of both the total ion current
(top) and the selected ion range (bottom).
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Selecting a Two-Dimensional Range on a Plot
Selecting a Two-Dimensional Range on a Plot
Use this procedure to isolate a small region of a plot, for example, to select a small peak.
 To select a two-dimensional range in the active plot
1. To activate the cross-hair cursor and status bar, move the cursor to the graphic region of a
plot. This is the region above the X-axis and to the right of the Y-axis.
The Xcalibur application displays a cross-hair cursor and the coordinates in the
appropriate units for the plot in the status bar at the bottom of the Qual Browser window.
This information appears in the status bar of these views:
• Chromatogram view: Time, Intensity, Filter
• Spectrum view: Mass (m/z), Intensity
• Map view: Time, Mass (m/z)
The application only displays the cross-hair and status bar when a view can be used to
pick a point, range, or scan filter for application to the active plot.
2. To use the cursor to outline a region of interest in the active plot, position the cross-hair
cursor where you want to begin outlining the area of interest. Then, drag the cursor to the
opposite corner of the area. To include the axis, extend the selected area so over the axis.
Use this procedure with the X-axis or Y-axis of the chromatogram, spectrum, and map
views.
The Xcalibur application replots the area of interest in the active plot and displays a red
area marker to indicate the area selected:
When you click any other cell, the application removes the red area marker.
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Figure 19. Position the cross-hair
Figure 20. Drag the cursor to define the area of interest
Figure 21. Xcalibur data system replots the area of interest in the active plot
If you do not obtain the desired result, click
and then repeat step 2.
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in the toolbar to restore the active plot,
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Using Scan Filters
Using Scan Filters
You can use a scan filter to specify that Xcalibur processing is to be applied to a subset of the
scans in a raw data file. The scan filter box is provided in all Xcalibur windows that display
raw files: the Home Page, Processing Method, Instrument Setup, Quan Browser, and Qual
Browser windows. You can either select a scan filter from the list of the filters that the Xcalibur
application creates from Instrument Setup settings or you can create a new filter using the
scan filter format.
 To use scan filters
1. Locate the appropriate scan filter list:
Locate the scan filter list in one of the following windows: Instrument Setup, Qual
Browser, Processing Method, Quan Browser, or Home Page.
2. Check the current filter:
The Xcalibur application displays the current scan filter in the Scan Filter list (see
Figure 22). To view other scan filters available in the raw file, click the down arrow to
display the list.
Figure 22. Example of the scan filter list (Qual Browser window)
• If you want to edit the current scan filter, type the correction in the Scan Filter box
and go to step 5.
• If you want to modify a different filter in the list, go to step 3.
• If you want to manually enter a new scan filter, go to step 4.
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Using Scan Filters
3. Select a scan filter from the Scan Filter list:
Use the scan filter format to determine the function of each filter in the scan filter list.
Click to select one of the scan filters in the list. The application displays your new
selection in the Scan Filter box. Edit the current scan filter to create a new scan filter, as
required. Go to step 5.
4. Enter a new scan filter by typing it over the current scan filter.
Use the scan filter format to create the scan filter that allows you to find only the scans
that contain the experiment settings of interest.
• Positive or negative charged ions
• Centroid or profile data
• Source CID
• Scan mode
• Scan power
• Parent maizes
• Product mass range
• TurboScan
• Constant neutral gain
• Constant neutral loss
5. Continue to enter other Xcalibur settings.
Scan Filter Format
The Xcalibur application creates scan filters from scan event settings and stores them with
each raw file. Users can select scan filters to specify that processing is to be applied to a subset
of the scans in a raw file. Make sure to use only fields that apply to your mass spectrometer.
You can define additional scan filters by adhering to the following scan filter format.
Note Not all features are applicable for every mass spectrometer.
Table 6. Scan filter format (Sheet 1 of 4)
Feature
Option
Interpretation
Polarity
+, –
Positive, Negative
Data type
p, c
Profile, Centroid
Dependent scans
d, !d
Include dependent scans, Exclude dependent scans
TurboScans
t, !t
Include TurboScan scans, Exclude TurboScan scans
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Table 6. Scan filter format (Sheet 2 of 4)
Feature
Option
Interpretation
Source CID
sid, !sid
Include Source CID scans, Exclude Source CID scans
Scan type
FULL, Z, SIM, SRM,
CRM, Q1MS, Q3MS
Full scan, ZoomScan, SIM, SRM, CRM, Q1MS, Q3MS
Scan mode
ms, ms2, ms3, ... MS10
MSn for n = 1 to 10
Each order can be followed by the appropriate number of
parents. The parents can also be omitted.
Example: “ms3 345.3, 253.2” indicates an MS3 scan with
parents with m/z 345.3 and 253.2.
pr
Parent (followed by the product mass)
cng
Constant Neutral Gain (followed by the mass of the neutral)
cnl
Constant Neutral Loss (followed by the mass of the neutral)
Mass Analyzer
ITMS, TQMS, SQMS, ITMS, TQMS, SQMS, TOFMS, FTMS, Sector
TOFMS, FTMS, Sector
Photo Ionization
pi, !pi
Include photo ionization scans, Exclude photo ionization scans
Compensation Voltage
cv, !cv
Include compensation voltage scans, Exclude compensation
voltage scans
Detector Valid
det, !det
Include detector valid scans, Exclude detector valid scans
Enhanced
E, !E
Include enhanced scans, Exclude enhanced scans
Wideband
w, !w
Include wideband scans, Exclude wideband scans
Supplemental Activation sa, !sa
Include supplemental activation scans, Exclude supplemental
activation scans
Multistate Activation
msa, !msa
Include multistate activation scans, Exclude multistate
activation scans
Product masses or mass
range of scan
[m1a–m1b, m2a–m2b,
m3a–m3b, ...]
Scans with a specific mass range or mass ranges, such as SIM,
SRM, and CRM.
Example: [50.00 – 1500.00] for a scan from m/z 50.00 to
1500.00
If a scan is exactly 1 u wide, it is displayed as a single value (the
center mass). This is typical for SIM, SRM, and CRM. Filters
for parents in dependent scans are matched with a tolerance of
m/z 1.0 so that minor differences in parent mass measurements
from scan to scan do not give different filters.
Segment/scan event
number pairs
{segment, scan number} Example “{3, 4} + c ms” indicates segment 3, scan event 4 for a
positive centroid MS scan
The curly brackets { } are required.
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Using Scan Filters
Table 6. Scan filter format (Sheet 3 of 4)
Feature
Option
Interpretation
Ionization mode
APCI, ESI, EI, CI, NSI, Example: “+ c ESI ms” indicates a positive centroid electrospray
FAB, TSP, FD, MALDI, MS scan
GD
Corona on/off
corona, !corona
Corona on, Corona off
Example: “+ APCI !corona ms” indicates a positive centroid
APCI scan with the corona off
Detector value
“det=## .##”
Detector value is “## .## with no spaces.
Example: “+ ESI det= –800.0” indicates a positive electrospray
scan at –800.0 detector units (usually volts)
MS/MS and MSn CID
energies
[email protected]
Mass is the parent mass and energy is the CID relative energy
(no units)
Example: “– c ms2 [email protected]” indicates a negative centroid
MS/MS scan of m/z 196.1 at 25.0 units of CID energy
Quadrupole
identification
Q1MS, Q3MS
Example: “+ c ESI Q3MS” indicates a positive centroid
electrospray MS scan using quadrupole 3
Accurate Mass
AM, !AM, AMI
Include accurate mass scans, Exclude accurate mass scans
Ultra
u, !u
Include ultra scans, Exclude ultra scans
Sector
BSCAN, !BSCAN
Include sector scans, Exclude sector scans
Sector
ESCAN, !ESCAN
Include sector scans, Exclude sector scans
LOCK
lock, !lock
Include lock scans, Exclude lock scans
Multiplex
msx, !msx
Include multiplexing scans, Exclude multiplexing scans
Electron Capture
Dissociation
ecd, !ecd
Include electron capture dissociation, Exclude electron capture
dissociation
Multi Photo
Dissociation
mpd, !mpd
Include photo dissociation, Exclude photo dissociation
Pulsed Dissociation
pqd, !pqd
Include pulsed dissociation scans, Exclude pulsed dissociation
scans
Electron Transfer
Dissociation
etd, !etd
Include electron transfer dissociation scans, Exclude electron
transfer dissociation scans
NPTR
nptr, !nptr
Include NPTR, Exclude NPTR
High Energy CID
hcd, !hcd
Include high energy scans, Exclude high energy scans
Source SID
cid, !cid
Include Source SID scans, Exclude Source SID scans
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Table 6. Scan filter format (Sheet 4 of 4)
Feature
Option
Interpretation
Insolation Width
iw ##, ##
Isolation Width value at ##, ##
Free Region
ffr1, ffr2
Applying a Scan Filter to a Plot
This procedure demonstrates the use of a scan filter view. For the routine application of scan
filters to chromatogram, spectrum, map, or spectrum list views, use the Ranges Dialog Boxes.
Choose Display > Ranges and select a scan filter from the Scan Filter box.
1. To open the chromatogram view, click
Chromatogram.
on the toolbar or choose View >
The Xcalibur data system displays a Chromatogram View in the cell.
2. To display the entire chromatogram run, choose Display > Zoom > Display All to
display the entire chromatogram.
If a filter has been applied to the chromatogram view, choose Display > Ranges. The
Chromatogram Ranges Dialog Box opens. Select the scan filter in the Scan Filter box and
press the DELETE key to remove the filter. Click OK.
3. To open the scan filter view, select another cell and choose View > Scan Filter. The Scan
Filter View opens in that cell.
4. To display all scan filters used in the sample, drag the cursor in the chromatogram view
parallel to the X-axis. To select all of the peaks in the chromatogram, start at the Y-axis
and stop at the end of the X-axis. See “Selecting a One-Dimensional Range on a Plot” on
page 43 for more information.
The application displays all of the scan filters used for the sample run in the scan filter
view.
5. To select and apply a scan filter to a plot in the active view, click the scan filter of interest
in the scan filter view and drag the scan filter to a view. Release the mouse button to apply
the filter.
The Xcalibur application outlines the selected scan filter with a box and changes the
cursor to
.
As you drag the scan filter, the following occurs:
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• The data system changes the cursor to
when the filter is in a compatible view.
• The data system changes the cursor to
when the filter is in an incompatible view.
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Applying a Scan Filter to a Plot
When you release the mouse button, the Xcalibur application applies the filter, redraws
the plot, and makes the view that contains the plot with the applied filter in the active
view.
Figure 23. Select a scan filter
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Figure 24. Drag the scan filter to a plot in another view
Figure 25. Xcalibur data system applies the scan filter and redraws the plot
If you do not obtain the desired result, click
and repeat step 4.
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in the toolbar to restore the previous plot
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Expanding Regions in the Same Plot
Expanding Regions in the Same Plot
Use the Xcalibur data system graphical interface to perform repeated expansions of a selected
region of a chromatogram view, spectrum view, or map view without needing to expand the
view each time.
 To repeat expansions of the same view
1. To choose the active plot, click the pin icon of a cell containing a plot.
The Xcalibur data system changes the pin icon from
active cell and therefore the active view.
to
to indicate that it is the
Click the plot to work with it.
2. To copy the view in the open cell to the computer clipboard, choose Edit > Copy Cell.
3. To choose another cell for the active view, click the cell where you want the expanded plot
or plots of the view of interest replotted.
The data system changes the pin icon from
and therefore the active view.
to
to indicate that it is the active cell
4. To paste the duplicate view to the active cell, choose Edit > Paste Cell.
5. To specify the region of interest, select from these options:
• For a chromatogram view or a spectrum view, drag the cursor in the plot parallel to
the X-axis or Y-axis. For more information about this procedure, see “Selecting a
One-Dimensional Range on a Plot” on page 43.
• For a Map display, drag the cursor in the plot to select an area from one corner of the
region of interest to the opposite corner of the region of interest. For more
information about this procedure, see “Selecting a Two-Dimensional Range on a
Plot” on page 47.
The data system replots the region of interest that you selected in the adjacent view into
the active view.
6. Repeat step 3 to expand other regions of interest by using the cursor in the adjacent view
to select other regions of interest.
Note Since the adjacent view does not change during this procedure, you do not need
to return to the previous view before selecting a new region of interest. Repeat this
step as many times as desired.
The data system displays the region of interest (one at a time) in the active view.
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A chromatogram view shows the intensities of one or more masses as a function of time.
These procedures describe how to manipulate chromatograms.
Contents
• Using Chromatogram Plots
• Setting Chromatogram Ranges
• Using the AutoFilter
• Setting Chromatogram Display Options
• Changing Peak Detection Settings
 To view a chromatogram
To view a chromatogram in the active cell, choose one of these options:
• Right-click the cell and choose View > Chromatogram from the shortcut menu.
• From the menu bar, choose View > Chromatogram.
• Click
on the toolbar.
Figure 26. An example of a Chromatogram view with the Chromatogram shortcut menu
displayed
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Using Chromatogram Plots
Using Chromatogram Plots
You can display up to eight plots within a chromatogram view.
 To insert a plot
1. Select the cell containing the view.
2. Right-click the chromatogram above the position for the new plot.
3. Choose Plot > Insert from the shortcut menu.
 To delete a plot
1. Select the cell containing the view.
2. Right-click the plot to delete.
3. Choose Plot > Delete from the shortcut menu.
You can also use the Ranges dialog box to add, delete, or enable plots.
Setting Up Chromatogram Display Options
Use one or more of these procedures to set up chromatogram display options:
• Setting Chromatogram Ranges
• Setting Automatic Processing Options
Setting Chromatogram Ranges
Use the Chromatogram Ranges dialog box to view and edit the mass range and time range for
all the plots in a chromatogram.
 To set the mass range and time range for a chromatogram
1. To open the Chromatogram Ranges Dialog Box (Figure 27), from the Qual Browser
window with a chromatogram view active, choose one of these options:
• Right-click a chromatogram plot in the cell and choose Ranges from the shortcut
menu.
• Choose Display > Ranges.
• Click
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on the Qual Browser toolbar.
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4 Using a Chromatogram View
Setting Up Chromatogram Display Options
Figure 27. Ranges page of the Chromatogram Ranges dialog box
2. To specify the time range in the Time range box, type the lower and upper time limits in
minutes, separated by a dash with no spaces.
3. To view or hide the chromatogram, select (or clear) the Type check boxes. A row of
settings in the Chromatogram Ranges dialog box describes the chromatogram.
4. To specify a raw file and change the source of the active plot, select from the Raw File list.
The list contains all the files active in the current cell. Choose from these options:
• Select a file from the list.
• Click Browse adjacent to the list and browse to the required file.
• Type the full path and filename of the required file.
5. To specify the scan filter, select from the Scan filter list to display filter options stored in
the .raw file. Select the desired filter.
6. To specify the chromatogram plot type, use the Plot Type lists. To change the current
chromatogram type, click the arrow to display a list of chromatogram type options and
select a type option.
7. To specify a range for the specified plot types, type the first mass/wavelength and
last mass/wavelength in the Ranges box. The format for multiple ranges is
First Mass/Wavelength (Range 1) – Last Mass/Wavelength (Range 1),
First Mass/Wavelength (Range 2) – Last Mass/Wavelength (Range 2).
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Setting Up Chromatogram Display Options
8. In the Plot Properties area, select a detector type and specify a peak algorithm type.
9. Specify the delay time between a component mass peak detected by the UV detector and
the time that the same component is detected by the application. To change the value,
enter the new delay time in the Delay box. The valid time range is –5.0 to +5.0 minutes.
10. To turn on, change, or turn off the fixed scale setting, choose one of these options:
• To turn on the maximum range for the Y-axis of the active chromatogram, select the
Fixed scale check box.
• To change the value, type the new maximum Y-axis value in the Fix scale to box.
• To turn off the fix scale setting, clear the Fixed scale check box.
11. To save the settings and close the dialog box, click OK.
Setting Automatic Processing Options
Use the Automatic processing page (Figure 28) to apply smoothing or baseline subtraction to
all the plots in the active chromatogram view. This page contains these areas:
• Setting Smoothing Area Options
• Setting Baseline Subtraction Area Options
• Setting Include Peaks Area Options
• Setting Mass Tolerance Area Options
• Setting Mass Precision Area Options
 To set automatic processing options for a chromatogram view
1. Open a chromatogram in an active chromatogram view of the Qual Browser window.
2. To open the Chromatogram Ranges Dialog Box (see Figure 28), choose one of these
options:
• Right-click a chromatogram plot in the cell and choose Ranges from the shortcut
menu.
• Choose Display > Ranges.
• Click
on the Qual Browser toolbar.
3. Click the Automatic Processing tab.
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Setting Up Chromatogram Display Options
Figure 28. Automatic Processing page of the Chromatogram Ranges dialog box
Setting Smoothing Area Options
Use the Smoothing area settings to smooth all scans defined by the mass range, time range,
and filter settings in the Spectrum Ranges dialog box.
 To set smoothing settings
1. To turn on chromatogram smoothing, select the Enable check box. To turn off
chromatogram smoothing, clear the Enable check box.
2. To change the type of smoothing, select either Boxcar or Gaussian from the Type list.
3. To specify the number of points for chromatogram smoothing, type a new number of
points in the Points box. The valid range for smoothing points includes odd values
between 3 (minimum smoothing) and 15 (maximum smoothing).
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Setting Up Chromatogram Display Options
Setting Baseline Subtraction Area Options
Use the Baseline subtraction settings to apply baseline subtraction to all chromatogram plots
in the active view. This algorithm fits a smooth curve through the noise in the chromatogram
and subtracts this curve from the chromatogram, leaving the peaks on a flat baseline.
 To set Baseline subtraction settings
1. To turn on baseline subtraction, select the Enable check box. To turn off baseline
subtraction, clear the Enable check box.
2. To choose a polynomial order, specify an order for the baseline curve in the Polynomial
order box. The normal operating range is 3 to 20. For complex chromatograms, use a
high polynomial order.
3. To choose a Below curve (%) value and move the baseline curve up or down in the
chromatogram noise, enter a value in the Below curve box. Normal operating range for
this parameter is 5 to 30%, depending on the abundance and width of peaks in the
chromatogram. For more or wider peaks, increase the value.
4. To change the algorithm’s precision, adjust the setting in the Tolerance box.
5. To choose how the algorithm fits the beginning and end of the chromatogram, use the
Flatten edges check box.
• To make sure the beginning and end of the plot are horizontal, select the check box.
• Clear the check box if this is not required.
6. To display the polynomial function with the chromatogram, select the Overlay graph of
fitted polynomial check box. Clear the check box to hide the display.
Setting Include Peaks Area Options
The Include peaks area has only one check box. Use this setting to include or exclude the
reference peaks (R) and exception peaks (E) for the mass data in all the cells in the
Qual Browser window.
 To set peaks area settings
To include reference and exception peaks in the chromatogram display, select the
Reference and exception peaks check box. To hide reference and exception peaks, clear
this check box.
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Setting Up Chromatogram Display Options
Setting Mass Tolerance Area Options
Use the Mass tolerance area to specify a value for mass tolerance. Settings in this area affect the
display of all the mass data in the Qual Browser window.
 To set Mass tolerance area settings
1. To use mass tolerance, select the Use user defined check box.
2. Enter a value from 0.1 to 50000.0 in the Mass Tolerance box. Select a unit type.
3. To turn off mass tolerance, clear the Use user defined check box (see Figure 29).
Figure 29. Mass Options page for default settings
Setting Mass Precision Area Options
Use the settings in the Mass precision area to apply mass precision to the mass data in all the
cells in the Qual Browser window.
 To set Mass precision settings
1. Specify the number of places after the decimal point that display in mass values in the
Decimals box.
2. To save the settings and close the dialog box, click OK.
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Using the AutoFilter
Using the AutoFilter
Use the Autofilter command to repopulate a chromatogram view with these possible
characteristics:
• A plot showing the chromatogram without any scan filters
• Plots for each scan filter applied to the chromatogram, up to the maximum of eight
chromatogram plots
 To use the Xcalibur AutoFilter command
1. To choose the cell for the view, click the cell where you want to apply the AutoFilter
command.
2. To make this cell active, click the pin icon.
The Xcalibur application changes the pin icon to indicate that it is the active cell.
3. To open a chromatogram view in the active cell, choose one of these options:
• Choose View > Chromatogram.
• Right-click the cell and choose View > Chromatogram from the shortcut menu.
• Click
on the toolbar.
The data system opens a Chromatogram View.
4. To apply the AutoFilter command to the current chromatogram view, choose one of these
options:
• Choose Actions > Autofilter.
• Right-click the cell and choose Autofilter from the shortcut menu.
• Click
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on the toolbar.
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Setting Chromatogram Display Options
The data system draws the chromatogram view with a plot for no scan filter applied and
one plot for every scan filter applied to the chromatogram up to a maximum of eight
chromatogram plots total.
5. Change chromatogram view options as follows:
• To change the ranges and chromatogram composition, choose Display > Ranges.
The Chromatogram Ranges Dialog Box opens.
• To change the style, color, labeling, axis titles and style, and normalization, choose
Display > Display Options. The Display Options Dialog Box opens.
Setting Chromatogram Display Options
The Display Options dialog box contains a small display area showing the active cell. Use this
display to preview the effects of different settings before applying them.
Use one or more of these procedures to set up chromatogram display options:
• Setting the Chromatogram Axis Options
• Setting the Chromatogram Color Options
• Setting the Chromatogram Label Options
• Setting the Chromatogram Normalization Options
• Setting the Chromatogram Style Options
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Setting Chromatogram Display Options
Setting the Chromatogram Axis Options
 To set the chromatogram axis options
1. Open a chromatogram in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Axis tab. The Chromatogram Axis Page – Display Options Dialog Box opens.
Figure 30. Axis page for a Chromattogram view in the Display Options dialog box
4. To change the name of the X- or Y-axis, type the new name in the appropriate axis
Name box.
5. To change the time when the data system displays the axis label, select Never, On Print,
or Always from the Show name list.
6. To move the displayed plot from the X- or Y-axis, select the appropriate axis Offset check
box. To turn off axis offset, clear the Offset check box.
7. To set time range splitting, select from these options:
a. To split the time scale, select the Split time range check box.
b. To change the number of divisions (subsections), type the new number in the
Divisions (time) box.
To display only one time range, clear the Split time range check box.
8. To save the settings and close the dialog box, click OK.
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Setting Chromatogram Display Options
Setting the Chromatogram Color Options
 To set the chromatogram color options
1. Open a chromatogram in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Color tab. The Chromatogram Color Page – Display Options Dialog Box
opens.
Figure 31. Color page for a Chromatogram view in the Display Options dialog box
4. To select the color of a particular plot, click the plot number button. The Xcalibur
application opens the Color dialog box with a color palette so that you can select a preset
color or customize a color.
5. To select the color of the backdrop, click Backdrop. The application opens the Color
dialog box with a color palette so that you can select a preset color or customize a color.
Backdrop options are available when you have selected the Overlay 3D style.
6. To save the settings and close the dialog box, click OK.
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Setting Chromatogram Display Options
Setting the Chromatogram Label Options
 To set the chromatogram label options
1. Open a chromatogram in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Labels tab. The Chromatogram Labels Page – Display Options Dialog Box
opens.
Figure 32. Labels page for a Chromatogram view in the Display Options dialog box
4. To define the location and contents of chromatogram labels, choose from these options:
• To display the retention time above chromatogram peaks, select the Retention time
check box. To hide the retention time, clear the Retention time check box.
• To display the active scan number above chromatogram peaks, select the Scan
number check box. To hide the scan number, clear the Scan number check box.
• To display the m/z for the base peak of the active scan above chromatogram peaks,
select the Base peak check box. To hide the base peak m/z, clear the Base Peak
check box.
• To display letters above chromatogram peaks to provide supplemental information
about the peak data, select the Flags check box. For example, if a peak is saturated,
the data system displays an S above the peak.
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Setting Chromatogram Display Options
5. To specify the style of the labels, choose from these options:
• To move a label from its normal position to avoid conflict with another label, select
the Offset check box. Specify the amount of the offset (in number of characters) in
the Size box.
• To write vertical labels, select the Rotated check box. To write horizontal labels, clear
the Rotated check box.
• To place a box around each peak label, select the Boxed check box. If you do not
want to have a box around the label, clear the check box.
6. To specify a percent of the base peak so that the Xcalibur application labels all peaks above
that percent, type a value in the Label threshold box.
7. To save the settings and close the dialog box, click OK.
Setting the Chromatogram Normalization Options
 To set the chromatogram normalization options
1. Open a chromatogram in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Select the Normalization tab. The Chromatogram Normalization Page – Display
Options Dialog Box opens.
Figure 33. Normalization page for a Chromatogram view in the Display Options dialog box
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Setting Chromatogram Display Options
4. To specify the normalization method, choose from these options:
• To automatically rescale the Y-axis to the minimum and maximum signal values,
select the Auto range option.
• To specify the range of values to be plotted on the Y-axis, select the Intensity range
option and type the minimum and maximum intensities you want to display in the
Intensity Range box. The valid range is 0.000 – 100.000 percent.
5. To specify the plot normalization option, select one of these options:
• To normalize (set the Y-axis maximum) to the largest peak in the subsection
(division), select the Largest peak in subsection option.
• To normalize (set the Y-axis maximum) to the largest peak in the time range, select
the Largest peak in selected time range option.
• To normalize (set the Y-axis maximum) to the largest peak at all times, select the
Largest peak in all times option.
6. To save the settings and close the dialog box, click OK.
Setting the Chromatogram Style Options
 To set the chromatogram style options
1. Open a chromatogram in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Select the Style tab. The Chromatogram Style Page – Display Options Dialog Box opens.
Figure 34. Style page for a Chromatogram view in the Display Options dialog box
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Detecting Peaks
4. To specify the graphic style, choose one of these options:
• To display point-to-point peak profiles, select the Point To Point option.
• To display the graphic as vertical lines, select the Stick option.
5. To specify the arrangement style, choose one of these options:
• To stack plots vertically with no overlap, select the Stack (2D) option.
• To overlay plots vertically with optional horizontal skew (time offset), choose the
Overlay (3D) option.
6. To set the elevation angle for 3D plots from 0 to 60 degrees, either drag the Elevation
slider or click the Elevation slider left or right arrow until you reach the desired angle.
7. To set the skew angle, either drag the Skew slider or click the Skew slider left or right
arrow until you reach the desired angle (from 0 to 45 degrees).
8. To add a backdrop to 3D plots, select the Draw backdrop check box.
9. To save the settings and close the dialog box, click OK.
Detecting Peaks
Qual Browser provides several ways for detecting chromatogram peaks in a cell. The three
most common are described here.
Note Detect peak buttons on the toolbar and detect peak menu commands are active
only when you have an open raw file.
 To detect and integrate peaks in a raw file
1. To open the raw file containing the peaks that you want to detect and integrate, choose
File > Open or click
.
2. Select a raw file and choose OK. The data system displays the raw file in the Qual
Browser window.
3. To display the Main or the Amplify Toolbars, choose View > Toolbars. The Toolbars
dialog box opens.
4. Select one of these peak detection options:
• Automatic Detection of One Plot
• Automatic Detection of All Plots
• Manual Detection
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Automatic Detection of One Plot
 To detect and integrate all peaks in a selected chromatogram plot using the current
peak detection and integration settings
1. Click the chromatogram plot in the active cell. The Xcalibur data system shades the
selected plot.
2. To detect and integrate all peaks in the selected chromatogram plot, click
on the
toolbar or choose Actions > Peak Detection > Toggle Detection in This Plot. This
option uses the current peak detection and integration settings.
3. To undo the peak detection, click the button on the toolbar a second time or choose
Actions > Peak Detection > Toggle Detection in This Plot from the menu bar.
Automatic Detection of All Plots
 To detect and integrate all peaks in all chromatogram plots in the active cell using
the current peak detection and integration settings
1. Click
Plots.
on the toolbar or choose Actions > Peak Detection > Toggle Detection in All
2. To undo all detected peaks, click the button on the toolbar a second time or choose
Actions > Peak Detection > Toggle Detection in All Plots from the menu bar.
Manual Detection
To manually detect and integrate all peaks in all chromatogram plots in the active cell, use
either the Add Peaks or the Delete Peaks button on the toolbar.
Adding Peaks
 To add a peak to a chromatogram plot
1. To detect and integrate any peak in the selected cell, click
Actions > Peak Detection > Add Peaks.
The Xcalibur application changes the cursor to the Add Peaks
on the toolbar or choose
cursor.
2. Drag the Add Peaks cursor horizontally across the peak to detect and integrate. The
application marks the added peak with a blue baseline and integrates the peak. To adjust
the positioning of the baseline markers, use the cursor to drag.
3. To restore the default cursor, click the Add Peaks button on the toolbar a second time, or
choose Actions > Peak Detection > Add Peaks from the menu bar.
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Changing Peak Detection Settings
Deleting Peaks
The active cell must have one or more peaks detected (as indicated by
buttons on the toolbar and delete menu commands to be active.
) for the delete
 To delete peaks in a raw file
or choose
1. To open the raw file containing the peaks that you want to delete, click
File > Open from the Qual Browser window. The Open Raw File dialog box opens.
2. Select a raw file and click OK. The Xcalibur application displays the raw file in the
Qual Browser window.
3. Choose View > Toolbars from the Qual Browser window to open the toolbar.
4. To delete specific peaks in an active cell, click
the delete peaks cursor
.
. The application changes the cursor to
5. To delete a specific peak, click within the peak’s boundary, indicated by the blue baseline
.
a second time,
6. To return the delete peaks cursor to the default cursor, click
choose Actions > Peak Detection > Delete Peaks, or right-click the plot and select
Peak Detection > Delete Peaks from the shortcut menu.
Changing Peak Detection Settings
Use the Peak Detection Settings page to change peak detection settings (Figure 35).
 To display the Peak Detection Settings page
Right-click an active chromatogram view and choose Peak Detection > Settings from
the shortcut menu, or choose Actions > Peak Detection > Settings from the menu bar.
For information on the settings on the Peak Detection Settings page, refer to the
Acquisition and Processing User Guide.
Note The default values on the Peak Detection Settings page are suitable for most
analysis requirements. Change these settings only if standard chromatogram detection
and integration options do not provide the desired result.
To apply the current chromatogram peak identification and integration settings to all
displayed plots in the active view, select the Apply To All Plots check box. To apply the
settings only to the active plot, clear the Apply To All Plots check box.
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Changing Peak Detection Settings
Figure 35. Peak Detection Settings page in Qual Browser
Peak Detection
Settings
page
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Using a Map View
A map is a 2D or 3D representation of an analysis showing all the mass/wavelength scans
acquired during an analysis (see Figure 36). Use the Qual Browser window to open a raw file,
create a grid of interactive cells, and display a map and related header information in any of
the cells. Use menu commands to select display options.
Contents
• Setting Map Ranges
• Setting Map Display Options
The Map view consists of a time (X-axis) versus m/z (Y-axis) versus relative abundance
(Z-axis) map plot. An example of a map view is shown below:
Figure 36. Map view
 To view a map
Choose one of these options:
• Right-click the cell and choose View > Map from the shortcut menu.
• From the menu bar, choose View > Map.
• Click
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Setting Map Ranges
Figure 37. An example of a Map view, showing the Map view shortcut menu
Setting Map Ranges
 To set the mass range and time range for a map
1. Make a map view the active view in the Qual Browser window.
2. To open the Map Ranges Dialog Box, right-click the map view and choose Ranges from
the shortcut menu.
Figure 38. Map Ranges dialog box
3. To specify the mass range, input the first mass and last mass of the scan in the Mass box.
The format is First Mass (Range 1) – Last Mass (Range 1) +
First Mass (Range 2) – Last Mass (Range 2).
4. Specify the time range in the Time box by typing the lower and upper time limits in
minutes, separated by a dash with no spaces.
5. Select a desired scan filter from the Scan filter list, which displays filter options stored in
the .raw file.
6. To save the settings and close the dialog box, click OK.
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Setting Map Display Options
Setting Map Display Options
 To change the style of a map view
1. Make a map view the active view in the Qual Browser window.
2. To open the Display Options dialog box, right-click the cell and choose Display
Options, or choose Display > Display Options from the menu bar.
The Display Options dialog box consists of five tabbed pages: Style, Color, Axis,
Normalization, and Band Width. It contains a small display area showing the active cell. Use
this set of options to preview the effects of different settings before applying them.
Figure 39. Style page for a Map view in the Display Options dialog box
Use one or more of these procedures to set up map display options:
• Setting the Map Style Options
• Setting the Map Axis Options
• Setting the Map Color Options
• Setting the Map Normalization Options
• Setting the Band Width
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Setting Map Display Options
Setting the Map Style Options
 To set the map style options
1. Make a map view the active view in the Qual Browser window.
2. To open the Display Options Dialog Box, choose Display > Display Options, or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Style tab (see Figure 39). The Map Style page opens.
4. To specify the arrangement style, choose from these options:
• To stack plots vertically with no overlap for the active map, select the Stack option.
• To overlay plots vertically with optional horizontal skew (time offset) for the active
map, select the Overlay (3D) option.
• To display a density map, showing different shades for each intensity, select the
Density map option.
5. To specify style options for overlaid (3D) plots, choose from these options:
• To set the elevation angle (from 0 to 60 degrees), drag the Elevation slider or click the
left or right arrow on the Elevation slider until you reach the desired angle.
• To set the skew angle (from 0 to 45 degrees), drag the Skew slider or click the left or
right arrow on the Skew slider until you reach the desired angle.
• To select a different fill option, select a fill option from the Fill list.
• To add a backdrop to 3D plots, select the Draw Backdrop check box. To remove a
backdrop, clear the Draw Backdrop check box.
6. To save the settings and close the dialog box, click OK.
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Setting Map Display Options
Setting the Map Axis Options
 To set the map axis options
1. Make a map view the active view in the Qual Browser window.
2. To open the Display Options Dialog Box, choose Display > Display Options, or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Axis tab. The Map or Ion Map Axis Page – Display Options Dialog Box opens.
Figure 40. Axis page for a Map view in the Display Options dialog box
4. To change the name of the X-, Y-, or Z-axis, type the new name in the X, Y, or
Z Name box.
5. To change the time when the data system displays the axis label, select Never, On Print,
or Always from the Show list.
6. To move the displayed plot from the X- or Y-axes, select the Offset check box for X or Y
or both. To turn off axis offset, clear the X or Y Offset check box.
7. To set time range splitting, select from these options:
a. To split the time scale, select the Split time range check box.
b. To change the number of divisions (subsections), type the new number in the
Divisions (time) box.
To display only one time range, clear the Split time range check box.
8. To save the settings and close the dialog box, click OK.
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Setting Map Display Options
Setting the Map Color Options
 To set the map color options
1. Make a map view the active view in the Qual Browser window.
2. To open the Display Options Dialog Box, choose Display > Display Options, or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Color tab. The Map or Ion Map Color Page – Display Options Dialog Box
opens.
Figure 41. Color page for a Map view in the Display Options dialog box
4. To select the color of the framing lines, click Line. The Color dialog box opens with a
color palette so that you can select a preset color or customize a color.
5. To select the color of the solid fill for the active map, click Fill solid. The Color dialog
box opens with a color palette so that you can select a preset color or customize a color.
6. To select the color of the backdrop (background), click Backdrop. The Color dialog box
opens with a color palette so that you can select a preset color or customize a color.
Backdrop is active only when you select the Overlay 3D style.
7. To select grayscale or color, choose one of these options:
• To plot the map in grayscale, select the Grayscale check box.
• To plot the map in color, clear the Grayscale check box.
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Setting Map Display Options
8. Use the shade buttons (0%, 20%, 40%, 60%, 80%, and 100%) to change the map’s color
at 0%, 20%, 40%, 60%, 80%, and 100% relative abundance.
9. To select log scale or linear scale, choose one of these options:
• To display the color of the map in a logarithmic scale, select the Log Scale check box.
The factor width that you set in the Factor box determines the scaling between color
bands.
• To display the map in a linear scale, clear the Log Scale check box.
10. To save the settings and close the dialog box, click OK.
Setting the Map Normalization Options
 To set the map normalization options
1. Make a map view the active view in the Qual Browser window.
2. To open the Display Options Dialog Box, choose Display > Display Options, or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Normalization tab. The Map or Ion Map Normalization Page – Display
Options Dialog Box opens.
Figure 42. Normalization page for a Map view in the Display Options dialog box
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Setting Map Display Options
4. To specify the mass grouping, choose one of these options:
• To use the largest peak within each band (mass range) to determine the intensity of
the band, select the Base peak option.
• To use the sum of the intensities within each band (mass range) to determine the
intensity of the band, select the Sum option.
5. To specify the normalization options, choose from these options:
• To normalize the map to the largest peak in the raw file, select the Normalize to
entire file check box.
• To normalize the map to a fixed intensity value, select the Fix scale check box. Type
an intensity value between 0.01 and 1e+20 in the Fix scale box.
• To determine the intensity range for normalizing the map, select the Auto range
option.
• To change the intensity range (Y-axis range), type the minimum and maximum
intensities you want to display in the Intensity Range box. The valid range is
–200.000 to 200.000 percent.
6. To specify a peak to normalize the Y-axis maximum, choose one of these options:
• To normalize (set the Y-axis maximum) to the largest peak in the subsection
(division), select the Largest peak in subsection option.
• To normalize (set the Y-axis maximum) to the largest peak in the time range (all
subsections), select the Largest peak in time range option.
• To normalize (set the Y-axis maximum) to the largest peak in all times, select the
Largest peak in all times option.
7. To specify the normalization option for multiple mass plots, choose one of the following:
• To normalize each mass plot individually, select the Individually option.
• To normalize all mass plots equally, select the All the same option.
8. To save the settings and close the dialog box, click OK.
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Setting Map Display Options
Setting the Band Width
Use the Band Width page to specify the size of the bands displaying relative abundance to
make the display clearer. The Band width value specifies the band width in amu units. The
range of acceptable values is from 0.001 to 50.0, with a default value of 1.0.
 To define the band width in a map view
1. Open a raw file and display a map view in Qual Browser.
2. Choose Display > Display Options or right-click the cell and choose Display Options
from the shortcut menu.
3. Click the Band Width tab. The Map or Ion Map Band Width Page – Display Options
Dialog Box opens.
Figure 43. Band Width page of the Display Options dialog box
4. Set the band width to determine the height of the band.
5. To save the setting and close the dialog box, click OK.
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Setting Map Display Options
The map view reflects the chosen band size.
Figure 44. Map view with changed band width
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Setting Spectrum Options
A spectrum view shows the intensities of one or more masses as a function of time. These
procedures describe how to manipulate spectra.
Contents
• Setting Spectrum Display Options
• Setting Spectrum List Display Options
• Setting Up Spectrum Plot Ranges
• Specifying Spectrum Composition
• Subtracting Background Spectra
Setting Spectrum Display Options
The Display Options dialog box consists of six tabbed pages: Style, Color, Label, Axis,
Normalization, and Composition. It contains a small display area showing the active cell.
Use these options to preview the effects of different settings before applying them.
Use one or more of these procedures to set up spectrum ranges and options:
• Setting the Spectrum Axis Options
• Setting the Spectrum Color Options
• Setting the Spectrum Label Options
• Setting the Spectrum Normalization Options
• Setting the Spectrum Style Options
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Setting Spectrum Options
Setting Spectrum Display Options
Setting the Spectrum Axis Options
 To set the spectrum axis options
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Axis tab. The Spectrum Axis Page – Display Options Dialog Box opens.
Figure 45. Axis page for a Spectrum view in the Display Options dialog box
4. To change the name of the X, Y, or Z axis, type the new name in the X, Y, or
Z Name box.
5. To change the time when the data system displays the axis label, select Never, On Print,
or Always in the Show name list.
6. To move the displayed plot from the X or Y axes, select the Offset check box for X or Y.
To turn off axis offset, clear the X or Y Offset check box.
7. To set up mass range splitting, choose from these options:
a. To split the mass range, select the Split range check box.
b. To change the number of divisions (subsections), type the new number in the
Divisions box.
To display only one mass range, clear the Split range check box.
8. To save the settings and close the dialog box, click OK.
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Setting Spectrum Display Options
Setting the Spectrum Color Options
 To set the spectrum color options
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Color tab. The Spectrum Color Page – Display Options Dialog Box opens.
Figure 46. Color page for a Spectrum view in the Display Options dialog box
4. To select the color of regular (unflagged) peaks, choose Regular. The Color dialog box
opens with a color palette so that you can select a preset color or customize a color.
5. To select the color of saturated peaks, choose Saturated. The Color dialog box opens with
a color palette so that you can select a preset color or customize a color.
6. To select the color of the profile style, choose Profile. The Color dialog box opens with a
color palette where you can select a preset color or customize a color.
7. To select the color of the low intensity areas of the spectrum, click 0% in the Shade area.
The Color dialog box opens with a color palette where you can select a preset color or
customize a color.
8. To select the color of the high intensity areas of the spectrum, click 100% in the Shade
area. The Color dialog box opens with a color palette where you can select a preset color
or customize a color.
9. To save the settings and close the dialog box, click OK.
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Setting Spectrum Options
Setting Spectrum Display Options
Setting the Spectrum Label Options
 To set the spectrum label options
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Labels tab. The Spectrum Labels Page – Display Options Dialog Box opens.
Figure 47. Labels page for a Spectrum view in the Display Options dialog box
4. To define the spectrum labels, choose from these options:
• To display an m/z label over spectrum peaks, select the Mass check box. Specify in the
Decimals text box the number of digits The application displays to the right of the
decimal when it displays m/z labels over the peaks in a spectrum. To hide an
m/z label, clear the Mass check box.
• To display letters above spectrum peaks to provide supplemental information about
the peak data, click the Flags check box. For example, if a peak is saturated, the
application displays an S above the peak. To hide supplemental information, clear the
Flags check box.
5. To specify the style of the spectrum labels, choose from these options:
• To move a label from its normal position to avoid conflict with another label, select
the Offset check box. Type the size of the offset (in number of characters) in the Size
box.
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Setting Spectrum Display Options
• To write vertical labels, select the Rotated check box. To write horizontal labels, clear
the Rotated check box.
• To place a box around each peak label, select the Boxed check box. If you do not
want to have a box around the label, clear the check box.
6. To specify a percent of the base peak so that the data system labels all peaks above that
percent, type a value in the Label Threshold box.
7. To save the settings and close the dialog box, click OK.
Setting the Spectrum Normalization Options
 To set the spectrum normalization options
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Normalization tab. The Spectrum Normalization Page – Display Options
Dialog Box opens.
Figure 48. Normalization page for a Spectrum view in the Display Options dialog box
4. To change the intensity range (Y-axis range), type the minimum and maximum
intensities you want to display in the Intensity Range box. The valid range is
0.000 – 100.000 percent.
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Setting Spectrum Options
Setting Spectrum Display Options
5. To specify the spectrum normalization option, choose one of these options:
• To normalize (set the Y-axis maximum) to the largest peak in the subsection
(division), select the Largest peak in subsection option.
• To normalize (set the Y-axis maximum) to the largest peak in the mass range, select
the Largest peak in range option.
• To normalize (set the Y-axis maximum) to the largest peak in the scan, select the
Largest peak in scan option.
6. To specify the multiple scan normalization option, choose one of these options:
• To normalize each mass plot individually, select the Individually option.
• To normalize all mass plots equally, select the All the same option.
7. To save the settings and close the dialog box, click OK.
Setting the Spectrum Style Options
 To set the spectrum style options
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Style tab. The Spectrum Style Page – Display Options Dialog Box opens.
Figure 49. Style page in the Spectrum view in the Display Options dialog box
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Setting Spectrum List Display Options
4. To specify the graphic style, choose one of these options in the Plotting area:
• To choose the graphic style based on the data acquisition method for the active
spectrum, select the Automatic option.
• To display point-to-point peak profiles, select the Point to point option.
• To display the graphic as vertical lines, select the Stick option.
• To display the spectrum as a shaded representation of intensity in each amu band for
the active spectrum, select the Shade option.
5. To specify the arrangement style, choose one of these options:
• To stack plots vertically with no overlap, select the Stack option.
• To overlay plots vertically with optional horizontal skew (time offset), select the
Overlay (3D) option.
6. To set the elevation angle (from 0 to 60 degrees) for 3D plots, drag the Elevation slider or
click the left or right arrow until you reach the desired angle.
7. To set the skew angle (from 0 to 45 degrees) for 3D plots, drag the Skew slider or click
the left or right arrow until you reach the desired angle.
8. To add a backdrop to 3D plots, select the Draw Backdrop check box. To remove a
backdrop, clear the Draw Backdrop check box.
9. To save the settings and close the dialog box, click OK.
Setting Spectrum List Display Options
Use one or more of these procedures to set up spectrum list display options:
• Setting the Spectrum List Normalization Options
• Setting the Spectrum List Style Options
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Setting Spectrum Options
Setting Spectrum List Display Options
Setting the Spectrum List Normalization Options
 To set the spectrum list normalization options
1. Open a spectrum list view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Normalization tab. The Spectrum List Normalization Page – Display Options
Dialog Box opens.
Figure 50. Normalization page for a Spectrum List view in the Display Options dialog box
4. To change the intensity range, type the minimum and maximum intensities you want to
display in the Intensity range box. The valid range is 0.000 – 100.000 percent.
5. To specify the spectrum list normalization option, choose one of these options:
• To normalize to the largest peak in the subsection, select the Largest peak in
subsection option.
• To normalize to the largest peak in the mass range, select the Largest peak in
selected time range option.
• To normalize to the largest peak in the scan, select the Largest peak in all times
option.
6. To save the settings and close the dialog box, click OK.
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Setting Spectrum List Display Options
Setting the Spectrum List Style Options
 To set the spectrum list style options
1. Open a spectrum list view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Style tab. The Spectrum List Style Page – Display Options Dialog Box opens.
Figure 51. Style page for a Spectrum List view in the Display Options dialog box
4. To specify the number of peaks in the spectrum list, choose one of these options:
• To display m/z, intensity, and relative intensity of all spectrum peaks in the range
specified in the Spectrum List Ranges dialog box or as specified in the active scan
filter, select the All peaks check box.
• To specify a maximum number of peaks in the spectrum list, clear the All peaks
check box and type a maximum number of peaks in the Top box.
5. To specify peak order, choose one of these options in the Order by area:
• To order the spectrum list by m/z (in ascending order), select the Mass option.
• To order the spectrum list by intensity (in descending order), select the Intensity
option.
6. To save the settings and close the dialog box, click OK.
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Setting Spectrum Options
Setting Up Spectrum Plot Ranges
Setting Up Spectrum Plot Ranges
Use one or more of these procedures to set up spectrum plot ranges:
• Setting Spectrum Ranges
• Setting Spectrum Automatic Processing
Setting Spectrum Ranges
Use the Spectrum Ranges dialog box to view and edit the mass range, time range, background
subtraction, and smoothing parameters for all the plots in a spectrum cell (see Figure 52).
 To set the mass range and time range for a spectrum plot
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Spectrum Ranges Dialog Box, choose one of these options:
• Right-click a spectrum plot in the cell and choose Ranges from the shortcut menu.
• Choose Display > Ranges.
• Click
on the Qual Browser toolbar.
3. Click the Ranges tab.
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Setting Up Spectrum Plot Ranges
Figure 52. Ranges page of the Spectrum Ranges dialog box
4. To choose a raw file, select from the table of all active files in the current cell. To change
the source of the active plot, choose one of these options:
• Select a file from the table.
• Click Browse adjacent to the Raw file list and browse to the required file.
• Type the full path and file name of the required file in the Raw file box.
5. To specify the mass/wavelength range, choose one of these options:
• To specify the mass range, type the first mass and last mass of the scan in the
Mass Range box. The format is First Mass (Range 1) – Last Mass (Range 1) +
First Mass (Range 2) – Last Mass (Range 2).
• To specify the wavelength range, type the shortest wavelength and longest wavelength
of the scan in the Wavelength Range box. The format is shortest wavelength – longest
wavelength.
6. To specify the time range, type the lower and upper time limits in minutes, separated by a
dash with no spaces, in the Time Range box.
7. To specify the scan filter, select from options in the Filter list that are stored in the
.raw file.
If your MS detector has the MSn Browser feature, first select the Filter Type. Select Scan
to display the scan filters or select Process to display the processing filters.
8. To specify the fix scale setting, choose one of these options in the Range area:
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Setting Spectrum Options
Setting Up Spectrum Plot Ranges
• To turn on the maximum range for the Y-axis of the active spectrum, select the
Fix scale check box.
• To change the value, type the new maximum Y-axis value in the Fix Scale box.
• To turn off the fix scale setting, clear the Fix scale check box.
9. To turn spectrum averaging on or off, choose one of these options in the Range area:
• To average all scans defined by the mass range, time range, and filter settings in the
Spectrum Ranges dialog box, select the Average check box.
• To turn off spectrum averaging, clear the Average check box.
10. To determine whether background subtraction has been performed, review these settings
under Background Subtraction:
The Time range 1 check box and Time range 2 check box indicate whether or not
background subtraction has been performed for the active spectrum. When the check box
is selected, the data system displays the time range used for background subtraction in the
Time Range 1 or Time Range 2 boxes.
The system enters these settings when you perform a background subtraction using the
Actions > Subtract Spectra commands from the Qual Browser window.
11. To save the settings and close the dialog box, click OK.
Setting Spectrum Automatic Processing
 To set the mass range and time range for a mass spectrum
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Spectrum Ranges Dialog Box, right-click a spectrum plot in the cell and
choose Ranges from the shortcut menu or choose Display > Ranges.
3. Click the Automatic Processing tab.
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6 Setting Spectrum Options
Setting Up Spectrum Plot Ranges
Figure 53. Automatic Processing page of the Spectrum Ranges dialog box
4. To smooth all scans defined by the mass range, time range, and filter settings in the
Spectrum Ranges dialog box, select the Enable check box under Smoothing. To turn off
spectrum smoothing, clear the Enable check box.
5. To change the type of smoothing, select either Boxcar or Gaussian from the Type list.
6. To change the number of smoothing points, type the new number of points in the Points
box. The valid range for smoothing points includes odd numbers from 3 for minimum
smoothing to 15 for maximum smoothing.
7. To refine all scans defined by the mass range, time range, and filter settings in the
Spectrum Ranges dialog box, select the Enable check box under Refine. To turn off
spectrum smoothing, clear the Enable check box.
8. Type a time range for Refine in the Window Size box. Set this parameter to the expected
peak width.
9. Type a limit for low intensity ions in the Noise threshold box. Start with a value of zero,
increasing the setting until the procedure eliminates spurious masses generated by
background noise.
10. To include reference and exception peaks in the display of spectra, select the Reference
and exception peaks check box. To exclude reference and exception peaks, clear the
Reference and exception peaks check box.
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Setting Spectrum Options
Specifying Spectrum Composition
11. To use mass tolerance, select the Use user defined check box. Type a value from 0.1 to
50000.0 in the Mass Tolerance box, and then select units. To turn off mass tolerance,
clear the Use user defined check box.
12. In the Decimals box under Mass precision, specify the number of digits the Xcalibur
application displays to the right of the decimal when it displays m/z labels over the peaks
in a spectrum.
13. To save the settings and close the dialog box, click OK.
Specifying Spectrum Composition
Use the Spectrum Composition page (Figure 54) to add chemical formulas and related labels
to the spectrum. The Xcalibur data system determines which chemical formulas have an
m/z value most like that of the experimental spectrum peaks.
 To specify spectrum composition
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box, choose Display > Display Options or
right-click the cell and choose Display Options from the shortcut menu.
3. Click the Composition tab. The Spectrum Composition page of the Display Options
dialog box opens.
Figure 54. Spectrum Composition page for a Spectrum view in the Display Options dialog box
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Subtracting Background Spectra
4. To displays the chemical formula labels at the top of spectrum peaks, select the Elemental
Composition check box. The application determines which chemical formulas have a
m/z value most like that of the spectrum peaks.
5. Specify how many of the most likely chemical formulas you want the application to
display at the top of spectrum peaks. Type a number in the Formulae box.
6. To display the theoretical m/z of the chemical formulas that the application determines,
select the Theo. mass check box. The Xcalibur application displays the theoretical m/z to
the right of the formula separated by an equal sign (=).
7. To display the value of the ring and double-bond equivalents that the data system
calculates for the chemical formulas, select the RDB equiv. check box. The Xcalibur
application displays the ring and double-bond equivalent value under the chemical
formula.
Ring and double-bond equivalents provide a measure of the number of unsaturated
bonds in a compound. They limit the calculated formulas to only those that make sense
chemically.
8. To label the peak with the difference between the theoretical and experimental m/z, select
the Delta check box.
9. To specify the units to use when calculating the difference between the theoretical and
experimental m/z, select amu, mmu, or ppm in the Delta units area.
10. To save the settings and close the dialog box, click OK.
Subtracting Background Spectra
Use a chromatogram view to subtract background from a spectrum view, subtracting
background from either one range (either side of the chromatogram peak of interest) or two
ranges (both sides of the chromatogram peak of interest).
 To subtract background spectra
1. Open a chromatogram view in Qual Browser.
2. Open a spectrum view in another cell. You might need to add a new cell to the window.
3. Pin the cell containing the spectrum view.
4. Drag the cursor through the chromatogram peak of interest. This action updates the
pinned spectrum view with an averaged spectrum using the scans in the indicated range.
5. To select one or two ranges for spectrum subtraction, choose one of these options:
• Choose Actions > Subtract Spectra > 1 (or 2) Range.
• Right-click the spectrum cell and choose Subtract Spectra > 1 (or 2) Range from the
shortcut menu.
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Setting Spectrum Options
Subtracting Background Spectra
6. Identify a representative baseline region in the chromatogram view close to the peak of
interest. Drag the new cursor to select a time range in this region.
7. If you have selected the 2 Range option, choose a region on the other side of the peak of
interest.
8. Release the mouse button. The data system subtracts an average of the selected scans and
redraws the spectrum view. The Spectrum view header shows the number of subtracted
scans. For example, SB: 12 indicates that Qual Browser has applied background
subtraction to the spectrum using 12 scans.
9. To see the selected time ranges of the scans that were subtracted, choose Display >
Ranges to open the Spectrum Ranges dialog box and review the Time Range 1 box.
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Qual Browser Reference
Use Qual Browser to open a raw or result file, display chromatograms, spectra, and maps of
the data, choose spectra from chromatograms, average scans, subtract background data, create
and save layouts, add text and graphics, apply filters, amplify regions, and print the resulting
graphic.
Contents
• Qual Browser Menus
• Qual Browser Toolbars
• Qual Browser Views
• Qual Browser Info Bar
• Qual Browser Dialog Boxes
Qual Browser Menus
The Qual Browser window menu bar has these menus:
• Actions Menu
• Display Menu
• Edit Menu
• File Menu
• Grid Menu
• Help Menu
• Tools Menu
• View Menu
• Window Menu
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Actions Menu
Table 7. Actions menu (Sheet 1 of 3)
Command
Description
Subtract Spectra
1 Range
Perform a peak-by-peak subtraction of selected scans contained in one background
region of a chromatogram view from the current spectrum view. Use this command
to eliminate background scans that might interfere with the display of spectrum
peaks of interest. The subtracted scans must use the same scan filter as the target
scans. For more information, see “Subtracting Background Spectra” on page 99.
2 Ranges
Perform a peak-by-peak subtraction of selected scans contained in two selected
background regions of a chromatogram view from the current spectrum view. Use
this command to eliminate background peaks that might be interfering with the
display of spectrum peaks of interest. The subtracted scans must use the same scan
filter as the target scans. For more information, see “Subtracting Background
Spectra” on page 99.
Clear
Remove all subtract spectra modifications to the spectrum view. The Xcalibur
application also removes the SB: xx notation in the spectrum view header to
indicate that the spectrum view has been returned to the original display before
application of the Subtract Spectra command.
Peak Detection
Settings
View a page specific to one of the Xcalibur peak detection algorithms displays and
change the parameters used by Qual Browser to identify and integrate
chromatogram peaks.
The Help button on the Genesis Peak Detection Settings Page appears at the
extreme bottom of the page.
Toggle Detection In
This Plot
Detect and integrate all peaks in the selected chromatogram plot using the current
peak detection and integration settings. The Xcalibur application adds a check mark
to the left of the menu command.
Choose this command a second time to undo the peak detection and remove the
check mark from the left of the menu command.
Open a raw file to make this command active.
Toggle Detection In
All Plots
Detect and integrate all peaks in all selected and unselected chromatogram plots in
the active cell using the current peak detection and integration settings. The
Xcalibur application adds a check mark to the left of the menu command.
Choose this command a second time to undo all detected peaks and remove the
check mark from the left of the menu command.
Open a raw file to make this command active.
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Table 7. Actions menu (Sheet 2 of 3)
Command
Set Peak Detection
Algorithm and Detect
In This Plot
Description
View a list of the Xcalibur data system peak detection algorithms. Click one of the
algorithm names in the list to display the page for that algorithm and to use the
algorithm to detect chromatogram peaks in the active chromatogram cell. See
Chromatogram View.
Open a raw file to make this command active.
Set Peak Detection
Algorithm and Detect
In All Plots
View a list of the Xcalibur data system peak detection algorithms. Click one of the
algorithm names in the list to display the page for that algorithm and to use the
algorithm to detect chromatogram peaks in all the cells that are currently displayed.
See Chromatogram View.
Open a raw file to make this command active.
Add Peaks
Detect and integrate any peak in the active cell. The Xcalibur data system changes
the cursor to the add peaks cursor,
. To detect and integrate a peak, drag this
cursor horizontally across the peak. The application marks the added peak with a
blue baseline,
, and integrates the peak. The application also adds a check
mark to the left of the menu command.
Choose Actions > Peak Detection > Add Peaks a second time to return the add
peaks cursor to the default cursor and remove the check mark from the left of the
menu command.
 To label all detected peaks with their respective area, retention time, or
other peak parameters
1. Choose Display > Display Options. The Display Options Dialog Box opens.
2. Click the Label tab, select peak label parameters.
3. Choose OK. The data system displays the selected labels at the top of all peaks
in the plot.
Open a raw file to make this command active.
Delete Peaks
Delete selected peaks in the active cell. The application changes the cursor to
Click this cursor within each peak boundary, indicated by the blue baseline,
, of the peak(s) that you want to delete.
One or more peaks must be detected (as indicated by
to be active.
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Table 7. Actions menu (Sheet 3 of 3)
Command
Manual Noise Region
Selection
Description
Choose this command and drag the cursor horizontally across the region of the
chromatogram that you want to select as the noise region. The Xcalibur application
marks the region with a red baseline.
The application calculates noise based on the data points you select. It uses all
selected data points as noise points and calculates noise based on those points. You
can select the noise region from an individual trace or different noise regions from
multiple traces.
Open a raw file and select a chromatogram to make this button active.
Delete Manual Noise
Selection
Choose this command and drag the cursor over the region that was previously
selected as the noise region. Release the mouse button to delete the noise region.
Peak Purity
Peak Purity
View Peak Purity settings.
Open a raw data file from a PDA analysis and select PDA from the Detector list in
the Ranges dialog box to make this command active.
Library
Search
Submit the active spectrum to a library search. The Xcalibur application displays the
results of the search in the Library Search Results window.
Export To Library
Browser
Exports the active spectrum to the Library Browser.
Export to AMDIS
Exports the active spectrum to AMDIS.
Options
Choose the libraries used during a library search. You can also change various
parameters that determine how the search is carried out.
AutoFilter
AutoFilter
Apply all of the scan filters in the current raw file and open an AutoFilter display in
the active cell.
The AutoFilter display consists of a vertical sequence of chromatogram plots. The
first chromatogram displays the TIC with no scan filter. Below the first
chromatogram are up to seven TIC scan filter chromatograms, one chromatogram
plot for each scan filter. For additional information, see the Scan Filter View.
You can also apply scan filters to one or more plots from the Chromatogram Ranges
Dialog Box.
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Display Menu
Table 8. Display menu (Sheet 1 of 3)
Command
Ranges
Description
Open a Ranges dialog box for the active view. There is a Ranges dialog box for each
of these view types:
Chromatogram view: Chromatogram Ranges Dialog Box
Spectrum view: Spectrum Ranges Dialog Box
Map view: Map Ranges Dialog Box (Map)
Ion Map: Map Ranges Dialog Box (Ion Map)
Spectrum List view: Spectrum List Ranges Dialog Box
Scan Header view: Scan Header Range Dialog Box
Scan Filter view: Scan Filter Range Dialog Box
The Ranges command is not available for Report views.
Mass Options
Specify parameters for mass tolerance and mass precision for the displayed
chromatogram, spectrum, and spectrum list plots.
Display Options
Select the style, color, label [chromatogram and spectrum only], axis, normalization,
and smooth [chromatogram only] options for your chromatogram, spectrum,
or map.
Annotate
Add Text
Add text to the active plot.
Add Graphics
Add simple graphic objects such as lines or boxes to the active plot.
Clear
cursor so that you can selectively remove text or graphics
Activate the
annotation entries. To remove graphics or text, drag the cursor horizontally above
or below the text or graphic. The data system removes the text or graphic(s) and
changes the cursor back to your default cursor. Repeat this procedure to remove
other annotations. To replace text, select the Undo command or click
in the
toolbar. To remove all of the annotations from the active cell, use the Clear All
command.
Clear All
Remove all text and graphics annotation entries in the active cell. To remove
annotations one at a time, use the Clear command.
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Table 8. Display menu (Sheet 2 of 3)
Command
Description
Zoom
Zoom In Y
Zoom in on the Y-axis by a factor of two (2) from the current baseline to show more
detail. For example, you can change the Y-axis range from 0–100 to 0–50.
Zoom Out Y
Open out on the Y-axis by a factor of two (2) to show more data. For example, you
can change the Y-axis range from 0–25 to 0–50.
Auto Range
View the chromatogram, which is normalized from the minimum to the maximum
signal. Auto Range is useful for PDA and UV data.
Normalize
Normalize the intensity scale of the data display to a fixed range on the Y-axis. For
example, from 0–25 percent to 0–100 percent.
Zoom In X
Make the X-axis larger by a factor of two (2) to show more detail. For example, you
can change the X-axis range from 0–20 to 5–15.
Zoom Out X
Make the X-axis smaller by a factor of two (2) from the center to show more data.
For example, you can change the X-axis range from 7.5–12.5 to 5–15.
Display All
View all data on the X-axis or all text in a report. For example, you can change the
X-axis range from 7.5–12.5 to 0–20.
Reset
Restores the data display to the full range of the X-axis and Y-axis.
Drag With Cursor
Change the cursor to
the plot left or right.
Forward
Display data to the left of the active displayed range. This command is incremental
so you might need to use it multiple times to display the region of interest. To move
the display to the right, use the Back command.
Back
Display data to the right of the active displayed range. This command is incremental
so you might need to use it multiple times to display the region of interest. To move
the display to the left, use the Forward command.
Next Scan
Display the next mass scan with its scan number.
Previous Scan
Display the previous mass scan with its scan number.
Pan
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Table 8. Display menu (Sheet 3 of 3)
Command
Description
Amplify
Other Factor
Enter an amplification factor in the range 1.1 to 1000.0. You can apply this factor to
a region of a chromatogram view, spectrum view, or map view. The value is placed
and displayed in the Amplify Factors combo box.
When you click OK, the Xcalibur application displays this cursor:
. To amplify a
region, drag the cursor horizontally over the region. The application amplifies the
region, places this label above the amplified region: ------x3.2------, and displays the
original cursor.
To turn off
before using it, click
.
To cancel one or more amplified regions of a graph, use the Cancel Amplified
Region button
or the Clear command.
To cancel all amplified regions of a graph, use the Clear All command.
Clear
Cancel one or more amplified regions of a plot. The Xcalibur application change the
cursor to
. To clear an amplified region, drag the cursor horizontally extending
slightly beyond the start and end of the region. The application removes the
amplification, removes the amplification labels (such as ------x5------), and displays
the original cursor.
To turn off
before using it, click
.
To remove all amplified regions from a graphic, see the Clear All command.
Clear All
Cancel all amplified regions of an active plot. The Xcalibur application removes the
amplification, removes the amplification labels (such as ------x5------), and displays
the original cursor.
To cancel one or more amplified regions of a graph, use the Cancel Amplified
Region button
or the Clear command.
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Edit Menu
Table 9. Edit menu
Command
Undo
Description
Cancel your previous action. For example, if you have just deleted an entry or
annotation, choose the Undo command to replace the deleted entry or annotation.
Also, if you have just completed an entry or annotation, choose the Undo command
to delete the entry or annotation.
If you complete two actions, the Undo command only undoes the previous action
and not the first action.
Copy Cell
Copy the active cell to the clipboard.
Paste Cell
Paste a cell that is stored on the clipboard to the active cell. This command is often
used after a Copy Cell command or after choosing the Copy Cell button.
Copy View
Copy the active view to the clipboard. You can then use the Paste command of
another application, such as Microsoft Word™ or Microsoft Excel™, to copy the view
object to a document or spreadsheet. To edit the view object after it is pasted, return
to the Xcalibur data system to edit the view object and repeat the copy/paste
procedure.
Copy Special
Enter the height and width to be used to format the output to the clipboard. You
can also specify the units for the height and width as either millimeters or inches.
File Menu
Table 10. File menu (Sheet 1 of 2)
Command
Description
Open
Open
Find and open a raw file or a layout file that already exists.
Open Sequence
Select a sequence file.
Open Result File
Select a result file. The Xcalibur application displays a warning message if your
selected results file does not contain any qualitative data.
To view the results file for a raw file in an opened sequence, right-click the filename
on the Sequence Information page of the Info Bar. Then, choose Open Results File
from the popup context menu. The results file is displayed in the Qual Browser
workspace and the Results File Information page of the Info Bar.
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Table 10. File menu (Sheet 2 of 2)
Command
Description
Layout
Apply
Select a layout file.
Apply Default
Apply the default layout to the active window.
Save
Save the current layout. If the file has not been named, The Save Layout File dialog
box opens. Provide a name. The Xcalibur application applies the .lyt layout file
extension.
Save As
Save the current layout with a new name. The Xcalibur application applies the .lyt
layout file extension.
Save As Default
Save the current layout as the default layout for new windows.
Summary Information
Read, modify, or delete file summary information about the active file.
Other Commands
Close All
Close all the windows in Qual Browser.
Save Composite
Spectrum Data
Save a document as a different name or location.
Change Dataset Name
Select a dataset from a predefined list of names.
Display composite spectrum data with MSn Browser to make this command active.
The text of this menu item might be different if the administrator chose to use
another name for a dataset. For example, this menu item might be
Change Job Name.
Audit Trail
View all auditable events and changes made to data files in the current application.
Print
Specify what you want to print and how to print it.
Print Preview
Preview the pages before printing.
Page Setup
Select from these options: printer, form, orientation, and margins.
Recent Files
View the paths and names of the most recently used four files. These are located
above the Exit command. The Xcalibur application displays both open and closed
files. Click a displayed file to load it. If the selected file was closed, the data system
opens it.
Exit
Close the active window. If you exit before clicking OK from an active dialog box,
the data system prompts you to save your changes.
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Grid Menu
Table 11. Grid menu (Sheet 1 of 4)
Command
Description
Insert Cells
Left
Insert a cell or cells to the left of the active cell.
Right
Insert a cell or cells to the right of the active cell.
Above
Insert a cell or cells above the active cell.
Below
Insert a cell or cells below the active cell.
Row
Delete the grid row containing the active cell.
Column
Delete the grid column containing the active cell.
All Cells
Delete all cells in the view except the active cell.
Delete
Cell Size
Cell Size
Adjust the column width and row height. You can make adjustments relative to
other columns and rows.
This menu item is not available if you have only one cell.
Expand Cell
110
Full Width
Expand a cell to the full width of the grid.
Full Height
Expand a cell to the full height of the grid.
Full View
Expand a cell to the full size of the grid.
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Table 11. Grid menu (Sheet 2 of 4)
Command
Description
Reduce Cell
10%
Temporarily reduce the grid column size of the active cell to 10% of the original size.
The Xcalibur data system responds by expanding the right or left neighboring grid
columns so that the cells in these grid columns can be viewed at increased
resolution.
If there is only one column in the grid, this command temporarily reduces the grid
row size of the active cell to 10% of the original size. The data system responds by
expanding the top or bottom neighboring grid rows so that the cells in these grid
rows can be viewed at increased resolution.
To restore the grid column size to the original width, click
20%
in the toolbar.
Temporarily reduce the grid column size of the active cell to 20% of the original size.
The Xcalibur data system responds by expanding the right or left neighboring grid
columns so that the cells in these grid columns can be viewed at increased
resolution.
If there is only one column in the grid, this command temporarily reduces the grid
row size of the active cell to 20% of the original size. The data system responds by
expanding the top or bottom neighboring grid rows so that the cells in these grid
rows can be viewed at increased resolution.
To restore the grid column size to the original width, click
50%
in the toolbar.
Temporarily reduce the grid column size of the active cell to 50% of the original size.
The Xcalibur data system responds by expanding the right or left neighboring grid
columns so that the cells in these grid columns can be viewed at increased
resolution.
If there is only one column in the grid, this command temporarily reduces the grid
row size of the active cell to 50% of the original size. The data system responds by
expanding the top or bottom neighboring grid rows so that the cells in these grid
rows can be viewed at increased resolution.
To restore the grid column size to the original width, click
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Table 11. Grid menu (Sheet 3 of 4)
Command
Description
Group Row
Group Row
Group a row containing two or more cells in a view containing two or more rows.
After you have grouped cells, the Xcalibur application updates any changes you
make to ungrouped cells in the same view to all of the grouped cells.
To insert and delete cells, use Grid > Insert cells and Grid > Delete commands
before you use the Group Row command.
To group a row, you must have at least two rows of cells in your view and the
grouped row need to have at least two cells.
The Xcalibur application makes the grouped row cells active, indicated by a gray
border around the grouped row cells and deactivates most menu commands and
buttons on the toolbar.
For example, consider the following view:
Chromatogram
Spectrum
Mass List
If you group spectrum and mass list cells using the Group Row command, the
application simultaneously updates mass list and spectrum cells as you make changes
in the Chromatogram cell.
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Table 11. Grid menu (Sheet 4 of 4)
Command
Description
Group Column
Group Column
Group a column containing two or more cells in a view containing two or more
columns. After you have grouped cells, the Xcalibur application updates any changes
you make to ungrouped cells in the same view to all of the grouped cells.
To insert and delete cells, use Grid > Insert cells and Grid > Delete before you use
the Group Column command. To group a column, you must have at least two
columns of cells in your view and the grouped column needs to have at least two
cells.
The application makes the grouped column cells active, indicated by a gray border
around the grouped cells, and deactivates most menu commands and buttons on the
toolbar.
For example, consider the following view:
Spectrum
Chromatogram
Mass List
If you group spectrum and mass list cells using the Group Column command, the
application simultaneously updates mass list and spectrum cells as you make changes
in the Chromatogram cell.
Grid Lines
Grid Lines
View or hide grid lines between cells.
Help Menu
Table 12. Help menu
Command
Description
Qual Browser Help
Open Xcalibur Help and display Help for the Qual Browser window.
Xcalibur Help
Open Xcalibur Help.
Glossary
Open the glossary.
How To Use Online Help
Open Help that describes how to use the Help viewer.
About Qual Browser
View the installed version number of the Qual Browser program and the Thermo
Fisher Scientific copyright notice.
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Qual Browser Menus
Tools Menu
Table 13. Tools menu
Command
Description
Background Subtract
Create a new raw file by subtracting one raw file from another.
Add Tools
Add and remove tools [programs] on the Qual Browser window menu bar. The
Xcalibur application displays the added programs as menu commands when you
choose the Tools menu from the Qual Browser window.
View Menu
Table 14. View menu (Sheet 1 of 2)
Command
Description
Views
Chromatogram
View one or more chromatograms in the active cell. The Xcalibur application
displays any chromatograms defined by the settings in the Chromatogram Ranges
Dialog Box.
Spectrum
View a spectrum in the active cell. The application displays the spectrum defined by
the settings in the Spectrum List Ranges Dialog Box.
Map
View a three-dimensional x, y, z map of the parameters time, relative peak height,
and m/z in the active cell. The application displays the map defined by the settings
in the Map Ranges Dialog Box.
Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak height,
and m/z in the active cell. The application displays the map defined by the settings
in the Map Ranges Dialog Box.
Spectrum List
View the instrument method in the active cell. The instrument method contains the
scan number and retention time for the scan and tabular data for m/z, intensity, and
relative intensity. The application displays the instrument method defined by the
settings in the Spectrum List Ranges Dialog Box.
Scan Header
View the scan header of the current scan in the active cell. The application displays
the scan header for the scan that is closest to the time set in the Scan Header Range
Dialog Box.
Scan Filters
View all of the scan filters used in all scans of the active raw file in the active cell.
The application displays the Scan Filter for the scan that is closest to the time set in
the Scan Filter Range Dialog Box.
Tune Method
View the tune method stored in the active raw file in the active cell.
Reports
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Table 14. View menu (Sheet 2 of 2)
Command
Description
Instrument Method
View the instrument method stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left arrows
located on the toolbar to browse to the pages of the instrument methods for the
other instruments.
These right and left arrow buttons are not active for raw files that contain only one
instrument method.
Sample Information
View the sample list information stored in the active raw file.
Status Log
View the status log stored with the active raw file.
Error Log
View the error log stored with the active raw file.
Other Commands
Add Plot
Activate automatic plot addition mode for grids containing multiple cells. Use this
option to build a layout quickly.
 To add a plot
1. Activate a mode (indicated by a check mark
alongside the menu item).
2. Pin the cell where you want to add a plot.
3. Click in another cell. A plot is added to the pinned cell.
4. Repeat this procedure to add further plots to pinned cells.
Toolbars
Show or hide the Main and Amplify toolbars. You can also turn ToolTips on or off
and choose to display large or small buttons on the toolbar.
Customize Toolbar
Customize the Main toolbar. You can add buttons for most Qual Browser menu
commands. You can also change the order of the buttons on the toolbar or remove
them from the toolbar.
Status Bar
Shows or hides the Status bar.
Info Bar
Shows or hides the Info bar.
Refresh
Update a view that is showing a chromatogram or a map from a raw file that is
currently being acquired. The Xcalibur application expands the display range to
show the full range of the data acquired so far. The range is reset only in the
currently active cell. The application refreshes other cells, but does not adjust their
ranges.
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Qual Browser Toolbars
Window Menu
Table 15. Window menu
Command
Description
New Window
Open a new data window in Qual Browser. The new window uses the default layout
and displays the most recently opened raw file.
Cascade
Arrange the current open windows in an overlapped arrangement with all the title
bars visible.
Tile
Arrange the current open windows in a tiled arrangement so that each window has
the same area of Qual Browser’s workspace.
Arrange Icons
Arrange iconized (minimized) windows along the bottom of the Qual Browser
workspace.
Qual Browser Toolbars
The Qual Browser window provides these toolbars:
• Qual Browser Amplify Toolbar
• Qual Browser Main Toolbar
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Qual Browser Amplify Toolbar
Use the Qual Browser window Amplify toolbar to amplify a region of a plot.
Table 16. Qual Browser Amplify toolbar
Button
Description
Amplify Factor
Set the Amplify Factor to apply to a region of a plot using the Amplify
button. Select an amplify factor from the preset values or type your
own.
For example, to amplify a region by a factor of 10.0, select:
.
Amplify
Enlarge a region of the active plot by the factor selected in the Amplify
Factor combo box. The Xcalibur application changes the cursor to
.
To amplify a region, drag the cursor horizontally over the region. The
application amplifies the region, places the following label above the
amplified region: ------x5------, and displays the original cursor.
To turn off
before using it, click
.
To cancel one or more amplified regions of a graph, use the
Clear command.
or the
To cancel all amplified regions of a graph, use the Clear All command.
Cancel Amplified Region
Cancel one or more amplified regions of a plot. The Xcalibur
application change the cursor to
. To clear an amplified region,
drag the cursor horizontally extending slightly beyond the start and
end of the region. The application removes the amplification, removes
the amplification labels (such as ------x5------), and displays the
original cursor.
To turn off
before using it, click
.
To remove all amplified regions from a graphic, use the Clear All
command.
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Qual Browser Toolbars
Qual Browser Main Toolbar
The Qual Browser window Main toolbar can be customized to display buttons for most menu
commands. The Qual Browser Amplify Toolbar is fixed. When you start Qual Browser for the
first time the Main toolbar contains buttons for some of the most frequently used commands.
You can fully customize the main toolbar.
To customize the main toolbar, choose the View > Customize Toolbar command. This opens
the Customize Toolbar dialog box .
All of the buttons available for the Qual Browser Main toolbar are displayed below under the
menu bar name that contains the corresponding command. Buttons on the toolbar are also
arranged in this manner in the Customize Toolbar dialog box.
Table 17. Qual Browser Main toolbar (Sheet 1 of 10)
Button
Description
File
118
Open
Find and open a file that already exists.
Open Sequence
Select a sequence file.
Open Result File
Select a results file.
Apply
Select a layout file.
Apply Default
Apply the default layout to the active data window.
Save
Enter audit information about the active file and select the location (disk and
directory) for the saved file. After you have entered audit information, press the
Continue button. The Save As dialog box opens.
Save As
Save the layout of the active data window. If it has not been saved before, the
Save Layout File dialog box opens. Provide a name for the layout.
Save As Default
Save the layout of the active data window as the default layout for new windows.
Summary Information
View summary information.
Close All
Close all data windows.
Print Preview
Specify what you want to print and how to print it before previewing the pages.
You can print your selection or return to Qual Browser.
Print
Select print range and print quality.
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Qual Browser Toolbars
Table 17. Qual Browser Main toolbar (Sheet 2 of 10)
Button
Description
Edit
Undo
Cancel your previous action. For example, if you have just deleted an entry or
annotation, choose the Undo command to replace the deleted entry or
annotation. Also, if you have just completed an entry or annotation, choose the
Undo command to delete the entry or annotation.
If you complete two actions, the Undo command only undoes the previous
action and not the first action.
Copy Cell
Copy the active cell to the clipboard.
Paste Cell
Paste a cell that is stored on the clipboard to the active cell.
Copy View
Copy the active grid to the clipboard.
Copy Special
Scale the output size of the clipboard image from the current cell or window.
Chromatogram
Change the view in the active cell to a chromatogram view.
Spectrum
Change the view in the active cell to a spectrum view.
Map
Change the view in the active cell to a map view.
Spectrum List
Change the view in the active cell to a spectrum list view.
Scan Header
Change the view in the active cell to a scan header view.
Scan Filters
Change the view in the active cell to a scan filters view.
Tune Method
Change the view in the active cell to a tune method view.
Instrument Method
Change the view in the active cell to an instrument method view.
Sample Information
Change the view in the active cell to a sample information view.
Status Log
Change the view in the active cell to a status log view.
Error Log
Change the view in the active cell to an error log view.
View
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Table 17. Qual Browser Main toolbar (Sheet 3 of 10)
Button
Description
Add Plot
Activate automatic plot addition mode for grids containing multiple cells. Use
this option to build a layout quickly.
 To add a plot
1. Activate a mode (indicated by a check mark
alongside the menu item).
2. Pin the cell where you want to add a plot.
3. Click in another cell. A plot is added to the pinned cell.
4. Repeat this procedure to add further plots to pinned cells.
When you have finished adding plots, click the button on the toolbar again.
Info Bar
View or hide the Info Bar.
The Help button on the Genesis Peak Detection Settings Page appears at the
extreme bottom of the page.
Refresh
Update a view that is showing a chromatogram or a map from a raw file that is
currently being acquired. The Xcalibur application expands the display range to
show the full range of the data acquired so far. The range is reset only in the
currently active cell. The application refreshes other cells, but does not adjust
their ranges.
Ranges
View ranges for the active view.
Display
The Ranges command is not available for Report views.
There is a Ranges dialog box for each of these view types:
Chromatogram view: Chromatogram Ranges Dialog Box
Spectrum view: Spectrum Ranges Dialog Box
Map view: Map Ranges Dialog Box (Map)
Ion Map: Map Ranges Dialog Box (Ion Map)
Spectrum List view: Spectrum List Ranges Dialog Box
Scan Header view: Scan Header Range Dialog Box
Scan Filter view: Scan Filter Range Dialog Box
Display Options
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Select the style, color, label [chromatogram and spectrum only], axis,
normalization, and smoothing [chromatogram only] options for your
chromatogram, spectrum, or map.
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Qual Browser Toolbars
Table 17. Qual Browser Main toolbar (Sheet 4 of 10)
Button
Description
Add Text
Add text to the active plot.
Add Graphics
Add simple graphic objects such as lines or boxes to the active plot.
Clear
cursor so that you can selectively remove text or graphics
Activates the
annotation entries. To remove graphics or text, drag the cursor horizontally
above or below the text or graphic. The Xcalibur application removes the text or
graphic(s) and changes the cursor back to your default cursor. Repeat this
procedure to remove other annotations.
To replace text or graphics, use the Undo command or click
in the toolbar.
To remove all of the annotations from the active cell, use the Clear All button
on the toolbar.
Clear All
Remove all text and graphics annotation entries in the active cell. To remove
annotations one at a time, use the Clear button on the toolbar.
Zoom In Y
Zoom in on the Y-axis by a factor of two (2) from the current baseline to show
more detail. For example, you can change the Y-axis range from 0–100 to 0–50.
Zoom Out Y
Zoom out on the Y-axis by a factor of two (2) to show more data. For example,
you can change the Y-axis range from 0–25 to 0–50.
Auto Range
View the chromatogram, which is normalized from the minimum to the
maximum signal. Auto Range is useful for PDA and UV data.
Normalize (0 to 100%)
Normalizes the intensity scale of the data display to a fixed range on the Y-axis.
For example, from 0–25 percent to 0–100 percent.
Zoom In X
Zoom in on the X-axis by a factor of two (2) to show more detail. For example,
you can change the X-axis range can from 0–20 to 5–15.
Zoom Out X
Zoom out on the X-axis by a factor of two (2) from the center to show more
data. For example, you can change the X-axis range from 7-5–12.5 to 5–15.
Display All
View all data on the X-axis or all text in a report. For example, you can change
the X-axis range from 7.5–12.5 to 0–20.
Reset
Restores the data display to the full range of the X-axis and Y-axis.
Drag With Cursor
Move (pan) the active plot horizontally left and right along the X-axis by
dragging the cursor. The Xcalibur application changes the cursor to
.
Click
Forward
Thermo Scientific
again to turn off
.
Display data to the left of the active displayed range. This command is
incremental so you might need to use it multiple times to display the region of
interest.
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Qual Browser Toolbars
Table 17. Qual Browser Main toolbar (Sheet 5 of 10)
Button
Description
Back
Display data to the right of the active displayed range. This command is
incremental so you might need to use it multiple times to display the region of
interest.
Next Scan
View the next mass scan with its scan number.
Previous Scan
View the previous mass scan with its scan number.
Left
Insert a cell or cells to the left of the active cell.
Right
Insert a cell or cells to the right of the active cell.
Above
Insert a cell or cells above the active cell.
Below
Insert a cell or cells below the active cell.
Row
Delete the grid row containing the active cell.
Column
Delete the grid column containing the active cell.
All Cells
Delete all the cells in the active window.
Cell Size
Adjust the column width and row height. You can make adjustments relative to
other columns and rows.
Full Width
Zoom the active cell to the full width of the grid.
Full Height
Zoom the active cell to the full height of the grid.
Full View
Zoom the active cell to the full size of the grid.
Reduce Cell
Temporarily reduces the grid column size of the active cell to 20% of the
original size. The Xcalibur application expands the right or left neighboring grid
columns so that you can view the cells in these grid columns at increased
resolution. This command is only active if the grid has two or more rows or
columns.
Grid
If there is only one column in the grid, this command temporarily reduces the
grid row size of the active cell to 20%. The system responds by expanding the
top or bottom neighboring grid rows so that the cells in these grid rows can be
viewed at increased resolution.
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Table 17. Qual Browser Main toolbar (Sheet 6 of 10)
Button
Description
Group Row
Group a row containing two or more cells in a view containing two or more
rows. After you have grouped cells, the Xcalibur data system updates any
changes you make to ungrouped cells in the same view to all of the grouped
cells.
To insert and delete cells, use Grid > Insert and Grid > Delete before you use
the Group Row command.
To group a row, you must have at least two rows of cells in your view and the
grouped row needs to have at least two cells.
The data system makes the grouped row cells active, draws a blue border around
the grouped row cells, and deactivates most menu commands and buttons on
the toolbar.
The data system also makes all ungrouped row cells in the view inactive.
For example, consider the following view:
Chromatogram
Spectrum
Mass List
If you group spectrum and mass list cells using the Group Row command, the
system simultaneously updates mass list and spectrum cells as you make changes
in the Chromatogram cell.
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Table 17. Qual Browser Main toolbar (Sheet 7 of 10)
Button
Description
Group Column
Group a column containing two or more cells in a view containing two or more
columns. After you have grouped cells, the Xcalibur data system updates any
changes you make to ungrouped cells in the same view to all of the grouped
cells.
To insert and delete cells, use Grid > Insert and Grid > Delete before you use
the Group Column command. To group a column, you must have at least two
columns of cells in your view and the grouped column needs to have at least two
cells.
The Xcalibur application makes the grouped column cells active, draws a blue
border around the grouped cells, and deactivates most menu commands and
buttons on the toolbar.
The application also makes all ungrouped column cells in the view inactive.
For example, consider the following view:
Spectrum
Chromatogram
Mass List
If you group spectrum and mass list cells using the Group Column command,
the application simultaneously updates mass list and spectrum cells as you make
changes in the Chromatogram cell.
Grid Lines
View or hide grid lines.
1 Range
Perform a peak-by-peak subtraction of selected scans contained in one
background region of a chromatogram view from the current spectrum view.
Use this command to eliminate background scans that might interfere with the
display of spectrum peaks of interest. The subtracted scans need to use the same
scan filter as the target scans. For more information, see “Subtracting
Background Spectra” on page 99.
2 Ranges
Perform a peak-by-peak subtraction of selected scans contained in two selected
background regions of a chromatogram view from the current spectrum view.
Use this command to eliminate background peaks that might be interfering
with the display of spectrum peaks of interest. The subtracted scans need to use
the same scan filter as the target scans. For more information, see “Subtracting
Background Spectra” on page 99.
Actions
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Table 17. Qual Browser Main toolbar (Sheet 8 of 10)
Button
Description
Clear
Remove all subtract spectra modifications to the spectrum view. The Xcalibur
application also removes the SB: xx notation in the spectrum view header to
indicate that the spectrum view has been returned to the original display before
applying the Subtract Spectra command.
Settings
View a page specific to one of the Xcalibur peak detection algorithms and
change the parameters used by Qual Browser to identify and integrate
chromatogram peaks.
The Help button on the Genesis Peak Detection Settings Page appears at the
extreme bottom of the page.
Toggle Detection In
This Plot
Detect and integrate all peaks in the selected chromatogram plot using the
current peak detection and integration settings.
Click the button a second time to undo the peak detection.
A raw file must be open for this button to be active.
Toggle Detection In
All Plots
Detect and integrate all peaks in all selected and unselected chromatogram plots
in the active cell using the current peak detection and integration settings.
Click the button a second time to undo all detected peaks.
A raw file must be open for this button to be active.
Add Peaks
Detect and integrate any peak in the active cell. The Xcalibur data system
changes the cursor to the add peaks cursor,
. To detect and integrate a peak,
drag this cursor horizontally across the peak. The data system marks the added
peak with a blue baseline,
, and integrates the peak.
Click the button a second time to return the add peaks cursor to the default
cursor.
 To label all detected peaks with their respective area, retention time, or
other peak parameters
1. Choose Display > Display Options. The Display Options Dialog Box
opens.
2. Click the Label tab, and select peak label parameters.
3. Choose OK. The application displays the selected labels at the top of all
peaks in the plot.
A raw file must be open for this button to be active.
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Qual Browser Toolbars
Table 17. Qual Browser Main toolbar (Sheet 9 of 10)
Button
Description
Delete Peaks
Delete selected peak(s) in the active cell. The Xcalibur application changes the
cursor to the delete peaks cursor
. Click this cursor within each peak
boundary, indicated by the blue baseline
of the peak(s) that you want
to delete.
Click
a second time to return the delete peaks cursor to the default cursor.
One or more peaks must be detected (as indicated by
to be active.
Add Manual Noise Region
) for this button
Select an area as the noise region. Click
and drag the cursor horizontally
across the chromatogram region you want to select. The Xcalibur application
marks the region with a red baseline.
The application calculates noise based on the data points you select. It uses all
selected data points as noise points and calculates noise based on those points.
You can select the noise region from an individual trace or different noise
regions from multiple traces.
Open a raw file and select a chromatogram to make this button active.
Delete Manual Noise
Region
and drag the cursor over the region
Delete a selected noise region. Click
that was previously selected as the noise region. Release the mouse button to
delete the noise region.
Search
Submit the active spectrum to a library search. The Xcalibur application
displays the results of the search in the Library Search Results window.
Export To Library Browser
Exports the active spectrum to the Library Browser.
Options
Choose the libraries used during a library search. You can also change various
parameters that determine how the search is carried out.
Autofilter
Apply all of the scan filters in the current raw file and open an AutoFilter display
in the active cell.
The AutoFilter display consists of a vertical sequence of chromatogram plots.
The first chromatogram displays the TIC with no scan filter. Below the first
chromatogram are up to seven TIC scan filter chromatograms, one
chromatogram plot for each scan filter. For additional information, see the Scan
Filter View.
You can also apply scan filters to one or more plots from the Chromatogram
Ranges Dialog Box.
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Qual Browser Views
Table 17. Qual Browser Main toolbar (Sheet 10 of 10)
Button
Description
Window
New Window
Open a new data window in Qual Browser. The new window uses the default
layout and displays the most recently opened raw file.
Cascade
Arrange the current open windows in an overlapped arrangement with all the
title bars visible.
Tile
Arrange the current open windows in a tiled arrangement so that each window
has the same area of Qual Browser’s workspace.
Qual Browser Help
Command
Open Xcalibur Help for Qual Browser. This window displays procedures and
reference topics for the Qual Browser window.
Help
Qual Browser Views
The Qual Browser window has these views:
• Chromatogram View
• Error Log View
• Instrument Method View
• Ion Map View
• Map View
• Result File Window
• Sample Information View
• Scan Filter View
• Scan Header View
• Spectrum List View
• Spectrum View
• Status Log View
• Tune Method View
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Qual Browser Views
Chromatogram View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and display
a chromatogram and related header information in any of the cells. Use menu commands to
select view options.
The chromatogram view consists of up to eight chromatogram plots. An example of a
chromatogram view plot with a retention time label is shown below:
View Header Information
• RT
• NL
• m/z [Mass Range]
• TIC
• Base Peak
• Analog UV 1
• Analog UV 2
• Analog UV 3
• Analog UV 4
• Scan Filter
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Right-click the chromatogram view to display the shortcut menu commands.
Table 18. Chromatogram view shortcut menu commands (Sheet 1 of 4)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur data
system displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The data system displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The data system displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The system displays the map defined by
the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The instrument method
contains the scan number and retention time for the scan and tabular data
for m/z, intensity, and relative intensity. The system displays the spectrum
list defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The Xcalibur
application displays the scan header for the scan that is closest to the time
set in the Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
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Table 18. Chromatogram view shortcut menu commands (Sheet 2 of 4)
Command
Description
Plot
Plot > Insert
Insert a copy of the selected (grayed) plot above the selected plot. Select a
plot.
Plot > Delete
Delete the selected (grayed) plot. Select a plot.
Plot > Move Up
Switch positions of the selected (grayed) plot with the one above it. Select a
plot.
Plot > Move Down
Switch positions of the selected (grayed) plot with the one below it. Select a
plot.
Peak Detection
Peak Detection > Settings
View or change the parameters used by Qual Browser to identify and
integrate chromatogram peaks.
The Help button on the Genesis Peak Detection Settings Page appears at
the extreme bottom of the page.
Peak Detection > Toggle Detection
In This Plot
Detect and integrate all peaks in the selected chromatogram plot using the
current peak detection and integration settings. The Xcalibur application
adds a check mark to the left of the menu command.
Choose Peak Detection > Toggle Detection In This Plot a second time
to undo the peak detection and remove the check mark from the left of the
menu command.
Open a raw file to make this command active.
Peak Detection > Toggle Detection
In All Plots
Detect and integrate all peaks in all selected and unselected chromatogram
plots in the active cell using the current peak detection and integration
settings. The Xcalibur application adds a check mark to the left of the
menu command.
Choose Peak Detection > Toggle Detection In All Plots a second time to
undo all detected peaks and remove the check mark from the left of the
menu command.
Open a raw file to make this command active.
Peak Detection > Set Peak Detection
Algorithm and Detect In This Plot
View a list of the Xcalibur peak detection algorithms. Click one of the
algorithm names in the list to display the page for that algorithm and to
use the algorithm to detect chromatogram peaks in the active
chromatogram cell. See Chromatogram View.
Open a raw file to make this command active.
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Table 18. Chromatogram view shortcut menu commands (Sheet 3 of 4)
Command
Description
Peak Detection > Set Peak Detection
Algorithm and Detect In All Plots
View a list of the Xcalibur peak detection algorithms. Click one of the
algorithm names in the list to display the page for that algorithm and to
use the algorithm to detect chromatogram peaks in all the cells that are
currently displayed. See Chromatogram View.
Open a raw file to make this command active.
Peak Detection > Add Peaks
Detect and integrate any peak in the active cell. The Xcalibur application
. To detect and integrate a
changes the cursor to the add peaks cursor,
peak, drag this cursor horizontally across the peak. The application marks
the added peak with a blue baseline,
, and integrates the peak.
The application also adds a check mark to the left of the menu command.
Choose Peak Detection > Add Peaks a second time to return the add
peaks cursor to the default cursor and remove the check mark from the left
of the menu command.
 To label all detected peaks with their respective area, retention
time, or other peak parameters
1. Choose Display > Display Options. The Display Options Dialog
Box opens.
2. Click the Label tab, and select peak label parameters.
3. Choose OK. The Xcalibur application displays the selected labels at
the top of all peaks in the plot.
Open a raw file to make this command active.
Peak Detection > Delete Peaks
Delete selected peaks in the active cell. The Xcalibur application changes
the cursor to
. Click this cursor within each peak boundary, indicated
by the blue baseline,
, of the peak(s) that you want to delete.
One or more peaks must be detected (as indicated by
command to be active.
) for this
Peak Purity
Peak Purity
View or change Peak Purity settings.
Open a raw data file from a PDA analysis and select PDA from the
Detector list in the Ranges dialog box to make this command active.
Library
Library > Search
Submit the active spectrum to a library search. The Xcalibur application
displays the results of the search in the Library Search Results window.
Library > Export To Library Browser
Export the active spectrum to the Library Browser.
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Table 18. Chromatogram view shortcut menu commands (Sheet 4 of 4)
Command
Description
Library > Options
Choose the libraries used during a library search. You can also change
various parameters that determine how the search is carried out.
Export
Export
Export the time vs. intensity values of the chromatogram to the clipboard.
AutoFilter
AutoFilter
Apply all of the scan filters in the current raw file and open an AutoFilter
display in the active cell.
The AutoFilter display consists of a vertical sequence of chromatogram
plots. The first chromatogram displays the TIC with no scan filter. Below
the first chromatogram are up to seven TIC scan filter chromatograms, one
chromatogram plot for each scan filter. For additional information, see the
Scan Filter View.
You can also apply scan filters to one or more plots from the
Chromatogram Ranges Dialog Box.
Ranges
Ranges
View and edit the mass range, time range and other properties of a
chromatogram plot.
Display Options
Display Options
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Error Log View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and view an
error log in any of the cells. Use menu commands to select view options.
The error log view lists errors that occurred during a sample run. An example of an error log
with no errors is shown below:
Right-click the error log view to open the Error view shortcut menu.
Table 19. Error view shortcut menu commands (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The instrument method
contains the scan number and retention time for the scan and tabular data
for m/z, intensity, and relative intensity. The application displays the
spectrum list defined by the settings in the Spectrum List Ranges Dialog
Box.
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Table 19. Error view shortcut menu commands (Sheet 2 of 2)
Command
Description
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
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Instrument Method View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and view the
instrument method for the current raw file in any of the cells.
If there is more than one instrument method, click the right and left arrows
located on
the toolbar to browse to the pages of the instrument method for the other instruments.
Note These right and left arrow buttons are not active for raw files that contain only one
instrument method.
An example of an instrument method view is shown below:
View Header Information
• Instrument Method: Drive:\Path
• Created
Instrument Method Information
• Creator
• Last Modified
• Summary
• MS Run Time
Autosampler Settings
• Injection Volume
• Divert Valve
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HPLC Settings
• LC Run Time
• Inner Diameter [of column]
• Length
• LC Pressure Limits [Minimum]
• LC Pressure Limits [Maximum]
• Number of Solvents: 1, 2, 3, or 4
• Solvent A
• Solvent B
• Solvent C
• Solvent D
• Program Steps: 1 through 20
Syringe Settings
• Syringe Type
• Flow Rate
• Volume
• Stop Syringe Pump at End of Run [Yes/No]
MS Detector Settings
• Segments
• Duration
• Tune Method
• Scan Events
• Scan Type
Dependent Data Settings
• Reject Spectrum List
• Parent Spectrum List
• Default Charge State
• Collision Energy
• Min Signal Required
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Right-click in the instrument method view to open the Instrument Method view shortcut
menu.
Table 20. Instrument Method view shortcut menu commands
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the spectrum list in the active cell. The spectrum list contains the
scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows,
, located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
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Ion Map View
Use the Ion Map view to analyze the parent, product, and neutral loss of MSn data. The Ion
Map view consists of three panes.
• Map Pane
• Control Pane
• Spectrum Pane
Note The Ion Map view in the Qual Browser window is not available for all MS
detectors.
Map Pane
The Map pane can display the MSn data as a Stack (2D), Overlay (3D), or
Density Map (2D). Choose Display > Display Options. The Display Options dialog box
opens. Click the Style tab to display the Style page and select one of the three options.
• The Density Map (2D) style displays the parent mass (X-axis) and product mass (Y-axis)
as a density map with different colors for each intensity. This is the default display style.
• The 2D Stack style displays the parent mass (X-axis) and stacks the individual product
mass spectra on the (Y-axis).
• The 3D Map style displays the parent mass (X-axis), product mass (Y-axis), and relative
abundance (Z-axis). Neutral loss masses are calculated using the formula
(parent – product).
Drag the cursor to the mass region of interest. The corresponding spectrum is displayed in the
Spectrum pane and the coordinates are displayed in the Control pane.
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Control Pane
Use the Control pane to specify that the parent, product, or neutral loss is to remain constant
while other parameters are varied.
Table 21. Control pane parameters (Sheet 1 of 3)
Parameter
Description
Product Spectrum
Create a product spectrum consisting of products from the specified parent mass. The
Activate the Parent Mass box opens.
Parent Mass
View the product spectrum for the selected parent in the Spectrum pane. This spectrum
consists of all of the products from the parent in the data that is the closest to the selected
parent mass coordinate.
Drag the cursor in the Map pane along the Parent axis. The Xcalibur application displays
the parent mass coordinate in the Parent Mass box. Also, you can enter the parent mass
coordinate in the Parent Mass box. The valid range is m/z 0.00 to 100000.00.
This box is only active if you select the Product Spectrum option.
Parent Map
Produce a parent map consisting of parents that decompose to form the specified product
mass. The Activate the Product Mass box opens.
Product Mass
View the parent map for the selected product in the Spectrum pane. This reconstructed
spectrum consists of all of the parents that produced the products defined in the product
mass window. The parents and products were extracted from the array of MS/MS data. The
product mass window is defined by the m/z value in the Product Mass box and the m/z value
in the Tolerance box, as follows: product mass +/- Tolerance.
Select the Parent Map option to activate this box.
Drag the cursor in the Map pane along the Product axis. The Xcalibur application displays
the product mass coordinate in the Product Mass box. Also, you can enter the product mass
coordinate in the Product Mass box. The valid range is m/z 0.00 to 100000.00.
Neutral Loss Map
Thermo Scientific
Activate the Neutral Loss box so that you can create a neutral loss map consisting of parents
that lose the specified neutral loss mass.
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Table 21. Control pane parameters (Sheet 2 of 3)
Parameter
Description
Neutral Loss
View the neutral loss map for the selected neutral loss mass in the Spectrum pane. This
reconstructed spectrum consists of all of the parents that produced product(s) within the
neutral loss mass window selected. The neutral loss window is defined by the m/z value in
the Neutral Loss box and the m/z value in the Tolerance box, as follows:
Neutral Loss Mass +/- Tolerance. The neutral loss mass is parent mass – product mass.
This box is only active if you select the Parent Map option. This box is only active if you
select the Parent Map option.
Drag the cursor in the Map pane along the diagonal neutral loss axis. The Xcalibur
application displays the neutral loss mass coordinate in the Neutral Loss box. Also, you can
enter the neutral loss coordinate in the Neutral Loss box. The valid range is
m/z –10 0000.00 to 10 0000.00.
Tolerance
Select the window where the Xcalibur application selects either product masses or neutral
loss masses, depending upon which option you select.
• If you select the Product Mass option, the product window is defined by the m/z value
in the Product Mass box and the m/z value in the Tolerance box, as follows:
product mass +/- Tolerance
• If you select the Neutral Loss option, the neutral loss window is defined by the
m/z value in the Neutral Loss box and the m/z value in the Tolerance box, as follows:
neutral loss mass +/- Tolerance. The neutral loss mass is parent mass – product mass.
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Table 21. Control pane parameters (Sheet 3 of 3)
Parameter
Description
Free Tracking
Disconnect the map pane from all controls provided by the spectrum pane and the control
pane. If you select the Free Tracking option, you can drag the cursor in the map pane to
select specific regions of the map.
Neutral Loss
Mass/Product Mass
Provide a double label at the top of each ion peak displayed in the Spectrum pane. The title
of this check box changes depending upon whether you have selected the Product Spectrum
option, Parent Map option, or Neutral Loss Map option in the Control pane.
• Product Spectrum option: The check box is labeled Neutral Loss Mass. The spectrum
displays all products from the specified parent mass. Peaks are labeled as follows:
Product Mass
(Neutral Loss Mass)
• Parent Map option: The check box is labeled Neutral Loss Mass. The spectrum displays
all parents that produce the specified product mass. Peaks are labeled as follows:
Parent Mass
(Neutral Loss Mass)
• Neutral Loss Map option: The check box is labeled Product Mass. The spectrum
displays all parents that produce a product by losing the specified neutral loss (NL)
mass. Peaks are labeled as follows:
Parent Mass
(Product Mass)
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Spectrum Pane
View the spectrum that you select using the cursor controls in the Map pane and the settings
in the Control pane. Depending on the settings, you can display the following:
• Product Spectrum
• Parent Map
• Neutral Loss Map
Right-click in the Ion Map view to open the Ion Map view shortcut menu.
Table 22. Spectrum pane parameters (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The instrument method
contains the scan number and retention time for the scan and tabular data
for m/z, intensity, and relative intensity. The application displays the
spectrum list defined by the settings in the Spectrum List Ranges Dialog
Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
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Table 22. Spectrum pane parameters (Sheet 2 of 2)
Command
Description
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
Ranges
Ranges
Set the parent mass range, product mass range, and scan filter for an ion
map.
Display Options
Display Options
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Select the Style, Color, Labels, Axis, and Normalization settings.
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Map View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and display
a map and related header information in any of the cells. Use menu commands to select
display options.
The map view consists of a time (X-axis) vs. m/z (Y-axis) vs. relative abundance (Z-axis) map
plot. An example of a map view is shown below:
View Header Information
• RT:
• Mass:
• NL:
• T:
• F:
Right-click the map view to open the Map view shortcut menu.
Table 23. Map view shortcut menu commands (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
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Table 23. Map view shortcut menu commands (Sheet 2 of 2)
Command
Description
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The spectrum list contains
the scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
Ranges
Ranges
Set the mass and time range and scan filter for a map.
Display Options
Display Options
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Select the Style, Color, Labels, Axis, and Normalization settings.
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Result File Window
Use the Qual Browser window to open a result file. A result file contains a list of detected
peaks from the chromatogram, and the processing results associated with each peak including
any library search results.
Qual Browser displays the result file in a fixed, two cell arrangement. This shows:
• A chromatogram plot in the upper cell with the detected peaks highlighted.
• The spectrum associated with the currently selected chromatogram peak in the lower cell.
Note Many of Qual Browser's features are not available for use with a result file because
the raw file is not directly available for processing.
Library search results for the displayed spectrum are shown in a separate library search results
window. It is not possible to submit the spectrum from the results display for library search. If
a library search has been carried out during processing (when the result file was created),
search results will be stored in the result file and displayed for each detected peak. To submit a
spectrum for library searching or to export a spectrum to the Library Browser, you must open
the raw file.
Sample Information View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and view
sequence information for the current sample in any of the cells.
An example of a sample information view is shown below:
View Header Information
• [Bracket] Type
• Level
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Table 24. Sample information view parameters
Parameter
Description
ID
View a unique identification (ID) number for each sample. Set this
number in the Sequence Setup view.
Row
Sequence Information
Sample Name
View the sample name of the sample selected from the sequence.
Heading
View information about a user-defined column heading that is pertinent to
the active sample row in the sequence. Set the headings in the Sequence
Setup view.
Instrument Method: Drive:\Path
Processing Method: Drive:\Path
Vial
View the position number of a sample in the autosampler.
Injection Volume
View the injection volume in microliters of the sample to be injected.
Sample Weight
View the amount of a component that has been placed in the sample.
Specify the unit for this sample weight in the Processing Setup window.
The Xcalibur data system reports only include this information. It does not
convert units. To change the sample weight, double-click the Sample
Weight box.
Sample Volume
View the volume of a component that has been placed in the sample.
Specify the unit for this sample weight in the Processing Setup window.
The Xcalibur data system reports only include this information. It does not
convert units.
ISTD Corr Amt
View the correction for the internal standard amount. If the value in this
box is not 0.000, the value is used in an algorithm to correct for a case
when any internal standard amounts specified in the active instrument
method are correct, but when the amount of internal standard actually in
one or more samples is different than the amount specified in the
instrument method.
This correction eliminates the necessity of remaking any samples to the
internal standard concentrations or amounts specified in the instrument
method and re-running the samples.
Dil Factor
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View the dilution factor that was used to prepare the sample.
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Right-click the sample information view to open the Sample Information view shortcut
menu.
Table 25. Sample Informtion view shortcut menu commands
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The spectrum list contains
the scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
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Scan Filter View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and display
a list of scan filters in the scan filter format. Use menu commands to select view options.
An example of a scan filters view is shown below:
View Header Information
• Start S#
• End S#
• Start Time
• End Time
Right-click the scan filter view to open the Scan Filter view shortcut menu
Table 26. Scan Filter view shortcut menu commands (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
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Table 26. Scan Filter view shortcut menu commands (Sheet 2 of 2)
Command
Description
View > Spectrum List
View the instrument method in the active cell. The spectrum list contains
the scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
Ranges
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Set the scan filter time.
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Scan Header View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and display
scan header information for a selected scan in any of the cells. Use menu commands to select
view options.
An example of a scan header view is shown below:
Display Header Information
• S#:
• RT:
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Scan Header Information
• Total Ion Current
• API Source CID Energy
• Scan Low Mass
• Resolution
• Scan Start Time
• Data Type
• Scan End Time
• Polarity
• Scan Number
• Average Scan by Inst.
• Micro Scan Count
• Backgd Subtracted by Instrument
• Base Peak Intensity
• Charge State
• Base Peak Mass
• Number of Data Packets
• Ion Injection Time
• MS Order
• Scan Mode
• Parent Mass(es)
• Scan Segment
• Isolation Width(s)
• Scan Event
• Collision Energy(s)
• Elapsed Scan Time
Right-click the scan header view to open the Scan Header view shortcut menu.
Table 27. Scan Header view shortcut menu commands (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the spectrum list in the active cell. The spectrum list contains the
scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
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Table 27. Scan Header view shortcut menu commands (Sheet 2 of 2)
Command
Description
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
Ranges
Ranges
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Set the scan header time.
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Qual Browser Views
Spectrum List View
The spectrum list view can display either:
• A list containing m/z, absolute intensity, and relative intensity for each of the selected
ions. If you have label stream data, you can also include Resolution, Charge, Baseline, and
Noise. If you have a profile scan, you can also display centroided data. An example of a
this spectrum list view is shown below:
• A list containing m/z, theoretical mass, delta (mms), RDB equivalents, and composition
from your simulation data.
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• S#
Scan number
• RT
Retention time
• AV
Averaged (followed by the number of averaged scans)
• SB
Subtracted (followed by subtraction information)
• NL
Neutral loss
• T
Scan type
• F
Scan filter
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To open the spectrum list view shortcut menu, right-click the spectrum list view.
Table 28. Spectrum List view shortcut menu commands (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the spectrum list in the active cell. The spectrum list contains the
scan number and retention time for the scan and tabular data for m/z,
intensity, and relative intensity. The application displays the spectrum list
defined by the settings in the Spectrum List Ranges Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all of the scan filters used in all scans of the active raw file in the
active cell. The application displays the scan filter for the scan that is
closest to the time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
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Table 28. Spectrum List view shortcut menu commands (Sheet 2 of 2)
Command
Description
Subtract Spectra
Subtract Spectra > 1 Range
Perform a peak-by-peak subtraction of selected scans contained in one
background region of a chromatogram view from the current spectrum
view. Use this command to eliminate background scans that might
interfere with the display of spectrum peaks of interest. The subtracted
scans need to use the same scan filter as the target scans. For more
information, see “Subtracting Background Spectra” on page 99.
Subtract Spectra > 2 Ranges
Perform a peak-by-peak subtraction of selected scans contained in two
selected background regions of a chromatogram view from the current
spectrum view. Use this command to eliminate background peaks that
might be interfering with the display of spectrum peaks of interest. The
subtracted scans need to use the same scan filter as the target scans. For
more information, see “Subtracting Background Spectra” on page 99.
Export
Export > Clipboard (Exact Mass)
Export the exact m/z vs. intensity values of the spectrum to the clipboard.
The Xcalibur application also copies the raw file name, scan filter, scan
number, and retention time information to the clipboard.
Export > Clipboard (Nominal Mass)
Export the rounded m/z vs. intensity values of the spectrum to the
clipboard. The application also copies the raw file name, scan filter, scan
number, and retention time information to the clipboard.
Elemental Composition
Elemental Composition
Determine which chemical formulas have m/z values most like that of the
spectrum peaks. The application then displays the chemical formula labels
at the top of the spectrum peaks.
If the application displays the elemental composition values in light gray,
close Qual Browser and choose Xcalibur Roadmap > Tools >
Configuration. The Configuration page opens. Click the Fonts tab and
set all font sizes to a minimum of 10 points.
Ranges
Ranges
View and edit the mass range, time range and other properties of a
spectrum list.
Display Options
Display Options
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Spectrum View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and display
a spectrum and related header information in any of the cells. Use menu commands to select
display options.
The spectrum view consists a relative abundance vs. m/z spectrum plot. An example of a
spectrum view is shown below:
View Header Information
• S#
Scan number
• RT
Retention time
• AV
Averaged (followed by the number of averaged scans)
• SB
Subtracted (followed by subtraction information)
• NL
Neutral loss
• T
Scan type
• F
Scan filter
To open the spectrum view shortcut menu, right-click the spectrum view.
Table 29. Spectrum view shortcut menu commands (Sheet 1 of 4)
Command
Description
View
View > Chromatogram
View one or more chromatograms in the active cell. The Xcalibur
application displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
View a spectrum in the active cell. The application displays the spectrum
defined by the settings in the Spectrum Ranges Dialog Box.
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Table 29. Spectrum view shortcut menu commands (Sheet 2 of 4)
Command
Description
View > Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Ion Map
View a three-dimensional x, y, z map of the parameters time, relative peak
height, and m/z in the active cell. The application displays the map defined
by the settings in the Map Ranges Dialog Box.
View > Spectrum List
View the instrument method in the active cell. The instrument method
contains the scan number and retention time for the scan and tabular data
for m/z, intensity, and relative intensity. The application displays the
instrument method defined by the settings in the Spectrum List Ranges
Dialog Box.
View > Scan Header
View the scan header of the current scan in the active cell. The application
displays the scan header for the scan that is closest to the time set in the
Scan Header Range Dialog Box.
View > Scan Filters
View all scan filters used in all scans of the active raw file in the active cell.
The application displays the Scan Filter for the scan that is closest to the
time set in the Scan Filter Range Dialog Box.
View > Reports
View > Reports > Tune Method
View any tune methods stored in the active raw file in the active cell.
View > Reports > Instrument Method
View any instrument methods stored in the active raw file in the active cell.
If there is more than one instrument method, click the right and left
arrows
located on the toolbar to browse to the pages of the
instrument methods for the other instruments.
These right and left arrow buttons are not active for raw files that contain
only one instrument method.
View > Reports > Sample Information
View the sample list information stored in the active raw file.
View > Reports > Status Log
View the status log stored with the active raw file.
View > Reports > Error Log
View the error log stored with the active raw file.
Plot
Plot > Insert
Insert a copy of the selected (grayed) plot above the selected plot. Select a
plot.
Plot > Delete
Delete the selected (grayed) plot. Select a plot.
Plot > Move Up
Switch positions of the selected (grayed) plot with the one above it. Select a
plot.
Plot > Move Down
Switch positions of the selected (grayed) plot with the one below it. Select a
plot.
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Table 29. Spectrum view shortcut menu commands (Sheet 3 of 4)
Command
Description
Subtract Spectra
Subtract Spectra > 1 Range
Perform a peak-by-peak subtraction of selected scans contained in one
background region of a chromatogram view from the current spectrum
view. Use this command to eliminate background scans that might
interfere with the display of spectrum peaks of interest. The subtracted
scans need to use the same scan filter as the target scans. For more
information, see “Subtracting Background Spectra” on page 99.
Subtract Spectra > 2 Ranges
Perform a peak-by-peak subtraction of selected scans contained in two
selected background regions of a chromatogram view from the current
spectrum view. Use this command to eliminate background peaks that
might interfere with the display of spectrum peaks of interest. The
subtracted scans need to use the same scan filter as the target scans. For
more information, see “Subtracting Background Spectra” on page 99.
Subtract Spectra > Clear
Remove all subtract spectra modifications to the spectrum view. The
Xcalibur application also removes the SB: xx notation in the spectrum
view header to indicate that the spectrum view has been returned to the
original display before application of the Subtract Spectra command.
Library
Library > Search
Submit the active spectrum to a library search. The application displays the
results of the search in the Library Search Results window.
Library > Export To Library Browser
Export the active spectrum to the Library Browser.
Library > Options
Choose the libraries used during a library search. You can also change
various parameters that determine how the search is carried out.
Export
Export > Clipboard (Exact Mass)
Export the exact m/z vs. intensity values of the spectrum to the clipboard.
The Xcalibur application also copies the raw file name, scan filter, scan
number, and retention time information to the clipboard.
Export > Clipboard (Nominal Mass)
Export the rounded m/z vs. intensity values of the spectrum to the
clipboard. The application also copies the raw file name, scan filter, scan
number, and retention time information to the clipboard.
Export > Write to Raw FIle
Save the spectrum as a raw data file.
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Table 29. Spectrum view shortcut menu commands (Sheet 4 of 4)
Command
Description
Elemental Composition
Determine which chemical formulas have m/z values most like that of the
spectrum peaks. The Xcalibur application then displays the chemical
formula labels at the top of the spectrum peaks.
Elemental Composition
If the data system displays the elemental composition values in light gray,
close Qual Browser and choose Xcalibur Roadmap > Tools >
Configuration. The Configuration page opens. Click the Fonts tab and
set all font sizes to a minimum of 10 points.
Ranges
Ranges
View and change the mass range, time range, and other properties of a
spectrum plot.
Display Options
Display Options
Select the style, color, labels, axis, and normalization settings.
Status Log View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and view
status log information for a selected scan in any of the cells.
An example of a status log view is shown below:
View Header Information
• S#:
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• Status Log Time
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Status Log Information
API Source
• Source Voltage
• Aux Gas Flow Rate
• Source Current
• Capillary RTD OK: [True/False]
• Vaporizer Thermocouple OK:
[True/False]
• Capillary Voltage
• Vaporizer Temp
• Sheath Gas Flow Rate
• Capillary Temp
• Tube Gate Voltage
• 8 kV Supply at Limit: [True/False]
Vacuum
• Vacuum OK: [True/False]
• Ion Gauge (Torr × 10^–5)
• Ion Gauge Pressure OK:
[True/False]
• Convectron Pressure OK: [True/False]
• Convectron Gauge
• Ion Gauge On: [True/False]
Turbo Pump
• Status
• Power
• Life
• Temperature
• Speed
Ion Optics
• Octapole Frequency On:
[True/False]
• Octapole 1 Offset
• Lens Voltage
• Trap DC Offset
• Analyzer Temperature
• Octapole 2 Offset
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Main RF
• Reference Sine Wave OK:
[True/False]
• Standing Wave Ratio Failed:
[True/False]
• Main RF DAC (steps)
• RF Detector Temperature
• Main RF Modulation
• Main RF Amplifier
• RF Generator Temp
• Main RF Detected
Ion Detection System
• Multiplier Actual
Power Supplies
• +5V Supply Voltage
• +35V Supply Voltage
• –15V Supply Voltage
• +36V Supply Voltage
• +15V Supply Voltage
• –150V Supply Voltage
• +24V Supply Voltage
• +150V Supply Voltage
• –28V Supply Voltage
• –205V Supply Voltage
• +28V Supply Voltage
• +205V Supply Voltage
• +28V Supply Current
• Ambient Temp
• Instrument: On/Off
• Retention Time
Instrument Status
• Analysis
Autosampler
• Status
• Number of Injections
• Current Vial Position
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LC Pump
• Status
• Pump Pressure [Minimum]
• Run Time
• Temperature [Maximum]
• Flow Rate
• Composition
Analog Inputs
• Number Activated
Syringe Pump
• Status
• Infused Volume
• Flow Rate
• Syringe Diameter
• Ready In is active:
[True/False]
• Divert/Inject Valve
Digital Inputs
• Start In is active:
[True/False]
UV Detector
• Status
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Tune Method View
Use the Qual Browser window to open a raw file, create a grid of interactive cells, and view a
tune method for a specified run segment in any of the cells. Use menu commands to select
view options.
An example of a Tune method view is shown below:
View Header Information
• Segment
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Tune Method Information
• Capillary Temp
• Trap DC Offset Voltage
• APCI Vaporizer Temp
• Multiplier Voltage
• Source Voltage (APCI)
• Maximum Ion Time
• Source Voltage (API)
• Ion Time
• Source Current (APCI)
• Data Type
• Source Current (API)
• Source Type
• Sheath Gas Flow
• Polarity
• Aux Gas Flow
• Zoom Micro Scans
• Capillary Voltage (API)
• Zoom AGC Target
• Tube Lens Offset (API)
• Full Micro Scans
• Octapole RF Amplifier
• Full AGC Target
• Octapole 1 Offset
• MSn Micro Scans
• Octapole 2 Offset
• MSn AGC Target
• InterOctapole Lens Voltage
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Qual Browser Info Bar
Qual Browser Info Bar
The Qual Browser Info Bar displays information about the active grid cell for chromatogram
or spectrum views. It consists of these pages:
Cell Information Page
Elemental Composition Page
MSn Browser Information Page
Avalon Peak Detection Settings Page
ICIS Peak Detection Settings Page
Genesis Peak Detection Settings Page
Result File Information Page
Sequence Information Page
Spectrum Simulation Page
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Cell Information Page
Use the Cell Information page of the Info Bar to view information about the active grid cell
for spectrum or chromatogram views:
Table 30. Cell Information page parameters (Sheet 1 of 2)
Parameter
Description
Spectrum Views
Plot type and Raw File Name
View information about a raw data file created by the mass spectrometer
when a sample is run, containing raw analysis data.
The icon changes to reflect the type of plot present.
Raw File Path
View a listing of the directories that lead from the current drive and
directory to the raw file.
Scan Filter
(if applied)
View scan filters used in a raw file. The Xcalibur application uses scan
filters to specify that processing is to be applied to a subset of the scans in a
raw file. The application creates scan filters from instrument method
settings and can be selected using Scan Filter combo boxes in the data
system windows.
Fix Scale
(if applied)
View the current maximum range for the Y-axis of the active spectrum.
This box is only active when you select the Spectrum Fix Scale check box.
The maximum Y-axis value can range from 10 to 1010. To change the
value, input the new maximum Y-axis value in the Spectrum Fix Scale box.
Background Subtraction:
Time Range 1, Time Range 2
(if applied)
The chromatogram time range or ranges used for background subtraction.
Chromatogram Views
Raw File Name
View information about a raw data file (.raw) created by the mass
spectrometer when a sample is run, containing raw analysis data.
Raw File Path
View a listing of the directories that lead from the current drive and
directory to the raw file.
Scan Filter (if applied)
View applied scan filters. The Xcalibur application uses scan filters to
specify that processing is to be applied to a subset of the scans in a raw file.
Scan filters are created by the application from instrument method settings
and can be selected using Scan Filter combo boxes in the data system
windows.
Fix Scale
(if applied)
View or change the current maximum range for the Y-axis of the active
chromatogram. This box is only active when you select the Spectrum Fix
Scale check box. The maximum Y-axis value can range from 10 to 1010. To
change the value, input the new maximum Y-axis value in the Spectrum
Fix Scale box.
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Table 30. Cell Information page parameters (Sheet 2 of 2)
Parameter
Description
Detector Delay
View the time difference in minutes between the UV detector and the mass
spectrometer. The Xcalibur application corrects the retention time so that
both the UV detector and mass spectrometer are detecting the same peak
at the same time.
Mass Range
(for mass range plot type only)
View the mass spectrometer mass ranges for a type of chromatogram where
the application sums all ions from one or more specified mass spectrometer
mass ranges plots them as a function of time.
Background Subtraction
Time Range 1, Time Range 2
(if applied)
View the chromatogram time range or ranges used for background
subtraction.
Right-click the Cell Information page to open a shortcut menu with these commands:
Table 31. Cell Infomation page shortcut menu commands
Command
Description
Ranges
View or change the properties of all the plots in the active cell. You
can view or modify the time and mass ranges and change
background subtraction and smoothing parameters.
Delete
Delete the selected plot from the cell.
Elemental Composition Page
Use the Elemental Composition page of the Info Bar to calculate the best matching chemical
formula for a mass or a list of masses from a spectrum.
Table 32. Elemental Composition page parameters (Sheet 1 of 5)
Parameter
Description
Elemental Composition
Elemental Composition
Specify the mass and the charge state and whether or not to include the Nitrogen Rule in
the calculation of possible formulas. See “Nitrogen Rule” on page 170 for more
information.
If the Xcalibur application displays the elemental composition values in light gray, close
Qual Browser and choose Xcalibur Roadmap > Tools > Configuration. The
Configuration page opens. Click the Fonts tab and set all font sizes to a minimum of 10
points.
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Table 32. Elemental Composition page parameters (Sheet 2 of 5)
Parameter
Description
Mass
View or change the mass you want the Xcalibur application to use to calculate probable
chemical formulas.
To change the mass value, enter a mass from 0.5 to 100 000. To calculate formulas and
display them in the Results box, click the Calculate button.
Max Results
View or change the maximum number of formulas you want the Xcalibur data system to
display. To increase or decrease the value, enter a number less than 400. To calculate
formulas and display them in the Results box, click the Calculate button.
Calculate
Calculate formulas and display them in the Results box after you enter a mass from 0.5 to
100,000 in the Mass box.
Results
Results
View a list displaying the results of the formula calculation using the values specified in the
Calculate Composition box. The list is presented in order of best fit and contains rows
that you can select to compute a spectrum or to print the results to a file.
Idx
The Index (Idx) column displays the number of the row in the Results List. The Index
column displays an incremental list of numbers in order of Best Fit after specifying that
the Xcalibur data system calculate probable chemical formulas. To select a formula, click a
number in the Index column and click the Calculate button to calculate probable
formulas.
Formula
This column displays the formulas calculated using the values specified in the Calculate
Composition box and the limits specified in the Limits In Use box.
RDB
View the ring and double-bond equivalents calculated for each of the formulas in the
Results List. See also Double Bond/Ring Equivalent box.
Delta [units]
View the difference between the specified mass and the calculated mass, in amu, mmu, or
ppm units, for each of the formulas in the Results List.
File
Write a formula or a group of formulas to a file. To select formulas, first click an index
number in the Idx column of the Results List. Then use CTRL+click or SHIFT+click to
select other results you want in the file.
List
View the information from the Results table in the Spectrum List View. The spectrum list
view consists of a list containing m/z, theoretical mass, delta (mmu), RDB equivalents,
and composition (formula) for each selected ion.
Simulate
Simulate the spectrum of a formula highlighted in the Results List. The spectrum is based
on the full isotope distribution for that formula.
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Table 32. Elemental Composition page parameters (Sheet 3 of 5)
Parameter
Description
Limits
Limits
Limit the number of possible elemental compositions. You can specify limits on peak
width and on sites of unsaturation (or double bond and ring equivalents.)
Charge
View or change the charge state you want IsotopeViewer to use to calculate probable
formulas. To change the charge state, enter a number from –99 to +99. To calculate
formulas and display them in the Results box, click the Calculate button.
Nitrogen Rule
Select whether or not to use the Nitrogen Rule in the formula calculation. The choices in
the list are as follows: Do Not Use, Even, and Odd.
For molecular ions of even or odd molecular weight, specify that formulas contain either
an even or an odd number of nitrogen atoms, respectively, in the Nitrogen-Rule list.
Conversely, for fragment ions of even or odd molecular weight, specify the reverse; that is,
specify odd or even, respectively, in the Nitrogen-Rule list.
McLafferty states the Nitrogen Rule as follows: “If an odd-electron ion contains no (or an
even number of ) nitrogen atoms, its molecular ion will be at an even mass
number...[Similarly,] an odd-electron ion will be at an odd mass number if it contains an
odd number of nitrogen atoms.”
Mass Tolerance
Specify a mass tolerance to restrict the number possible elemental compositions. The
Xcalibur application returns results of the elemental composition search only if the
computed formula matches the entered mass within the specified tolerance. The value
must be between 0.00 and 1000.00.
Units
View the units that you can associate with mass tolerance: amu (atomic mass units), mmu
(millimass units), and ppm (parts-per-million).
If specify error limits in ppm, the errors are mass-dependent and get larger at low masses
and smaller at high masses.
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Table 32. Elemental Composition page parameters (Sheet 4 of 5)
Parameter
Description
Double Bond/Ring
Equivalents
View or change a range of values for double bonds and ring equivalents—a measure of the
number of unsaturated bonds in a compound—and limits the calculated formulas to only
those that make sense chemically. You can specify limits in a range from –1000.0 to
+1000.0.
The value is calculated by the following formula:
imax
 Ni ( Vi – 2 )
i
D = 1 + ---------------------------------------2
where
D is the value for the RDB
imax is the total number of different elements in the composition
Ni is the number of atoms of element i
Vi is the valence of atom i
The calculation results in an exact integer such as 3.0, indicating an odd-electron ion, or
an integer with a remainder of 0.5, indicating an even-electron ion. A value of –0.5 is the
minimum value and corresponds to a protonated, saturated compound (for
example, H3O+).
Elements in Use
Elements in Use
Defines which isotopes, and the number of occurrences for each isotope, to consider when
the data system calculates possible elemental compositions for a specified mass value.
Isotope
View the isotopes that you want the data system to consider when it calculates elemental
compositions for a given mass.
To add an isotope, click in an empty area in the Isotope column. The Select Isotopes
Dialog Box opens. Also, you can right-click in the grid and choose Add Isotopes from the
shortcut menu.
To remove an isotope, right-click an isotope and choose Delete Isotope from the shortcut
menu.
Min
View the minimum number of occurrences of a specified isotope for a determination of
formula composition.
Max
View the maximum number of occurrences of a specified isotope for a determination of
formula composition.
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Table 32. Elemental Composition page parameters (Sheet 5 of 5)
Parameter
Description
DB Eq.
View the values of the lower and upper limits for double bond and ring equivalents that
IsotopeViewer calculates for each isotope in the Elements In Use List. See also Double
Bond/Ring Equivalent box.
Mass
View the exact isotopic mass for each isotope specify in the Elements In Use List.
Buttons
Load
Select a file (.lim) that contains a set of isotope limits.
Save As
Save a list of isotopes to a file with a .lim extension.
 To select multiple isotopes in the Elements In Use list
1. Click an isotope symbol.
2. Use CTRL+click or SHIFT+click to select other isotope symbols you want in the
isotope limits file.
Apply
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Apply the Elemental Composition box settings to the spectrum.
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MSn Browser Information Page
Use the MSn Browser Information page of the Info Bar to display and analyze MSn
experimental data.
Note The MSn Browser Information page is not available for all mass spectrometers.
Table 33. MSn Browser Information page parameters (Sheet 1 of 4)
Parameter
MS2 Precursor
Description
Select MSn spectra. The
icon is the top of the tree view displayed in the Info bar of
the MSn Browser feature available in the Qual Browser window. A typical starting view
is shown below:
The MS2 precursor ion m/z is displayed to the right of the icon. The MS2 precursor ion
is the parent ion mass from the MS1 experiment that is used for the MS2 (MS/MS)
experiment.
If you click the plus (+) sign, all of the MS3 precursor icons appear and the icon for the
MS2 average spectrum appears. See the example below:
To view a spectrum, click the
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icon of interest.
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Table 33. MSn Browser Information page parameters (Sheet 2 of 4)
Parameter
Composite
Spectrum
Description
View a spectrum that is the sum of all MS2, MS3, MS4, MS5,…MS10 spectra, as
defined by your instrument method.
• A spectrum that has not been normalized
When the Normalize Composite Spectrum check box is unavailable on the MSn
page of the Info bar, the Xcalibur data system normalizes the composite spectrum
(NL) to the highest intensity of the MS2 experiment. When you choose this option,
the data system displays the intensities of consecutive MS experiments at lower and
lower intensities.
An example follows for a processing filter for a composite spectrum (not
normalized) of an MS3 experiment where four microscans were averaged. The
parent mass of the MS2 experiment is m/z 1108.16 and the parent mass of the MS3
experiment is m/z 775.98. The relative collision energy used for both experiments
was 30 percent:
Msnbrows#38–185 RT:0.98–4.91 AV:4 NL: 2.73E3
T: + c CMP ms3 [email protected] [email protected] [200.00–1560.00]
These peaks are labeled: (Parent Mass) PM MS2 and PM MS3.
• Normalized spectrum
When the Normalize Composite Spectrum check box is active on the MSn page of
the Info bar, each MSn spectrum is individually normalized (NL) so that its highest
peak is displayed at Relative Abundance 100. The relative peak heights of this
display are therefore not meaningful. For example, a composite spectrum (CMP) for
an MS3 experiment displays both the MS2 base peak and the MS3 base peak at
Relative Abundance 100 and maintains all other relative abundances of the other
ions in each spectrum. Use this display normalization option to view multiple
spectra simultaneously, even if the absolute value of the intensities are significantly
different.
An example follows for a process filter for a normalized composite spectrum of an
MS3 experiment in which four microscans were averaged. The parent mass of the
MS1 experiment is m/z 1108.16 and the parent mass of the MS2 experiment is
m/z 775.98. The relative collision used was 30 percent:
Msnbrows#38–185 RT:0.98–4.91 AV:4 NL: 2.73E3
T: + c CMP ms3 1108.16 775.98 [200.00–2000.00]
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Table 33. MSn Browser Information page parameters (Sheet 3 of 4)
Parameter
Average Spectrum
Description
View a spectrum that is the sum of all of the microscans taken for a particular MSn
experiment. An average spectrum can be independently displayed for MS2, MS3, MS4,
MS5, …MS10 experiments. The average spectrum is displayed normalized (NL) to the
average base peak.
In the event that there is only one spectrum with one scan to average, the Xcalibur data
system displays the term single spectrum instead of average spectrum. In other words,
single spectrum is a special case of average spectrum.
An example of a processing filter for the average spectrum of an MS3 experiment in
which two microscans were averaged follows. The parent mass of the MS1 experiment is
m/z 1108.07 and the parent mass of the MS2 experiment is m/z 776.03:
Msnbrows#38–185 RT:1.01–4.91 AV:2 NL: 2.73E3
T: + MS3 [email protected] [email protected] [200.00–1560.00]
Scan Number At RT Select single scans (individual scans) on the MSn Browser Information page if you
right-click the MSn Information page and choose Include Single Scans.
Time Range
Enter a chromatogram time range. The MSn browser changes the Time axis on the
chromatogram (View > Chromatogram) and limits the spectra available for display to
those taken during the specified time range.
There are two ways to change the Time Range:
• Enter the time range in minutes in the Time Range box. The valid range is 0.00 to
999.0 minutes. The format is From–To. For example, to view the chromatogram
time range from 0.01 to 5.10 minutes, enter 0.01-5.10.
• Select the Track check box to track the time range using the chromatogram view.
Then, drag the cursor horizontally across the chromatogram view from the
minimum time to the maximum time of interest. The data system changes the
range in the Time Range box and displays the chromatogram with its revised range.
To return to the original range, click the zoom reset button.
Track
Track the time range using the chromatogram view. Then, drag the cursor horizontally
across the chromatogram view (View > Chromatogram) from the minimum time to
the maximum time of interest. The data system changes the range in the Time Range
box and displays the chromatogram with its revised range.
To return to the original range, click the zoom reset button.
Mass Range
Enter the mass range that you are interested in viewing. The MSn browser limits the
viewable spectra to the specified mass range.
To change the mass range, enter the range in the Mass Range box. The valid range is
m/z 65.00 to 2000.00. The format is From–To. For example, to view spectra having
mass range m/z 100 to 500, enter 100.00 – 500.00.
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Table 33. MSn Browser Information page parameters (Sheet 4 of 4)
Parameter
Mass Tolerance
Description
View or change the current mass range over which spectra are not distinguished
(grouped). The valid range is m/z 0.00 to 10.00. The default value is m/z 0.50.
• If the mass tolerance is large (m/z >0.50), the data system groups scans that meet the
range tolerance so that the number of individual scans can be reduced.
• If the mass tolerance is small (m/z <0.50), the data system displays each scan from
the specified precursor
Normalize
Composite
Spectrum
Normalize the composite spectrum displayed in the spectrum view (View > Spectrum).
This option results in a composite of individual spectra (MS2, MS3, MS4, and so on),
normalizing each spectrum to the highest intensity in the MS2 experiment, not using
the relative number of counts. This option provides easy comparison of MSn
experimental data. However, the Xcalibur data system does not retain the peak ratio of
the MSn data.
Clear this check box if you do not want to normalize the composite spectrum displayed
in the spectrum view (View > Spectrum). This option results in a composite of
individual spectra (MS2, MS3, MS4, and so on), normalizing the MS2 spectrum to
Relative Abundance 100 and displaying all other spectra relative to their actual number
of counts. This option increases the difficulty of comparison of MSn experimental data,
however it retains the peak ratio information.
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Table 34. MSn Browser Information page shortcut menu commands
Command
Description
Ranges
View or change the properties of all the plots in the active cell. You can
view or modify the time and mass ranges and change background
subtraction and smoothing parameters.
Include Individual Scans
If you clear this command, the MSn Browser displays the MS2 Average
Spectrum and all MSn Average Spectra and Composite Spectra that are
included in the raw file.
If you select this command, the MSn Browser displays the MS2 Average
Spectrum and all of the individual scans that make up the average
spectrum. The number of individual scans is controlled by the selection of
the Mass Tolerance value.
If the Mass Tolerance is small (<0.50), individual scans are available for
display. Individual scans might be grouped if the Mass Tolerance is large
(m/z >0.50). In addition, the MSn Browser displays MSn Average Spectra,
MSn Composite Spectra, and all of the MSn individual scans. The
functionality of the Mass Tolerance value is the same for all MSn scans as
that for MS2 scans as described above.
Individual scans appear in the following format:
Scan Number at Retention Time
For example, the icons for scan numbers 76, 115, and 154 appear below:
Normalize Composite Spectrum
View the selected spectrum as either normalized or not normalized.
Expand/Collapse List
View or hide the subentries in the list.
Export
Export the information to your computer clipboard.
Print
Open the Print dialog box.
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Avalon Peak Detection Settings Page
Use the Avalon Peak Detection Settings page of the Info Bar to specify peak identification and
peak integration criteria to be applied to the active chromatogram displayed in the Qual
Browser window.
Table 35. Avalon Peak Detection Settings page parameters (Sheet 1 of 4)
Parameter
Description
Application of Settings
Apply To All Plots
Apply the current chromatogram peak identification and integration settings to all
displayed plots. To apply criteria to all plots, select the Apply to All Plots check box. To
apply the criteria to only the active plot, clear this option.
Event List
Event List
View or change the settings for initial events and user-defined timed events in the event
list. To calculate values for initial events, open a raw file, make the chromatogram view
active, and then click the Auto Calculate Initial Events button. To change the settings in
the event list, highlight the row and then enter the revised settings in the boxes below
the list. You can then click Change to update automatically both the event list and the
chromatogram display.
There are seven initial entry integration events, identified by the initial value setting in
the Time column. These are the default integration events required by the Avalon
integration algorithm. You can change the value of an initial entry integration event,
but you cannot delete it or change its time value.
Time
View or change either the term initial value or values of time in minutes.
 To change the time of a timed event
1. Highlight the row in the event list.
2. Enter the revised setting in the Time box (below the event list).
3. Click Change to update automatically both the event list and the chromatogram
display.
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Table 35. Avalon Peak Detection Settings page parameters (Sheet 2 of 4)
Parameter
Description
Event
View or change descriptions of detection parameters for initial events and timed events.
 To change a timed event in the Event column
1. Highlight the row in the event list.
2. Click the Event drop-down list (below the event list) to display the available events.
3. Select an event.
4. Click Change to update automatically both the event list and the chromatogram
display.
You cannot change an event associated with an initial value.
Value
View or change the values associated with initial events or timed events. The range of
factors allowed for each value is specific to each event.
 To change a value in the Value column
1. Highlight the row in the event list.
2. Enter the revised setting in the Value box (below the event list).
3. Click Change to update automatically both the event list and the chromatogram
display.
Event List Entry
Time
View or change the currently highlighted entry from the Time column in the event list.
 To change the time setting for a timed event
1. Enter the new value in the box.
2. Click Change to update automatically both the event list and the chromatogram
display.
You cannot change the time entry for events that are listed with an Initial Value.
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Table 35. Avalon Peak Detection Settings page parameters (Sheet 3 of 4)
Parameter
Description
Event
View the currently highlighted entry in the Event column of the event list. To change
the description of a timed event, select a description from the list. Then, click Change
to update automatically both the event list and the chromatogram display.
Events that are listed with Initial Values cannot be changed.
The Xcalibur application provides these events:
Start/End Threshold: Directly related to the RMS noise in the chromatogram, this
value is Threshold, the fundamental control used for peak detection.
Bunch Factor: The Bunch Factor is the number of points grouped together during
peak detection. It controls the bunching of chromatographic points during integration
and does not affect the final area calculation of the peak. The Bunch Factor must be an
integer between 1 and 6; a high bunch factor groups peaks into clusters.
Area Threshold: Controls the area cutoff. The application does not detect any peaks
with a final area less than the area threshold. This control is in units of area for the data.
P-P Resolution: The peak to peak resolution threshold controls 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 option 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 should follow 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. Set a value in minutes.
Tangent Skim: For fused peaks that are significantly different in size, the tangent skim
method provides a method of allocating area to the various peaks. By default, the
application chooses the tallest peak in a cluster as the parent (solvent). You can also
identify which peak in the cluster is the parent. The application detects tangent skim
peaks on either side (or both sides) of the parent peak. Tangent skim automatically
resets at the end of the peak cluster.
The Threshold and Bunch Factor parameters are the most important ones in
controlling peak detection.
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Table 35. Avalon Peak Detection Settings page parameters (Sheet 4 of 4)
Parameter
Description
Value
View or change the currently highlighted entry from the Value column in the event list.
The range of factors allowed for each value is specific to each event.
 To change the value setting for an initial event or a timed event in this box
1. Highlight the row in the event list.
2. Enter the revised setting in the Value box.
3. Click Change to update automatically both the event list and the chromatogram
display.
Buttons
Auto Calc Initial Events
Search for the best values of initial events that detect peaks in the data. This button is
active with the event list of the Avalon peak detection algorithm only if you have a raw
file open. When you click the button, Avalon automatically estimates the initial values
for the detection of peaks based on the data in the current raw file, and then displays
those initial values in the event list. Any timed event in the event list is unchanged when
you click this button.
Auto Calculate Initial Events determines initial values for the following events only:
Start Threshold, End Threshold, Area Threshold, P-P [Resolution] Threshold, Bunch
Factor, Negative Peaks, and Tension. Additionally, you can specify timed events for
these events in the same event list.
Add
Add a time/event/value entry for a timed event in the event list. When you click the
Add button, both the event list and the chromatogram display update automatically
with the added specification in the currently selected chromatogram.
Delete
Remove a highlighted event from the event list. You cannot delete initial values.
Change
Update a highlighted time/event/value entry in the event list. When you click the
Change button, peak detection with the updated specification occurs automatically in
the currently selected chromatogram. For initial events, the application changes only
the values, and not the events.
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ICIS Peak Detection Settings Page
Use the ICIS Peak Detection Settings page of the Info Bar to specify peak detection and
integration criteria that the Xcalibur application applies to the active raw file displayed in the
Qual Browser window.
Table 36. ICIS Peak Detection Settings page parameters (Sheet 1 of 3)
Parameter
Description
Application of Settings
Apply To All Plots
Apply the current chromatogram peak identification and integration settings to all
displayed plots. To apply criteria to all plots, select the Apply to All Plots check box.
To apply the criteria to only the active plot, clear this option.
Peak Parameters
Baseline Window
Specify the number of scans to review, looking for a local minima. The valid range
is 1 through 500. The default value is 40 scans. This value is used by the ICIS peak
detection algorithm.
Area Noise Factor
Specify the noise level multiplier used to determine the peak edge after the location
of the possible peak. The valid multiplier range is 1 through 500. The default
multiplier is 5. This value is used by the ICIS peak detection algorithm.
Peak Noise Factor
Specify the noise level multiplier used to determine the potential peak signal
threshold. The valid multiplier range is 1 through 1000. The default multiplier is
10. This value is used by the ICIS peak detection algorithm.
Constrain Peak Width
Limit the peak width of a component during peak integration of a chromatogram.
You can then set values that control when peak integration is turned on and off by
specifying a peak height threshold and a tailing factor. To constrain a peak width,
click the Constrain Peak Width check box and enter values in the Peak Height (%)
box and the Tailing Factor box.
Peak Ht (%)
View or change the percent of the total peak height (100%) that a signal needs to
be above the baseline before integration is turned on or off. This box is active only
when you select the Constrain Peak Width check box. The valid range is 0.0 to
100.0%. To enter a height, type the appropriate value in the Peak Ht box.
Tailing Factor
View or change a factor that controls how the data system integrates the tail of a
peak. This factor is the maximum ratio of the trailing edge to the leading side of a
constrained peak. This box is active only when you select the Constrain Peak
Width check box. The valid range is 0.5 through 9.0.
Advanced
Advanced
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Specify advanced criteria to detect your chromatographic peak. The Xcalibur
application provides these advanced settings: Manual Noise Region, INCOS Noise,
Repetitive Noise, RMS, Minimum Peak Width, Multiplet Resolution, Area Tail
Extension, and Area Scan Window.
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Table 36. ICIS Peak Detection Settings page parameters (Sheet 2 of 3)
Parameter
Description
Manual Noise Region
Specify a region of the chromatogram that the Xcalibur data system uses to
determine noise. You can enter the retention time (RT) in the RT Range box.
and drag the cursor horizontally across the region of the
Also, you can click
chromatogram that you want to select as the noise region. The application marks
the region with a red baseline.
RT Range
Enter the retention time (RT) range in the RT Range box that you want the data
system to use to determine noise. The RT range should be within the
chromatogram range.
Also, you can click
and drag the cursor horizontally across the region of the
chromatogram that you want to select as the noise region. The application marks
the region with a red baseline.
INCOS Noise
Use a single pass algorithm to determine the noise level. This value is used by the
ICIS peak detection algorithm.
Repetitive Noise
Use a multiple pass algorithm to determine the noise level. This value is used by the
ICIS peak detection algorithm. In general, this algorithm is more accurate in
analyzing the noise than the INCOS Noise algorithm, but it takes longer.
RMS
Calculate noise as RMS. By default, the data system uses Peak To Peak for the noise
calculation. If you determine the noise region manually, the application
automatically selects RMS.
Min Peak Width
Enter the minimum number of scans required in a peak. The valid range is 0 to 100
scans. The default value is 3 scans. This value is used by the ICIS peak detection
algorithm.
Multiplet Resolution
Enter the minimum separation in scans between the apexes of two potential peaks.
This criteria determines if two peaks are resolved. The valid range is 1 to 500 scans.
The default value is 10 scans. This value is used by the ICIS peak detection
algorithm.
Area Tail Extension
Enter the number of scans past the peak endpoint to use in averaging the intensity.
The valid range is 0 to 100 scans. The default value is 5 scans. This value is used by
the ICIS peak detection algorithm.
Area Scan Window
Enter the number of scans on each side of the peak apex to include in the area
integer. The valid range is 0 to 100 scans. The default value of 0 scans specifies that
all scans from peak start to peak end are to be included in the area integration. This
value is used by the ICIS peak detection algorithm.
Buttons
Apply
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Apply the settings displayed in the dialog box.
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Table 36. ICIS Peak Detection Settings page parameters (Sheet 3 of 3)
Parameter
Description
Save As Default
Use the current settings as default settings. If you save the settings as defaults, you
can restore these values at any time by using the Load Default button.
Load Default
Restore the current default settings. To set default settings, click Save As Default.
Genesis Peak Detection Settings Page
Use the Genesis Peak Detection Settings page of the Info Bar to specify peak identification
and peak integration criteria to be applied to active raw file displayed in the Qual Browser
window.
Table 37. Genesis Peak Detection Settings page parameters (Sheet 1 of 4)
Parameter
Description
Application of Settings
Apply To All Plots
Apply the current chromatogram peak identification and integration settings to all
displayed plots. To apply criteria to all plots, select the Apply to All Plots check box. To
apply the criteria to only the active plot, clear this option.
Peak Parameters
Percent Of Highest Peak
Enter a percentage threshold to limit the number of peaks submitted for further
processing. The Xcalibur application discards any detected peaks with an intensity less
than the threshold percentage of the most intense peak.
Minimum Peak Ht (S/N)
View or change the peak signal-to-noise criteria to equal or exceed as a criteria for peak
detection. The application ignores all chromatogram peaks that have signal-to-noise
values that are less than the Minimum Peak Height (S/N) value. To enter a peak
signal-to-noise criteria, type the value in the Minimum Peak Height (S/N) box. The
valid range is 1.0 (all peaks) to 999.0.
S/N Threshold
View or change the threshold for detecting peak edges. The default value is 0.5 and the
valid range is 0.0 to 999.0. The Xcalibur application calculates the signal-to-noise ratio
using only baseline signal. Any extraneous, minor, detected peaks are excluded from the
calculation.
Valley Detection Enabled
Use the Xcalibur 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.
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Table 37. Genesis Peak Detection Settings page parameters (Sheet 2 of 4)
Parameter
Description
Expected Width
View or change the expected peak width parameter (in seconds). This value controls the
minimum width that a peak is expected to have if valley detection is selected.
With valley detection selected, any valley points nearer than the expected width/2 to the
top of the peak are ignored. If a valley point is found outside the expected peak width,
the Xcalibur application terminates the peak at that point. The application always
terminates a peak when the signal reaches the baseline, independent of the value set for
the expected peak width. The valid range is 0.0 to 999.0 seconds. To change the current
value, type a new width in the Expected Width box.
Constrain Peak Width
Limit the peak width of a component during peak integration of a chromatogram. You
can then set values that control when peak integration is turned on and off by specifying
a peak height threshold and a tailing factor. To limit a peak width, click the Constrain
Peak Width check box.
Peak Ht
View or change the Peak Height where the data system tests the width of target peaks.
You can enter any value from 0 to 100%. The default value is 5.0%.
Tailing Factor
View or change a factor that controls how the data system integrates the tail of a peak.
This factor is the maximum ratio of the trailing edge to the leading side of a constrained
peak. This box is active only when you select the Constrain Peak Width check box. The
valid range is 0.5 through 9.0.
Advanced
RMS
Calculate noise as RMS.
Peak to Peak
Calculate noise as peak-to-peak.
Manual Noise Region
Specify a region of the chromatogram that the Xcalibur application uses to determine
noise. You can enter the retention time (RT) in the RT Range box.
Also, you can click
and drag the cursor horizontally across a region of the
chromatogram to select the region as the noise region. The application marks the region
with a red baseline.
RT Range
Enter the retention time (RT) range in the RT Range box that you want the Xcalibur
data system to use to determine noise. The RT range should be within the
chromatogram range.
and drag the cursor horizontally across a region of the
Also, you can click
chromatogram to select the region as the noise region. The application marks the region
with a red baseline.
Baseline Noise Tolerance
Thermo Scientific
View or change a value that 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. The valid range is 0.0 to 100.0. To change the baseline noise tolerance, enter
the new value in the Baseline Noise Tolerance box. When you click Apply, the data
system applies the new peak integration parameter.
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Table 37. Genesis Peak Detection Settings page parameters (Sheet 3 of 4)
Parameter
Description
Min Number Of Scans In
Baseline
View or change the minimum number of scans that the Xcalibur application uses to
calculate a baseline. A larger number includes more data in determining an averaged
baseline. The valid range is 2 to 100.0. To change the minimum number of scans, enter
the new value in the Minimum Number of Scans in Baseline box. When you click
Apply, the application applies the new baseline parameter.
Baseline Noise Rejection
Factor
View or change the current baseline noise rejection factor. This factor controls the
width of the rms noise band above and below the peak detection baseline. This factor is
applied to the raw rms noise values to raise the effective rms noise used by the Xcalibur
data system during peak detection. The system responds by assigning the left and right
peak boundaries above the noise and therefore closer to the peak apex value in minutes.
This action effectively raises the peak integration baseline above the rms noise level. The
valid range of this factor is 0.1 to 10.0. The default value is 2.0.
Peak S/N Cutoff
View or change the signal-to-noise level that the data system defines as the top of 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 will define the right and left edges of the peak when
the S/N reaches a value less than 200. The valid range is 50.0 to 10000.0. To change the
cutoff value, enter the new value in the Peak S/N Cutoff box. When you click Apply,
the application applies the new peak detection parameter.
Rise Percentage
View or change the percentage that the peak trace can rise above the baseline after
passing through a minimum (before or after the peak). If the trace exceeds this value,
the Xcalibur data system applies valley detection peak integration criteria. This test is
applied to both the left and right edge of the peak. This criteria is useful for integrating
peaks with long tails. The valid range is 0.1 to 500.0. To change the rise percentage,
enter the new value in the Rise Percentage box. When you click Apply, the Xcalibur
system applies the new peak detection criteria.
Valley S/N
View or change the signal-to-noise criteria that the Xcalibur data system uses for valley
detection. The valid range is 1.0 to 100.0. To change the valley detection
signal-to-noise criteria, enter the new value in the Valley S/N box. When you click
Apply, the system applies the new peak detection criteria.
Background
Recomputation Interval
The Xcalibur application periodically recalculates the representative background scan it
uses for background subtraction. This is to compensate for the possibility that the
composition of the background might change over the course of a run. The
Background Recomputation Interval is the time interval in minutes between these
recalculations.
To change the interval, enter the new value in the Background Recomputation Interval
box. The valid range is 0.5 to 10.0 minutes.
Number Of Scans In
Background
186
View or change the number of background scans used to determine the background.
The valid range is 2 to 100. To change the number of background scans, enter the new
value in the Number of Scans in Background box. When you click Apply, the Xcalibur
system applies the new baseline parameter.
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Table 37. Genesis Peak Detection Settings page parameters (Sheet 4 of 4)
Parameter
Description
Buttons
Apply
Apply the settings displayed in the dialog box.
Save As Default
Specify to use the current settings as default settings. Once the settings are saved as
defaults, you can restore these values at any time by using the Load Default button.
Load Default
Restore the current default settings. To set default settings, use the Save As Default
button.
Result File Information Page
The Result File Information page contains a peak list for the selected result file.
Table 38. Result File Information page parameters
Thermo Scientific
Command
Description
Retention Time
Specify the time after injection when an analyte elutes. This is the
total time that the analyte is retained on the chromatographic
column. If the maximum signal from an analyte is detected 5 min
and 14 s after injection, then the analyte has a retention time of
5:14.
Left
View the retention time corresponding to the start of the
chromatographic peak, where the detection signal increases
beyond the threshold criteria.
Apex
The retention time corresponding to the uppermost point of a
chromatogram peak.
Right
The retention time corresponding to the end of the
chromatographic peak, where the detection signal decreases below
the threshold criteria.
Height
The number of counts at the peak apex.
Area
The area of the peak in units of counts * seconds.
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Sequence Information Page
The Sequence Information page of the Info Bar lists the file name and path of the sequence. It
also lists the raw files in the sequence.
Double-click any file in the sequence to open it in the active window, replacing the plots in all
cells with equivalent spectra, chromatograms, or maps.
Right-click any file within the Sequence Information page to display a shortcut menu.
Table 39. Sequence Information page parameters
Command
Description
Open-Replace
All in Current Window
Open the selected file in the active window, replacing the plots in all cells with
equivalent spectra or chromatograms (you can also double-click a file).
All in Current Cell
Replace all plots in the active cell with equivalent plots from the selected file.
Current Plot
Replace the current plot in the active window with an equivalent from the selected
file.
Open-Add
New Window
Open the selected raw file in a new window.
New Plot
Open the selected file as a plot in the active cell.
Other
Open Result File
Open a result file associated with the selected raw file.
Properties
View basic information about the selected sample including the row, filename,
sample ID, name, sample type and result file name.
The dialog box closes if you click anywhere outside it. Click the pin icon to keep
the Sample Properties dialog box open. You must then click the close icon to close
the dialog box or unpin the dialog box (by clicking the pin icon again) and click
anywhere outside the dialog box.
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Spectrum Simulation Page
Use the Spectrum Simulation page to create a simulated isotopic distribution spectrum of a
chemical formula.
Table 40. Spectrum Simulation page parameters (Sheet 1 of 5)
Parameter
Description
New
Place the simulated spectrum in a new view.
Insert
Place the simulated spectrum above the selected (highlighted) spectrum.
Select a spectrum to make the Insert button active.
Replace
Replace the selected (highlighted) spectrum with the simulated spectrum.
Select a spectrum to make the Replace button active.
Chemical Formula
Enter or select the chemical formula for the simulated spectrum. Then, click the Insert or
Replace button to display the spectrum. The maximum molecular weight for the formula is
less than 600,000 amu.
You can enter both upper and lower case letters, however the Xcalibur data system interprets
all lower case input as two-letter symbols. For example, the string inau will be parsed as
In Au. You can force other interpretations by being more specific in capitalization, namely
INAu or INaU. The application interprets all upper case input as single-letter element
names. For example, COSI is interpreted as C O S I.
Specify a specific isotope by naming it in the following fashion: [13]C using square brackets
about the isotope mass number.
You can specify mixtures of substances by using additional symbols + (addition) and *
(multiplication). Both symbols are required to specify a mixture. A valid mixture has the
format substance*quantity + substance* quantity, for example, C4H8*2+H2O*5.
Peptide/Protein
Enter or select the peptide/protein formula for the simulated spectrum. Then, click the
Insert or Replace button to display the spectrum. The maximum molecular weight for the
formula is less than 600,000 amu.
You can use both single capital letter abbreviations for amino acids (for example, CAT), and
the standard three letter abbreviations with the first letter capitalized. To enter multiple
copies of an amino acid, type a number directly after the one- or three-letter abbreviation.
For example: Tyr3 represents 3 Tyrosines.
You can specify mixtures of substances by using additional symbols '+' (addition) and '*'
(multiplication). Both symbols are required to specify a mixture. A valid mixture has the
format substance*quantity + substance* quantity, for example, A*2+C*5.
List of common one- and three-letter abbreviations.
List of less common three-letter abbreviations.
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Table 40. Spectrum Simulation page parameters (Sheet 2 of 5)
Parameter
Description
Plus H2O
Specify that the simulated spectrum for a peptide formula includes a water molecule.
This check box becomes active when you select the Peptide/Protein option.
Mass readback
View the sum of the masses of the lightest naturally occurring isotopes of the elemental
formula in amu. When mixtures are simulated, the value of Mass readback will be blank.
Change Mixture
Specify the compounds and amounts you want to include in the mixture in the
Change Mixture for Simulation dialog box. Click the Change Mixture button to open
the Change Mixture for Simulation dialog box.
Adduct
Adduct
Specify that the simulated spectrum is an adduct.
The Spectral Simulation feature in the Xcalibur data system supports two general modes of
ionization: addition or subtraction of protons and addition/subtraction of electrons.
If you clear the Adduct check box, the data system calculates the mass to charge ratio based
on the loss or addition of electrons according to this general formula:
formula mass – (sign of charge * the number of charges * electron mass) / number of charges
If you select the Adduct check box, the data system calculates the mass to charge ratio based
on protonation/deprotonation according to this general formula:
formula mass + (sign of charge * the number of charges * proton mass) / number of charges
When a formula does not contain any hydrogen atoms, the system does not subtract the
mass of a proton even though the you select the Adduct check box. See Concentration
below for more information on how the data system calculated the mass to charge ratio for
multiply charged ions when an adduct without any hydrogen atoms is selected.
Identity
190
Select the adduct for the simulated spectrum. Choose from H, K, or Na.
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Table 40. Spectrum Simulation page parameters (Sheet 3 of 5)
Parameter
Description
Concentration
There are four possibilities for how the adduct is added to the ion:
• one adduct:
For positive charge states and positively charged adducts, the Xcalibur data system
creates the specified charge state by adding the positive adduct for the first charge and
H+ ions for subsequent charges. For example, a charge distribution of Most
abundant=2 and Half width = 2 (2,2) and a K+ adduct shows these ions:
+1 C10K+
+2 C10HK+2
+3 C10H2K+3
+4 C10H3K+4
For negative charge states, each charge state shows loss of H+ to attain the specified
charge. If the molecule does not contain hydrogen, nothing is removed. For example,
for 2 ions C6H6 and C4 and a K adduct, the (–2,2) charge state gives:
–1 C6H5K– C4K–
–2 C6H4K–2 C4K–2
–3 C6H3K–3 C4K–3
–4 C6H2K–4 C4K–4
The second and third cases produce a distribution of adducts for charges where the
absolute values are greater than 1. It is possible to specify both a distribution of charge
states and a distribution of adducts. This case can result in an extremely complicated
spectrum when the adduct distribution overlaps the charge state distribution.
• low: the ion with no adduct will be included at 100% intensity, 1 adduct at 25%
intensity, 2 adducts at 11% intensity, and so on. (To the limit of the charge
distribution.)
• high: the ion with N adducts are included at 100% intensity, N-1 adduct at 25%
intensity, N-2 adducts at 11% intensity, and so on, where N is the absolute value of the
maximum charge simulated. (To the limit of the charge distribution.)
• 100%: the ion of charge N contains M adducts (where M is the absolute value of N.)
Charge Distribution
Charge Distribution
Specify limits on charge distribution. Change the values of the settings to simulate the effect
on ions. See Adduct for more information.
Most Abundant
Select the most abundant charge of the ion, and the Xcalibur application calculates the
masses accordingly. The range will be –99 to +99, and the default value is +1.
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Table 40. Spectrum Simulation page parameters (Sheet 4 of 5)
Parameter
Description
Half Width
Simulate the number of additional charges on each side of the most abundant. Select a value
from 0 to 99.
For example: If you simulate charge 10 and a half width of 3, then the Xcalibur application
draws charges 10 +/- 3, giving 7, 8, 9, 10, 11, 12, 13 (with the largest peak at charge 10).
If you simulate charge 2 and a half width of 3, then the application draws positive charges
from the range 2 +/- 3, giving 1, 2, 3, 4, 5. (with the largest peak at charge 2).
If you simulate charge 1 and a half width of 3, then the application draws charges 1, 2, 3, 4.
To simulate an intensity distribution, the peaks at the edge of the distribution are shown at
5% of the height of the most abundant peak.
Output Style
Output Style
Select how you want the Xcalibur application to display the simulated spectrum. The
options are pattern, profile, and centroid.
Pattern
Plot the exact pattern of isotopic peaks generated by the simulation.
Profile
Plot the pattern spectrum convolved with a gaussian, cosine, triangular, or lorentzian
broadening function (see below). Use the Samples Per Peak box to specify the number of
data points across the peak.
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Table 40. Spectrum Simulation page parameters (Sheet 5 of 5)
Parameter
Description
Samples/Peak
Set the Samples Per Peak to the number of data points across the width of the peak.
The peak definition depends on which valley option you selected:
• FWHM: the width of the peak is measured at 50% height
• 10% Valley: the width of the peak is measured at 5% height
• 5% Valley: the width of the peak is measured at 2.5% height
After resolving 2 peaks, the Xcalibur application creates a valley by the sum of the signals
from the newly resolved peaks, so the peak height of each contributing peak at the valley
bottom is half of the valley height.
Centroid
Select this option to apply the same algorithm used in the firmware to convert from
profile data to centroid. When you select centroid, both the Samples/Peak box and the
Choose Algorithm button become active.
Choose Algorithm
Select a centroiding algorithm.
Resolution
Specify the type of unit for peak width to associate with the value in the adjacent boxes. You can select resolution in
Daltons, parts per million (ppm), or resolving power. Simulate MS results from a quadrupole detector with a fixed
mass peak width (Daltons), or simulate results from a magnetic sector detector with a relative mass peak width
(ppm or resolving power).
Daltons
Specify a value for simulated peak width in Daltons. When you select the option, the box
becomes active.
PPM
Specify a value for simulated peak width in parts per million. When you select the option,
the box becomes active.
Resolving Power
Specify the resolving power for simulated peak width. When you select the option, the box
becomes active.
Resolving power is a measurement of the ability of a mass spectrometer to resolve close
peaks. For example: A resolving power of 1000 at 10% valley implies that if there are 2 equal
height peaks at mass 1000 and 1001, then there will be a valley between those peaks at
10% of the peak height, at mass 1000.5 (and that at 999.5 and 1001.5 the profile will be at
5% of the peak height).
Valley
FWHM
Select this option to make the peak width at half maximum equal to the resolution. For
example, if you select a resolution of 1 Dalton, then the peak is 1 Dalton wide at half
maximum.
10%
Select this option to simulate a valley at 10% height between just resolved peaks.
5%
Select this option to simulate a valley at 5% height between just resolved peaks.
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List of Common One- and Three-Letter Abbreviations
Table 41. Common one- and three-letter abbreviations
194
One letter
Name
Formula
Three letter
A
Alanine
C3H5NO
Ala
C
Cysteine
C3H5NOS
Cys
D
Aspartate
C4H5NO3
Asp
E
Glutamate
C5H7NO3
Glu
F
Phenylalanine
C9H9NO
Phe
G
Glycine
C2H3NO
Gly
H
Histidine
C6H7N3O
His
I
Isoleucine
C6H11NO
Ile
K
Lysine
C6H12N2O
Lys
L
Leucine
C6H11NO
Leu
M
Methionine
C5H9NOS
Met
N
Asparagine
C4H6N2O2
Asn
O
Ornithine
C5H11N2O
Orn
P
Proline
C5H7NO
Pro
Q
Glutamine
C5H8N2O2
Gln
R
Arginine
C6H12N4O
Arg
S
Serine
C3H5NO2
Ser
T
Threonine
C4H7NO2
Thr
V
Valine
C5H9NO
Val
W
Tryptophan
C11H10N2O
Trp
Y
Tyrosine
C9H9NO2
Tyr
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List of Less Common Three-Letter Abbreviations
Table 42. Less common three-letter abbreviations (Sheet 1 of 3)
Three letter
Name
Formula
Abu
2-Aminobutyric acid
(2-aminobutanoic acid)
C4H7NO
Aec
Aminoethylcysteine
C5H10N2OS
Aib
Aminoisobutyric acid
C4H7NO
Aln
Aly
C13H11NO
Alveolysin
Amc
C6H10N2O2S
Bcy
C10H11NOS
Bgl
C12H13NO3
Bly
C16H26N4O3S
Bse
C10H11NO2
Bth
C11H13NO2
Cmc
Carboxymethylcysteine
Cml
C5H7NO3S
C8H14N2OS
Cph
Chlorophenylalanine
C9H8NOCl
Cya
Cysteic acid
C3H5NO4S
Dha
Dehydroalanine
C3H3NO
Dhb
Dehydro-2-aminobutyric acid
C4H5NO
Dpr
D-proline
C5H5NO
Dty
Diiodotyrosine
C9H7NO2I2
Fcy
C18N29NOS
Fph
C9H8NOF
Ftr
C12H10N2O2
Gaa
C4H7NO
Gcg
C5H5NO4
Gla
Carboxyglutamic acid
Glp
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C12H22N2O6
C6H7NO5
C5H5NO2
Hse
Homoserine
C4H7NO2
Hsl
Homoserine lactone
C4H5NO
Hya
Beta-hydroxyaspartate
C4H5NO4
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Table 42. Less common three-letter abbreviations (Sheet 2 of 3)
Three letter
Name
Formula
Hyg
Hydroxyglycine
C5H7NO4
Hyl
Hydroxylysine
C6H12N2O2
Hyp
Hydroxyproline
C5H7NO2
Ils
Isolysine
C9H18N2O
Ity
Iodotyrosine
C9H8NO2I
Iva
Isovaline
C5H9NO
Mar
C7H14N4O
Mas
C5H7NO3
Mbt
C17H17NO2
Mes
C5H9NO3S
Mga
C6H10N2O2
Mgl
C6H9NO3
Mhi
C7H9N3O
Mls
C7H14NO
Mme
C6H11NOS
Mph
C10H11NO
Mso
Methioninesulfoxide
Mty
C10H11NO2
Nle
Norleucine
C6H11NO
Nls
Norlysine
C12H15N3O2
Pal
C8H8N2O
Pcy
C19H35NO2S
Pec
C10H12N2OS
Pip
2-Piperidinecarboxylic acid
C6H9NO
Psr
Phosphoserine
C3H6NO5P
Pth
Phosphothreonine
C4H8NO5P
Pty
Phosphotyrosine
C9H10NO5P
Pyr
Pyroglutamic acid
C5H5NO2
Sar
sarcosine
C3H5NO
Sas
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Table 42. Less common three-letter abbreviations (Sheet 3 of 3)
Three letter
Name
Formula
Tml
E-amino trimethyl-lysine
C9H19N
Tys
Tyrosinesulfonic acid Tyr(SO3H)
C9H9NO5S
Qual Browser Dialog Boxes
The Qual Browser window has these dialog boxes:
• Add Graphics Dialog Box
• Add Programs To Tool Menu Dialog Box
• Add Text Dialog Box
• Add Tool Dialog Box
• Amplify by Other Factor Dialog Box
• Average Filter Selection Dialog Box
• Cell Size Dialog Box
• Choose Centroiding Algorithm Dialog Box
• Color Dialog Box
• Copy to Clipboard Dialog Box
• Display Options Dialog Box
• Global Mass Options Dialog Box
• Heading Editor Dialog Box
• Library Search Constraints Page (Qual View)
• Peak Purity Dialog Box
• Print Dialog Box
• Ranges Dialog Boxes
• Select Isotopes Dialog Box
• Specify Mixture for Simulation Dialog Box
• Subtract Background Dialog Box
• Toolbars Dialog Box
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Add Graphics Dialog Box
Use the Add Graphics dialog box to add graphic elements to a spectrum, chromatogram, or
map.
Table 43. Add Graphics dialog box parameters (Sheet 1 of 3)
Parameter
Description
Style
Horizontal Line
Draw a horizontal line on a plot.
 To draw a horizontal line
1. Choose the Horizontal Line option and choose a line color.
2. Click OK to close the Add Graphics dialog box.
3. Drag the cursor on the plot to draw the horizontal line. You can drag from right-to-left
or from left-to-right.
Vertical Line
Draw a vertical line on a plot.
 To draw a vertical line
1. Choose the Vertical Line option and choose a line color.
2. Click OK to close the Add Graphics dialog box.
3. Drag the cursor on the plot to draw the vertical line. You can drag from bottom-to-top
or from top-to-bottom.
Diagonal Line
Draw a diagonal line on a plot.
 To draw a diagonal line
1. Choose the Diagonal Line option and choose a line color.
2. Click OK to close the Add Graphics dialog box.
3. Drag the cursor on the plot to draw the diagonal line. You can drag from left-to-right or
from right-to-left. Move the cursor before you release the mouse button to position the
angle of the line.
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Table 43. Add Graphics dialog box parameters (Sheet 2 of 3)
Parameter
Description
Box
Draw a rectangular box on a plot.
 To draw a box
1. Choose the Box option and choose a line color.
2. Click OK to close the Add Graphics dialog box.
3. Drag the cursor diagonally to draw the box. You can click to start at any corner of the
box and then drag the cursor to the opposite corner. The Xcalibur application draws a
box similar to the following:
Filled Box
Draw a rectangular box on a plot.
 To draw a filled box
1. Choose the Filled Box option and choose a line color and a fill color.
2. Determine whether the filled box is behind or not behind a graph.
3. Click OK to close the Add Graphics dialog box.
4. Drag the cursor diagonally to draw the box. You can click to start at any corner of the
box and then drag any cursor to the opposite corner. These filled boxes have a black box
and a brown fill and demonstrate the use of the Behind Graph check box feature.
Behind graph
Not behind graph
Colors
Line
Select the color of the added line or box outline.
The current color for an added line or box outline is displayed to the right of the Line
button. The Color dialog box opens with a color palette so you can select a preset color or
customize a color. Use the adjacent graphic to view the result of the current color selection.
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Table 43. Add Graphics dialog box parameters (Sheet 3 of 3)
Parameter
Description
Fill
Select the color of the added filled box.
The current color for the added filled box is displayed to the right of the Fill button. The
Color dialog box opens with a color palette so you can select a preset color or customize a
color. Use the adjacent graphic to view the result of the current color selection.
Behind Graph
Draw a filled box either in front of a plot or behind a plot. To draw a filled box behind a
graph, select the Behind Graph check box. To draw an opaque filled box in front of (on top
of ) a graph, clear the Behind Graph check box. This figure shows the difference between
the two options:
Behind graph
Not behind graph
Add Programs To Tool Menu Dialog Box
Use the Add Programs To Tool Menu dialog box to add and to remove application programs
from the Tool menu and to adjust the sequence of the menu.
Table 44. Add Programs To Tool Menu dialog box parameters (Sheet 1 of 2)
Parameter
Description
Menu Contents
View or change the names of the current list of tools (programs) that have been added to
the Tool menu. These names appear when you choose the Tools menu. You can use the
Add, Remove, Move Up, and Move Down buttons in the Add Programs To Tool Menu
dialog box to edit the current list of programs.
Menu Text
View or change the name of the tool (program) selected in the Menu Contents box. To
change the name, type the new name in the Menu Text box.
Program
Enter the path and file name of the tool (program) that you want to add to the Tools menu
or you can click Browse to select the path and file name.
Arguments
Add command line arguments.
Initial Directory
View or change the path that the data system uses to find the tool (program) selected in the
Menu Contents box. To change the path, type the new path in the Initial Directory box.
Close
Save all changes and to close the current page or dialog box.
Add
Add a tool (program) to the Tools menu.
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Table 44. Add Programs To Tool Menu dialog box parameters (Sheet 2 of 2)
Parameter
Description
Remove
Remove the name of the tool (program) selected in the Menu Contents box from the list of
tools.
Move Up
Change the current sequence of tools (programs) are displayed in the Menu Contents box.
This order is the sequence displayed when you choose the Tools menu.
Click Move Up to select a tool and move it up in the list sequence.
Move Down
Change the current sequence of tools (programs) are displayed in the Menu Contents box.
This order is the sequence displayed when you choose the Tools menu.
Click Move Down to select a tool and move it down in the list sequence.
Add Text Dialog Box
Use the Add Text dialog box to type, format, and position text on a spectrum, chromatogram,
or map plot.
Table 45. Add Text dialog box parameters (Sheet 1 of 6)
Parameter
Description
Annotation Text
View the annotation text that the Xcalibur data system adds to your plot if you click OK
and click your plot with the Add Text cursor
.
Text alignment and position options in the Add Text dialog box are not displayed until you
select the position on the plot. To change the text, select the current text and type the new
caption. Use the ENTER key for multiple lines.
Boxed
Include a visible box around the annotation text you add to a plot. To add a box around the
text, select the Annotation text: Boxed check box. If you do not want to include a box with
the text, clear the Boxed check box.
Rotated
Rotate the annotation text you add to a plot so that it reads vertically from bottom to top.
To rotate the text, select the Annotation text: Rotated check box. If you want your text to
read horizontally from left to right, clear the Rotated check box.
Annotation Text
A sample of rotated text follows:
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Table 45. Add Text dialog box parameters (Sheet 2 of 6)
Parameter
Description
Pointer
Draw a pointer line from the annotation text to a point on the plot. To include a pointer
with your annotation text, select the Annotation text: Pointer check box. If you do not want
your annotation text to include a pointer, clear the Pointer check box.
To point above the annotation text, use the Below Marked Position option. To point below
the annotation text, use the Above Marked Position option. These precautions make sure
the pointer line does not cross over the annotation text. An example of the proper use of
pointers is shown below:
Marked Position Is
Left
Orient annotation text so that the position marked with the
text cursor is to the left of
the placed text. In other words, the text is to the right of the point that you position the
arrow of the text cursor. The Xcalibur application activates the text cursor when you click
OK from the Add Text dialog box.
If you choose the Marked Position is Left option, the exact placement of annotation text
also depends upon the option you select in the Height Drawn box, as follows:
If you also select the Just Above Graph option, the text is placed as follows:
If you also select the Above Marked Position option, the text is placed as follows:
If you also select the Below Marked Position option, the text is placed as follows:
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Table 45. Add Text dialog box parameters (Sheet 3 of 6)
Parameter
Description
Center
Orient annotation text so that the position marked with the text cursor
is in the center
of the placed text. The Xcalibur application activates the text cursor when you click OK
from the Add Text dialog box.
If you choose the Marked Position is Center option, the exact placement of annotation text
also depends upon the option you select in the Height Drawn box, as follows:
If you also select the Just Above Graph option, the text is placed as follows:
If you also select the Above Marked Position option, the text is placed as follows:
If you also select the Below Marked Position option, the text is placed as follows:
Right
Orient annotation text so that the position marked with the
text cursor is to the right
of the placed text. In other words, the text is to the left of the point that you position the
arrow of the text cursor. The Xcalibur application activates the text cursor when you click
OK from the Add Text dialog box.
If you choose the Marked Post ion is Left option, the exact placement of annotation text
also depends upon the option you select in the Height Drawn box, as follows:
If you also select the Just Above Graph option, the text is placed as follows:
If you also select the Above Marked Position option, the text is placed as follows:
If you also select the Below Marked Position option, the text is placed as follows:
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Table 45. Add Text dialog box parameters (Sheet 4 of 6)
Parameter
Description
Multiple Lines Aligned
Left
Align multiple rows of annotation text so that each row is aligned on the left side. The
Xcalibur application does not display the left alignment of the text until it is placed onto the
plot with the text cursor, as follows:
Line One
This is Line Two
Line Three
Center
Align multiple rows of annotation text so that each row is aligned on a center axis. The
application does not display the center alignment of the text until it is placed onto the plot
with the text cursor, as follows:
Line One
This is Line Two
Line Three
Right
Align multiple rows of annotation text so that each row is aligned on the right side. The
application does not display the right alignment of the text until it is placed onto the plot
with the text cursor
, as follows:
Line One
This is Line Two
Line Three
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Table 45. Add Text dialog box parameters (Sheet 5 of 6)
Parameter
Description
Height Drawn
Just Above Graph
Orient the height of annotation text so that it is positioned directly above the plot position
marked with the
text cursor.
If you choose the Just Above Graph option, the exact placement of annotation text also
depends upon the option you select in the Marked Position Is box, as follows:
If you also select the Left option, the text is placed as follows:
If you also select the Center option, the text is placed as follows:
If you also select the Right option, the text is placed as follows:
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Table 45. Add Text dialog box parameters (Sheet 6 of 6)
Parameter
Description
Above Marked Position Orient the height of annotation text so that it is positioned above the position marked with
the
text cursor.
If you choose the Above Marked Position option, the exact placement of annotation text
also depends upon the option you select in the Marked Position Is box, as follows:
If you also select the Left option, the text is placed as follows:
If you also select the Center option, the text is placed as follows:
If you also select the Right option, the text is placed as follows:
Below Marked Position Orient the height of annotation text so that it is positioned below the position marked with
the
text cursor.
If you choose the Below Marked Position option, the exact placement of annotation text
also depends upon the option you select in the Marked Position Is box, as follows:
If you also select the Left option, the text is placed as follows:
If you also select the Center option, the text is placed as follows:
If you also select the Right option, the text is placed as follows:
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Add Tool Dialog Box
Use the Add Tool dialog box to add a program with a specified path to the Tools menu.
Table 46. Add Tool dialog box parameters
Parameter
Description
Program
Enter the path and file name of the tool (program) to add to the
Tools menu or click Browse to select the path and file name.
Browse
Find an existing file.
Amplify by Other Factor Dialog Box
Use the Amplify by Other Factor dialog box to specify an amplification factor to apply to a
region of an active plot.
The valid range is 1.1 to 1000.0. When you click OK, the Xcalibur application changes the
so that you can drag the cursor horizontally to amplify a region of the active
cursor to
graph or type a value into the Amplify Factor combo box.
Table 47. Amplify by Other Factor dialog box parameters
Thermo Scientific
Parameter
Description
Amplification Factor
Enter an amplification factor to be applied to a region of an active
plot. The valid range is 1.1 to 1000.0.
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Average Filter Selection Dialog Box
The Average Filter Selection dialog box opens whenever you try to average scans in a
chromatogram time range in which two or more types of scan types are defined. Use this
dialog box to select one of the scan filters defined for the selected time range.
Table 48. Average Filter Selection dialog box parameters
Parameter
Description
Filter
View the current scan filter for the active raw file. You can use a scan filter to specify that
processing is to be applied to a subset of the scans in a raw file.
To apply a different scan filter, select a new filter from the scan filter list (most common
method), select a new filter from a list and edit the scan filter or type a new scan filter
command string into the combo box using the scan filter format.
 To select from the list of scan filters used to create the raw file
1. Click the arrow on the combo box to display the list.
2. Select one of the scan filters. The Xcalibur application displays the scan filter in the
Filter combo box.
For example, this scan filter:
c full ms [26.81–251]
finds all scans in a raw file that have these properties:
centroid data
Scan Mode: Full
Scan Power: MS
Product Ion Mass Range: m/z 26.81 to 251.00
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Cell Size Dialog Box
Use the Cell Size dialog box to define the size of a cell.
Table 49. Cell Size dialog box parameters
Parameter
Description
Column Width
To set the column width of a cell, drag the Column Width scroll
box or click the scroll box left and right arrows until you reach the
desired width within the range 5 to 300%. The current width is
displayed below the scroll box. To quickly set the column width to
100%, choose the Default Width button. Use the adjacent
graphic to view the result of the column width setting.
Changing the Column Width has no effect if you have only one
column of cells.
Row Height
To set the row height of a cell, drag the Row Height scroll box or
click the scroll box left and right arrows until you reach the desired
height within the range of 5 to 300%. The current height is
displayed below the scroll box. To quickly set the column height
to 100%, choose the Default Height button. Use the adjacent
graphic to view the result of the column height setting.
Changing the Row Height has no effect if you have only one row
of cells.
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Choose Centroiding Algorithm Dialog Box
Use the Choose Centroiding Algorithm dialog box to choose which algorithm the Xcalibur
data system uses to calculate the centroid of profile data and to specify values of parameters
used by the centroiding algorithm.
Table 50. Choose Centroiding Algorithm dialog box parameters
Parameter
Description
Centroiding Algorithm Choose which algorithm the Xcalibur data system uses to convert the simulated spectrum
from profile data to centroid data.
Choose the algorithm associated with the mass spectrometer whose spectrum you want to
simulate. Your choices are:
• LCQ/TSQ/Quantum/ICIS
• DSQ/PolarisQ/GCQ
• Valley Detection (default)
Measure Resolution At Specify where to measure the resolution of a peak. The valley detection algorithm can
measure the resolution of each peak (resolving power) by determining when the signal
crosses a threshold on both sides of the peak. The Xcalibur application measures the
threshold relative to the apex height of the peak.
This option is available only when you are using the Valley Detection algorithm.
Noise Filter
Noise Filter
Check this box to turn on a filter to reject noise on peaks and prevent splitting peaks with a
dip in the peak apex.
A moving mean filter is applied to the signal, averaging the indicated number of points. The
filter is repeatedly applied, as set by the Repeat parameter.
This filtered data is only used to determine the start and end points of peaks. After this has
been determined, peaks are centroided from the original (unfiltered) signal.
For example: If peaks are being split at the apex, turn on filtering, and increase the points
value until peaks are no longer split.
Points
The number of points to consider in filtering. The value must be between 3 and 99.
Repeat
The repeat count to use in filtering. The value must be between 1 and 9.
Other
Merge Width
Merge data points that are within this range. The value can be between 0.0 and 100.0.
Merge Width is used only for the LCQ/TSQ/Quantum/ICIS and DSQ/PolarisQ/GCQ
algorithms.
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Color Dialog Box
Use the Color dialog box to select one of 48 basic colors or 16 (maximum) preselected custom
colors.
The Basic Colors have been preselected by the Xcalibur system. The palette of optional colors
include those that are commonly used for chromatograph, mass spectrograph, and map
graphics.
Use the Custom Options extension of the Color dialog box to choose colors from a
continuous palette containing millions of colors. A selected color can then be added to your
palette of 16 preselected colors that are displayed in the Color dialog box.
When you choose a point in the Color Space Spectrum box, the selected color appears in the
Color/Solid box and the Xcalibur application displays the corresponding Hue, Saturation,
Luminosity, as well as Red, Green, and Blue color coordinates. You can change the
Luminosity (amount of white) of the selected color by dragging the triangular cursor located
to the right of the Luminosity Scale up or down while monitoring the corresponding color in
the Color/Solid box.
You can also define a particular color by typing its Hue, Saturation, and Luminosity or Red,
Green, and Blue color coordinates into the corresponding boxes.
Copy to Clipboard Dialog Box
Use the Copy to Clipboard dialog box to copy either the current cell or the entire grid in the
active window to the clipboard. You can also specify the height and width of the copied object
in either millimeters or inches.
Table 51. Copy to Clipboard dialog box parameters
Parameter
Description
Copy
Current Cell
Copy the active cell to the clipboard or copy all the cells in the active window grid by using
the Grid option.
Grid
Copy the entire grid within a window to the clipboard or you can copy just the active cell by
using the Cell option.
Output Size
Width
View the current width of an object copied to the clipboard. The units of the value are
either millimeters or inches, depending upon the selected units option.
Height
View the current height of an object copied to the clipboard. The units of the value are
either millimeters or inches, depending upon the selected units option.
Millimeters
View the units used for the size of a cell or grid copied to the clipboard as millimeters.
Inches
View the units used for the size of a cell or grid copied to the clipboard as inches.
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Display Options Dialog Box
Use the pages of the Display Options dialog box to select Style, Color, Labels, Axis,
Band Width, Normalization, and Composition settings. The options presented by these pages
depend on whether the view in the active cell is a chromatogram, spectrum, map, ion map, or
spectrum list:
• Page options if a chromatogram is the active view
Style Page
Color Page
Axis Page
Normalization Page
Labels Page
• Page options if a spectrum is the active view
Style Page
Color Page
Axis Page
Normalization Page
Labels Page
• Page options if a map (or ion map) is the active view
Style Page
Color Page
Normalization Page
Band Width Page
Axis Page
• Page options if a spectrum list is the active view
Style Page
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Chromatogram Axis Page – Display Options Dialog Box
Use the Axis page of the Display Options dialog box to modify the appearance of your
chromatogram. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 52. Chromatogram Axis page parameters (Sheet 1 of 3)
Parameter
Description
X
Name
View or change the current axis names for the X, Y, and Z axes, as appropriate for the active
chromatogram, spectrum, or map. To change an axis name, type the new name in the Name
box. The Xcalibur application displays the results of the current settings in the adjacent
graphic.
The default axis names are as follows:
• X: Time
• Y: Relative Abundance
Show name
View or change when the data system displays the axis name next to the corresponding axis.
The data system can display the axis label displayed in the axis Name box at the following
times:
• Never: The Xcalibur application does not display the axis label when the graphic is
displayed or printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.
The current option is displayed in the list.
To change the time when the application displays the axis label, select from the Show name
list of options. Click Never, On Print, or Always.
Since standard reports are not displayed on the screen, the On Print and Always Show name
list options for standard reports are identical.
Offset
Set the location for the displayed plot a specified distance from the X- and/or Y-axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
Split time range
Split the time scale of the active chromatogram into two or more divisions. To split the time
scale, select the Split time range check box. The Xcalibur application activates the divisions
box so that you can select the number of divisions.
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Table 52. Chromatogram Axis page parameters (Sheet 2 of 3)
Parameter
Description
Divisions
View or change the current number of divisions for a chromatogram with a split time range.
This box is only active if you select the Split time range check box. The number of divisions
can be two, three, or four. To change the number of divisions, type the new number in the
Divisions (time) box. The Xcalibur data system displays the multiple chromatograms in the
adjacent graphic.
Y
Separate labels
Apply a distinct label to the Y-axis of each plot in the active chromatogram view. To label
the chromatogram plots separately, select the Separate labels check box. The Xcalibur
application activates the Plot box so you can specify the plot to get a specific label. Select
multiple plots on the Ranges Page – Chromatogram Ranges Dialog Box.
Plot
Specify a plot to apply a particular label to.
Source
Specify that the Xcalibur application apply either a custom (user-defined) label or a label
from the detector to the Y-axis of a map plot.
When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If no.lyt file exists, the application retrieves the parameters from the
default values you specified on the Labeling And Scaling Page.
Units
Apply absolute or relative scaling to the Y-axis of a chromatogram plot.
Name
View or change the current axis names for the X, Y, and Z axes, as appropriate for the active
chromatogram, spectrum, or map. To change an axis name, type the new name in the Name
box. The Xcalibur application displays the results of the current settings in the adjacent
graphic.
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Table 52. Chromatogram Axis page parameters (Sheet 3 of 3)
Parameter
Description
Show name
View or change when the data system displays the axis name next to the corresponding axis.
The data system can display the axis label displayed in the axis Name box at the following
times:
• Never: The Xcalibur system does not displays the axis label when the graphic is
displayed or printed.
• On Print: The system displays the axis label whenever the graphic is printed as a report.
• Always: The system displays the axis label whenever the graphic is displayed or printed.
The current option is displayed in the list.
To change the time when the data system displays the axis label, select from the Show name
list of options. Click Never, On Print, or Always.
Since standard reports are not displayed on the screen, the On Print and Always Show name
list options for standard reports are identical.
Offset
Thermo Scientific
Set the location for the displayed plot a specified distance from the X- and/or Y-axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves 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 Color Page – Display Options Dialog Box
Use the Color page of the Display Options dialog box to modify the appearance of a
chromatogram view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 53. Chromatogram Color page parameters
Parameter
Description
Plots
Change the colors of any of the plots within a chromatogram view.
In Processing Setup, the chromatogram preview corresponds to Plot 1. Plot buttons 2
through 8 are not used.
Plots 1to 8
Change the color of a plot. The current plot color is displayed to the right of its plot
number button.
To select the color of a plot, click the Plot number button, for example, Plot 3. The
Xcalibur application opens the Color Dialog Box with a color palette so that you can select
a preset color or customize a color.
Backdrop
Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. Click the Backdrop button to display a
background.
The Xcalibur application displays the current plot color to the right of the Backdrop button.
To select the color of the backdrop, click Backdrop. The application opens the Color
Dialog Box with a color palette so that you can select a preset color or customize a color.
The application displays the results of the current settings in the adjacent graphic.
Chromatogram Labels Page – Display Options Dialog Box
Use the Labels page of the Display Options dialog box to modify the appearance of your
chromatogram. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 54. Chromatogram Labels page parameters (Sheet 1 of 3)
Parameter
Description
Label with
Retention time
Add a retention time label above chromatogram peaks.
The order of chromatogram labels for an undetected peak, from top to bottom, is scan
number, retention time, and base peak. The application displays the retention time on all
peaks that meet the selection criteria set in the Label threshold box.
The retention time of a detected peak is indicated by the letters RT to the left of the value.
Decimals
216
View or change the number of decimal places in the retention time label. The range is
0 to 5.
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Table 54. Chromatogram Labels page parameters (Sheet 2 of 3)
Parameter
Description
Name
Add the component name in a Quan view.
Scan number
Add the active scan number in the label above chromatogram peaks.
The scan number of a detected peak is indicated by the letters S# to the left of the value.
Base Peak
Add m/z for the base peak of the active scan above chromatogram peaks.
The base peak of a detected peak is indicated by the letters BP to the left of the value.
Signal-To-Noise
Add the signal-to-noise ratio above chromatogram peaks.
When you select this check box and use the Genesis peak detection algorithm, The Xcalibur
application displays the calculated signal-to-noise ratio above the peaks. When you select
this check box and use either the ICIS or the Avalon peak detection algorithm, the
application displays SN: NA (not applicable) above the peaks, because these algorithms do
not calculate a value for signal-to-noise ratio.
The signal to noise of a detected peak is indicated by the letters SN to the left of the value.
Flags
Add letters above chromatogram peaks to provide supplemental information about the peak
data.
For chromatograms, the only possible flag is S, which indicates that a peak is saturated—
the signal is too large to measure (over range from A to D converter).
Area
Add m/z labels for the area of each integrated peak in the chromatogram peaks.
The integrated area of a detected peak is indicated by the letters MA or AA to the left of the
value. MA indicates manual integration, and AA indicates automatic integration.
Height
Show the peak height above chromatogram peaks.
The height of a detected peak is indicated by the letters MH or AH to the left of the value.
MH indicates manual integration. AH indicates automatic integration.
Label Styles
Offset
Set the location for the displayed plot at a specified distance from the X- or Y-axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
The amount of the offset is specified in the Size box.
Rotated
Thermo Scientific
Select whether or not the Xcalibur data system writes peak labels vertically upwards or
horizontally. For vertical labels, select the Rotated check box. For horizontal labels, clear the
Rotated check box. Use the adjacent graphic to view the result of the current label settings.
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Table 54. Chromatogram Labels page parameters (Sheet 3 of 3)
Parameter
Description
Boxed
Select whether or not the Xcalibur data system places a box around each peak label. To box
your label, select the Boxed check box. If you do not want to have a box around the label,
clear the check box. Use the adjacent graphic to view the result of the current label settings.
Size
View or change the amount that the data system moves a label from its normal position to
avoid conflict with another label. This box is only activated when you select the Offset
check box. The valid range is 0.1 to 15.0. The default value is 2.0.
Label threshold (%)
View or change the percent of the base peak so that the data system labels peaks above that
percent. The valid range is 0.0 to 100.0%. For example, if the base peak is 100% and the
label threshold setting is 50.0%, the Xcalibur system labels all peaks at or above 50%.
Chromatogram Normalization Page – Display Options Dialog Box
Use the Normalization page of the Display Options dialog box to modify the appearance of
your chromatogram. The Xcalibur application displays the results of the current settings in
the graphic on the right side of the page.
Table 55. Chromatogram Normalization page parameters
Parameter
Description
Normalize method
Auto range
Select the auto range normalization method for chromatograms. The
Xcalibur application reviews the chromatogram data, detects the minimum
and maximum signal data points, and assigns these values to the extremes
on the Y-axis. The entire dynamic range of the chromatogram is then
displayed in the active view, normalized over the full range of the Y-axis.
Intensity range
Specify the minimum and maximum ranges of the chromatogram plot to
display in the Y-axis. The valid range of values is –200.000 to 200.000%.
The default range is 0.000–100.000%.
Normalize each plot to
Largest peak in subsection
Set the Y-axis maximum for each subsection (division) equal to the largest
peak in the subsection (division). Set the number of subsections on the
Axis page.
Largest peak in selected time range
Set the Y-axis maximum equal to the largest peak in the time range. The
time range is the sum of all subsections [divisions]. Each subsection
(division) has the same Y-axis maximum. Set the number of subsections on
the Axis page.
Largest peak in all times
Set the Y-axis maximum equal to the largest peak in all times. Each
subsection (division) has the same Y-axis maximum. Set the number of
divisions on the Axis page.
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Chromatogram Style Page – Display Options Dialog Box
Use the Style page of the Display Options dialog box to modify the appearance of a
chromatogram view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 56. Chromatogram Style page parameters
Parameter
Description
Plotting
Point To Point
Select a graphic style that displays the active chromatogram or spectrum using a
point-to-point peak profile.
Stick
Select a graphic style that displays the active chromatogram or spectrum using vertical lines.
Arrangement
Stack (2D)
Stack plots vertically, with no overlap, for plots in the active cell.
Overlay (3D)
Overlay plots vertically with optional horizontal skew (time offset) for chromatogram or
spectrum plots in the active cell.
3D
Elevation
Set the elevation angle (amount of overlay) to a value from 0 to 60 degrees for an overlay
arrangement of plots in the active cell. To set the elevation angle, either drag the Elevation
slider or click the Elevation slider left or right arrow until you reach the desired angle.
The Xcalibur application displays the current angle setting below the scroll box.
Skew
Set the skew angle (time offset) to a value from 0 to 45 degrees for an overlay arrangement
of plots in the active cell. To set the skew, either drag the Skew slider or click the Skew slider
left or right arrow until you reach the desired angle.
The application displays the current angle setting below the scroll box.
Draw Backdrop
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Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.
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Map or Ion Map Axis Page – Display Options Dialog Box
Use the Axis page of the Display Options dialog box to modify the appearance of your Map or
Ion Map view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 57. Map or Ion Map Axis page parameters (Sheet 1 of 2)
Parameter
Description
X
Name
View or change the current axis names for the X, Y, and Z axes, as appropriate for the active
chromatogram, spectrum, or map. To change an axis name, type the new name in the Name
box. The Xcalibur application displays the results of the current settings in the adjacent
graphic.
The default axis names are as follows:
• X: Time
• Y: Relative Abundance
• Z: m/z
Show
View or change when the data system should display the axis name next to the
corresponding axis. The data system can display the axis label displayed in the axis Name
box at the following times:
• Never: The Xcalibur application does not display the axis label when the graphic is
displayed or printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.
The current option is displayed in the list.
To change the time when the Xcalibur data system displays the axis label, select from the
Show name list of options and click Never, On Print, or Always.
Since standard reports are not displayed on the screen, the On Print and Always Show
Name list options for standard reports are identical.
Offset
Set the location for the displayed plot at a specified distance from the X- and/or Y-axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
The amount of the offset is specified in the Size box.
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Table 57. Map or Ion Map Axis page parameters (Sheet 2 of 2)
Parameter
Description
Y
Source
Specify that the Xcalibur application apply either a custom (user-defined) label or a label
from the detector to the Y axis of a map plot.
When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If no.lyt file exists, the application retrieves the parameters from the
default values you specified on the Labeling And Scaling Page of the Xcalibur Configuration
dialog box.
Units
Apply absolute or relative scaling to the Y axis of a chromatogram plot.
Other
Grid Lines
Determine whether or not to display lines from major tic marks on the axis scale.
Split time range
Split the time scale of the active chromatogram into two or more divisions. To split the time
scale, select the Split time range check box. The Xcalibur application activates the divisions
box so that you can select the number of divisions. If you want to display only one time
range, clear the Split time range check box.
Divisions
View or change the current number of divisions for a spectra with a split mass range. This
box is only active if you select the Split time range check box. The number of divisions can
be two, three, or four. To change the number of divisions, type the new number in the
Divisions (m/z) box. The Xcalibur application displays the multiple spectra in the adjacent
graphic.
Map or Ion Map Band Width Page – Display Options Dialog Box
Use the Band Width page of the Display Options dialog box to modify the appearance of a
Map or Ion Map view. You can specify the size of the bands displaying relative abundance to
make the display clearer. The band width value specifies the band width in amu units.
Table 58. Map or Ion Map Band Width page parameters
Parameter
Description
m/z Band Width (amu) View or change the current value for the map view band width.
Set a value for the width of bands displayed in the Map view. The range of acceptable values
is from 0.001 to 50.0, with a default value of 1.0.
To see specific resolution detail, set the value as large as is necessary.
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Map or Ion Map Color Page – Display Options Dialog Box
Use the Color page of the Display Options dialog box to modify the appearance of a Map or
Ion Map view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 59. Map or Ion Map Color page parameters
Parameter
Description
Line
Change the color of framing lines for the active map. The current color is displayed to the
right of the Line button.
To change the color of the framing lines, click Line. The Xcalibur application opens the
Color Dialog Box with a color palette so that you can select a preset color or customize a
color. The application displays the results of the current settings in the adjacent graphic.
Fill solid
Change the color of the solid fill for the active map. The current color is displayed to the
right of the Fill solid button.
To change the color of the solid fill, click Fill solid. The Xcalibur application opens the
Color Dialog Box with a color palette so that you can select a preset color or customize a
color. The application displays the results of the current settings in the adjacent graphic.
Backdrop
Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. Click Backdrop to display a background. The
Xcalibur application displays the current plot color to the right of the Backdrop button.
To select the color of the backdrop, click Backdrop. The application opens the Color
Dialog Box with a color palette so that you can select a preset color or customize a color.
The application displays the results of the current settings in the adjacent graphic.
Gray scale
Turn off all color choices and display the map as a gray scale.
Log scale
Display the color of the map in a logarithmic scale. The factor width that you set in the
Factor box determines the scaling between color bands.
Factor
View or change the Factor that determines the scaling between color bands. The valid values
are 1.1 to 20. Selecting the Log scale check box activates the Factor box.
Shade
Shade %
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Change the color of the map at 0%, 20%, 40%, 60%, 80%, and 100% relative abundance.
To change the color, click a Shade % button. The Xcalibur data system opens the Color
Dialog Box with a color palette so that you can select a preset color or customize a color.
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Map or Ion Map Normalization Page – Display Options Dialog Box
Use the Normalization page of the Display Options dialog box to modify the appearance of a
Map or Ion Map view. The Xcalibur application displays the results of the current settings in
the graphic on the right side of the page.
Table 60. Map or Ion Map Normalization page parameters (Sheet 1 of 2)
Parameter
Description
Mass grouping
Specify the mass grouping compression method. Mass grouping describes how the Xcalibur data system compresses
mass data to form the colored bands in the 3D plot. Masses from a scan are compressed for each colored band using
one of two methods: Base peak or Sum.
Base peak
Use the largest peak within each band (mass range) to determine the intensity of
the band.
Sum
Use the sum of the intensities within each band (mass range) to determine the
intensity of the band.
Normalize to entire file
Select this check box to have the data system normalize the map to the largest peak
in the raw file.
Fix scale
Select this check box to have the data system normalize the map to a fixed intensity
value. Type an intensity value between 0.01 and 1e+20 in the Fix scale box.
Normalize method
Auto range
Select the Auto range normalization method for chromatograms. The Xcalibur
application reviews the chromatogram data, detects the minimum and maximum
signal data points, and assigns these values to the extremes on the Y-axis. The entire
dynamic range of the chromatogram is then displayed in the active view,
normalized over the full range of the Y-axis.
Intensity Range
Display the relative abundance range of mass peaks that the Xcalibur system
includes in the current Map or Ion Map view. The valid range must fall between
–200.000 and 200.000 percent.
To change the range of relative abundances, type the minimum and maximum
relative abundance you want to display in the Intensity Range box, separated by a
dash. For example, to display all peaks in a mass spectrum with relative abundances
ranging from 50 to 100 percent, type 50.000 – 100.000. The Xcalibur application
then excludes spectrum peaks with relative abundances that range from 0.000 to
49.999 from the displayed Map or Ion Map view.
Normalize each mass to
Largest peak in subsection
Set the Y-axis maximum for each subsection (division) equal to the largest peak in
the subsection (division). Set the number of subsections on the Axis page.
Largest peak in time range
Set the Y-axis maximum equal to the largest peak in the time range. The time range
is the sum of all subsections (divisions). Each subsection has the same Y-axis
maximum. Set the number of subsections on the Axis page.
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Table 60. Map or Ion Map Normalization page parameters (Sheet 2 of 2)
Parameter
Description
Largest peak in all times
Set the Y-axis maximum equal to the largest peak in all times. Each subsection
(division) has the same Y-axis maximum. Set the number of divisions on the
Axis page.
Normalize mass plots
Individually
Normalize mass plots individually.
All the same
Normalize all mass plots equally.
Map or Ion Map Style Page – Display Options Dialog Box
Use the Style page of the Display Options dialog box to modify the appearance of a Map or
Ion Map view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 61. Map or Ion Map Style page parameters
Parameter
Description
Stack
Stack plots vertically, with no overlap, for plots in the active cell.
Overlay (3D)
Overlay plots vertically with optional elevation and horizontal skew (time offset) for the
active map.
Density map
Display a density map that shows different shades for each intensity for the active map.
3D
Elevation
Set the elevation angle (amount of overlay) to a value of 0 to 60 degrees for an overlay
arrangement of plots in the active cell. To set the elevation angle, either drag the Elevation
slider or click the Elevation slider left or right arrow until you reach the desired angle.
The data system displays the current angle setting below the scroll box.
Skew
Set the skew angle (time offset) to a value of 0 to 45 degrees for an overlay arrangement of
plots in the active cell. To set the skew, either drag the Skew slider or click the Skew slider
left or right arrow until you reach the desired angle.
The data system displays the current angle setting below the scroll box.
Fill
View or change the current fill option for the active map. The Xcalibur application fill
options are Plain Lines, Colored Lines, None, Solid color, Intensity shaded, and Shaded
with frame.
Draw backdrop
Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.
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Spectrum Axis Page – Display Options Dialog Box
Use the Axis page of the Display Options dialog box to modify the appearance of your
spectrum. The Xcalibur application displays results of the current settings in the graphic on
the right side of the page.
Table 62. Spectrum Axis page parameters (Sheet 1 of 2)
Parameter
Description
X, Y, Z
Name
View or change the current axis names for the X, Y, and Z axes, as appropriate for the active
chromatogram, spectrum, or map. To change an axis name, type the new name in the Name
box. The Xcalibur application displays results of the current settings in the adjacent graphic.
The default axis names are as follows:
• X: m/z
• Y: Relative Abundance
• Z: Scan
Show (name)
View or change when the Xcalibur data system displays the axis name next to the
corresponding axis. The data system can display the axis label displayed in the axis Name
box at the following times:
• Never: The Xcalibur application does not display the axis label when the graphic is
displayed or printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.
The current option is displayed in the list.
To change the time when the system displays the axis label, from the Show list of options,
select Never, On Print, or Always.
Since standard reports are not displayed on the screen, the On Print and Always Name list
options for standard reports are identical.
Offset (X and/or Y)
Set the location for the displayed plot at a specified distance from the X and/or Y axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
The amount of the offset is specified in the Size box.
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Table 62. Spectrum Axis page parameters (Sheet 2 of 2)
Parameter
Description
Split time range
Split the m/z scale of the active spectrum into two or more divisions. To split the mass scale,
select the Split time range check box. The Xcalibur data system activates the Divisions box
so that you can enter the number of divisions.
Divisions
View or change the current number of divisions for a spectra with a split mass range. This
box is only active if you select the Split time range check box. The number of divisions can
be two, three, or four. To change the number of divisions, type the new number in the
Divisions (m/z) box. The Xcalibur application displays the multiple spectra in the adjacent
graphic.
Y-axis
Source
Specify that the Xcalibur system apply either a custom (user-defined) label or a label from
the detector to the Y-axis of a map plot.
When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If no .lyt file exists, the application retrieves the parameters from the
default values you specified on the Labeling and Scaling page of the Xcalibur Configuration
dialog box.
Units
Apply absolute or relative scaling to the Y-axis of a chromatogram plot.
Spectrum Color Page – Display Options Dialog Box
Use the Color page of the Display Options dialog box to modify the appearance of a
Spectrum view. The Xcalibur system displays the results of the current settings in the graphic
on the right side of the page.
Table 63. Spectrum Color page parameters (Sheet 1 of 2)
Parameter
Description
Centroid
Regular (peaks)
Change the color of regular, unflagged, peaks. The current color for regular peaks is
displayed to the right of the Regular (peaks) button. To select the color of regular peaks,
click Regular. The Xcalibur application opens the Color Dialog Box with a color palette so
that you can select a preset color or customize a color. It displays the results of the current
settings in the adjacent graphic.
Saturated (peaks)
Change the color of saturated peaks (amplitude is greater than range). The current color is
displayed to the right of the Saturated (peaks) button. To change the color of saturated
peaks, click Saturated. The Xcalibur application opens the Color Dialog Box with a color
palette so that you can select a preset color or customize a color. It displays the results of the
current settings in the adjacent graphic.
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Table 63. Spectrum Color page parameters (Sheet 2 of 2)
Parameter
Description
Reference/Lock
Change the color of reference peaks. The current color is displayed to the right of the
Ref/Lock button. To change the color of reference peaks, click Ref/Lock. The Xcalibur data
system opens the Color Dialog Box with a color palette so that you can select a preset color
or customize a color. The data system displays the results of the current settings in the
adjacent graphic.
Exception
Change the color of the exception peak. The current color is displayed to the right of the
Exception (peaks) button. To change the color of exception peaks, click Exception. The
Xcalibur data system opens the Color Dialog Box with a color palette so that you can select
a preset color or customize a color. The system displays the results of the current settings in
the adjacent graphic.
Other
Profile
Change the color of the profile style. The Xcalibur data system displays the current color to
the right of the Profile button. To change the color of the profile, click Profile. The Color
Dialog Box opens with a color palette. You can select a preset color or customize a color.
The application displays the results of the current settings in the adjacent graphic.
Backdrop
Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. The Xcalibur application displays the current
plot color to the right of the Backdrop button. To select the color of the backdrop, click
Backdrop. The application opens the Color Dialog Box with a color palette so that you can
select a preset color or customize a color. It displays the results of the current settings in the
adjacent graphic.
Shade
Shade %
Change the color of the map at 0%, 20%, 40%, 60%, 80%, and 100% relative abundance.
To change the color, click a Shade % button. The Xcalibur application opens the Color
Dialog Box with a color palette so that you can select a preset color or customize a color.
These changes are only visible if you have selected the Shade option on the Spectrum Style
Page – Display Options Dialog Box.
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Spectrum Labels Page – Display Options Dialog Box
Use the Spectrum Labels page of the Display Options dialog box to modify the appearance of
your spectrum. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 64. Spectrum Labels page parameters (Sheet 1 of 3)
Parameter
Description
Label with
Mass (MS data only)
Display a m/z label at the top of spectrum peaks. To turn on peak mass labeling, select the
Mass check box. The Decimals box becomes active.
The data system displays the Mass check box only if you are using MS data.
Relative to
Move the m/z label at the top of spectrum peaks by the amount typed in the Relative to box.
Wavelength
(non-MS data only)
Display a wavelength label at the top of spectrum peaks. The Decimals box becomes active.
Flags
The data system displays the Wavelength check box only if you are not using MS data.
Display letters above the colored spectrum peaks. The letters indicate why the peaks are
colored.
The possible flags are as follows:
• S
Saturated peaks are peaks with a signal too large to measure (over range from A to
D converter).
• R Reference peaks are peaks from a reference compound used for an internal
recalibration of a scan (for example, in MAT95 series).
• L
Lock peaks are local references used to calculate accurate mass of nearby peaks (for
example, in Quantum™ AM).
• E
Exception peaks are also peaks from a reference compound, but not used for
recalibration. These are typically small isotopes or fragments of the main references.
Decimals
View or change the number of digits the Xcalibur application displays to the right of the
decimal when it positions m/z labels over the peaks in a spectrum. This box is only active if
you select the Mass check box. The valid range is 0 to 5.
Resolution
Display the resolution information that is stored in the .raw file. The resolution is stored in
the .raw file only when your instrument is set to acquire additional peak labeling
information.
This check box is available only if resolution information is stored in the .raw file.
If you acquire profile data and the instrument has not acquired the resolution information,
you can select to have the Xcalibur application centroid the data after acquisition by
selecting the centroid check box. This action turns on the Resolution check box.
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Table 64. Spectrum Labels page parameters (Sheet 2 of 3)
Parameter
Description
Charge
Display the charge state information that is stored in the raw file. The charge is stored in
the raw file only when your instrument is set to acquire additional peak labeling
information.
This check box is available only if charge state information is stored in the raw file.
Baseline
Display the baseline information that is stored in the raw file. The baseline is stored in
the raw file only when your instrument is set to acquire additional peak labeling
information.
This check box is available only if baseline information is stored in the raw file.
Noise
Display the noise information that is stored in the raw file. The noise is stored in the raw file
only when your instrument is set to acquire additional peak labeling information.
This check box is available only if noise information is stored in the raw file.
Width (m/r)
Specify the peak width (mass ÷ resolution) at the peak height used for the resolution
measurement.
For example: With profile data, select the Centroid check box, select the Valley Detection
algorithm, and type 50.0 for Measure resolution at (%). With this method, the peak width
shown on labels is at 50% (also called FWHM).
This check box is available only if resolution information is stored in the raw file or if you
have applied a centroiding algorithm.
Centroid
Use centroid data for mass labels. This check box is active only if you display profile data
(this is not true for LTQ-FT, Orbitrap, and Exactive Instruments, because they already have
centroid data used for mass labels).
If you acquire profile data, select the Centroid check box to have the Xcalibur data system
centroid the data after acquisition for use in the labels feature. This action turns on the
Resolution check box. In this case, the Resolution and Width settings are available.
Choose algorithm
Activate the Choose algorithm button. This button is activated only when you select the
Centroid check box. To turn on the Centroid check box, you must display profile data.
Label styles
Offset
Make the location for the displayed plot a specified distance from the X- and/or Y-axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
The amount of the offset is specified in the Size box.
Size
Thermo Scientific
View or change the amount that the Xcalibur application moves a label from its normal
position to avoid conflict with another label. This box is activated when you select the
Offset check box. The valid range is 0.1 to 15.0. The default value is 2.0.
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Table 64. Spectrum Labels page parameters (Sheet 3 of 3)
Parameter
Description
Rotated
Select whether or not the data system writes peak labels vertically upwards or horizontally.
For vertical labels, select the Rotated check box. For horizontal labels, clear the Rotated
check box. Use the adjacent graphic to view the result of the current label settings.
Only the peak labels are rotated. The flags are not rotated.
Boxed
Select whether or not the Xcalibur data system places a box around each peak label. To box
your label, select the Boxed check box. If you do not want to have a box around the label,
clear the check box. Use the adjacent graphic to view the result of the current label settings.
Only the peak labels are boxed. The flags are not boxed.
Threshold
Label peaks that are at or above a minimum percent of the base peak. This option sets the minimum percent. The
valid range is 0.0 to 100.0%. For example, if the base peak is 100% and the label threshold setting is 50.0%, the
Xcalibur application labels all peaks at or above 50%. To change the label threshold, type a different percent value in
the Label Threshold box. Use the adjacent graphic to view the result of the current label settings.
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Spectrum Normalization Page – Display Options Dialog Box
Use the Spectrum Normalization page of the Display Options dialog box to modify the
appearance of your spectrum by specifying the following normalization parameters. The
Xcalibur application displays the results of the current settings in the graphic on the right side
of the page.
Table 65. Spectrum Normalization page parameters
Parameter
Description
Normalize method
Auto range
Select the auto range normalization method for chromatograms. The Xcalibur
application reviews the chromatogram data, detects the minimum and maximum
signal data points, and assigns these values to the extremes on the Y-axis. The entire
dynamic range of the chromatogram is then displayed in the active view,
normalized over the full range of the Y-axis.
Intensity Range
View or change the relative abundance range of mass spectrum peaks that the
Xcalibur data system includes in the current Spectrum view. The valid range must
fall between 0.000 and 200.000 percent.
To change the range of relative abundances, type the minimum and maximum
relative abundance you want to display in the Intensity Range box, separated by a
dash. For example, to display all peaks in a mass spectrum with relative abundances
ranging from 50 to 100 percent, enter 50.000 – 100.000. The Xcalibur application
then excludes spectrum peaks with relative abundances that range from 0.000 to
49.999 from the displayed spectrum.
Normalize spectrum to
Largest peak in subsection
Set the Y-axis maximum for each subsection (division) equal to the largest peak in
the subsection (division). Set the number of subsections on the Axis page.
Largest peak in mass range
Set the Y-axis maximum equal to the largest peak in the mass range. (The mass
range is the sum of all subsections [divisions]). Each subsection (division) has the
same Y-axis maximum. Set the number of divisions on the Axis page.
Largest peak in scan range
Set the Y-axis maximum equal to the largest peak in the scan range. (The scan range
is all m/z in the scan.) Each subsection (division) has the same Y-axis maximum. Set
the number of divisions on the Axis page.
Normalize multiple scans
Individually
Normalize mass plots individually.
All the same
Normalize all mass plots equally.
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Spectrum Style Page – Display Options Dialog Box
Use the Spectrum Style page of the Display Options dialog box to modify the appearance of a
Spectrum view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 66. Spectrum Style page parameters
Parameter
Description
Plotting
Automatic
Have the Xcalibur data system choose the graphic style based upon the data acquisition
method used for the active spectrum.
Point to point
Select a graphic style that displays the active chromatogram or spectrum using a
point-to-point peak profile.
Stick
Select a graphic style that displays the active chromatogram or spectrum using vertical lines.
Shade
Select a graphic style that uses a shaded representation of intensity in each amu band for the
active spectrum.
Arrangement
Stack (2D)
Stack plots vertically, with no overlap, for plots in the active cell.
Overlay (3D)
Overlay plots vertically with optional horizontal skew (time offset) for chromatogram or
spectrum plots in the active cell.
3D
Elevation
Set the elevation angle (the amount of overlay) to a value between 0 and 60 degrees for an
overlay arrangement of plots in the active cell. To set the elevation angle, either drag the
Elevation slider or click the Elevation slider left or right arrow until you reach the desired
angle.
The Xcalibur application displays the current angle setting below the scroll box.
Skew
Set the skew angle (time offset) to a value between 0 and 45 degrees for an overlay
arrangement of plots in the active cell. To set the skew, either drag the Skew slider or click
the Skew slider left or right arrow until you reach the desired angle.
The Xcalibur application displays the current angle setting below the scroll box.
Draw Backdrop
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Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.
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Spectrum List Composition Page – Display Options Dialog Box
Use the Spectrum List Composition page of the Display Options dialog box to calculate
elemental compositions and to add columns containing the results to your Spectrum List. The
Xcalibur application determines which chemical formulas have a m/z value most like that of
the experimental spectrum peaks. It displays the results of the current settings in the graphic
on the right side of the page.
Table 67. Spectrum List Composition page parameters (Sheet 1 of 2)
Parameter
Description
Label with
Elemental comp.
Select whether the Xcalibur application displays the chemical formula labels at the top of
spectrum peaks. The application determines which chemical formulas have a m/z value most
like that of the spectrum peaks. To turn on elemental composition labeling, select the
Elemental comp. check box.
If the Xcalibur application displays the elemental composition values in light gray, close
Qual Browser and choose Xcalibur Roadmap > Tools > Configuration to display the
Configuration page. Click the Fonts tab and set all font sizes to a minimum of 10 points.
Formulae
Type a number that specifies how many of the most likely chemical formulas you want the
Xcalibur data system to display at the top of spectrum peaks in the Formulae box.
Theo. mass
View the theoretical m/z of the chemical formulas that the Xcalibur application determines.
The application displays the theoretical m/z to the right of the formula separated by =.
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Table 67. Spectrum List Composition page parameters (Sheet 2 of 2)
Parameter
Description
RDB equiv.
View the value of the ring and double-bond equivalents that the Xcalibur application
calculates for the chemical formulas. The application displays the ring and double-bond
equivalent value under the chemical formula.
Ring and double-bond equivalents measure the number of unsaturated bonds in a
compound—and limit the calculated formulas to only those that make sense chemically.
You can specify limits in a range from –100.0 to +100.0.
The value is calculated by the following formula:
imax
 Ni ( Vi – 2 )
i
D = 1 + ---------------------------------------2
where
D is the value for the RDB
imax is the total number of different elements in the composition
Ni is the number of atoms of element i
Vi is the valence of atom i
The calculation results in an exact integer such as 3.0, indicating an odd-electron ion, or an
integer with a remainder of 0.5, indicating an even-electron ion. A value of –0.5 is the
minimum value and corresponds to a protonated, saturated compound (for example,
H3O+).
Label the peak with the difference between the theoretical and experimental m/z.
Delta
Delta units
Specify the units used to calculate the difference between the theoretical and experimental m/z. Select from these
options: amu, mmu, or ppm.
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Spectrum List Normalization Page – Display Options Dialog Box
Use the Spectrum List Normalization page of the Display Options dialog box to modify the
appearance of your Spectrum List. The Xcalibur application displays the results of the current
settings in the graphic on the right side of the page.
Table 68. Spectrum List Normalization page parameters
Parameter
Description
Intensity range
View or change the relative abundance range of mass spectrum peaks that the
Xcalibur data system includes in the current Spectrum List view. The valid range
must fall within 0.000 to 200.000 percent.
To change the range of relative abundances, type the minimum and maximum
relative abundance you want to display in the Intensity range box, separated by a
dash. For example, to display all peaks in a mass spectrum with relative abundances
ranging from 50 to 100 percent, type 50.000 – 100.000. The Xcalibur application
then excludes spectrum peaks with relative abundances that range from 0.000 to
49.999 from the displayed Spectrum List.
Normalize list to
Largest peak in subsection
Set the value listed in the Relative column equal to a percentage of the largest peak
in the subsection (division).
Largest peak in (mass) range
Set the value listed in the Relative column equal to a percentage of the
mass-to-charge ratio of the largest peak in the mass range. (The mass range is the
sum of all subsections [divisions].)
Largest peak in scan
Set the value listed in the Relative column equal to a percentage of the largest peak
in the full mass range.
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Spectrum List Style Page – Display Options Dialog Box
Use the Spectrum List Style page of the Display Options dialog box to modify the appearance
of a Spectrum view. The Xcalibur application displays the results of the current settings in the
graphic on the right side of the page.
Table 69. Spectrum List Style page parameters (Sheet 1 of 2)
Parameter
Description
Display
All peaks
List m/z, intensity, and relative intensity of all spectrum peaks (in the range specified in the
Spectrum List Ranges dialog box or as specified in the active scan filter) in the Spectrum
List. To display all peaks, select the All peaks check box.
Top
View or change the current maximum number of peaks to include in the Spectrum List.
This box is only active if the All peaks check box is clear. The valid range is 1 to 1000.
If you order the list by mass (m/z), the Xcalibur application displays the specified number of
peaks having the greatest intensity in ascending mass (m/z) order. For example, if you type
the value 10 in the Top box, the application displays a Spectrum List with the 10 greatest
intensity peaks sorted in ascending order by m/z.
If you order the list by intensity, the Xcalibur data system displays the specified number of
peaks having the greatest intensity in descending intensity order. For example, if you type
the value 10 in the Top box, the data system displays a spectrum list with the 10 greatest
intensity peaks sorted in descending order by intensity.
Flags
Specify whether or not the Xcalibur application displays letters in the Flags column of the
Spectrum List view to provide supplemental information about the peak data.
The possible flags are as follows:
S
Saturated peaks are peaks with a signal too large to measure (over range from A to
D converter).
R Reference peaks are peaks from a reference compound used for an internal recalibration
of a scan (for example, in MAT95 series).
L
Lock peaks are local references used to calculate accurate mass of nearby peaks
(for example, in Quantum AM).
E
Exception peaks are also peaks from a reference compound, but not used for
recalibration. These are typically small isotopes or fragments of the main references.
#
Mathematically modified peaks are peaks where the peak mass was recalculated by the
instrument, usually due to a calibration process.
M Merged peaks are peaks where the centroider combined two nearby peaks.
F
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Table 69. Spectrum List Style page parameters (Sheet 2 of 2)
Parameter
Description
Resolution
Specify whether or not the Xcalibur data system displays resolution information in the
Spectrum List.
Resolution is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.
Resolution can also be active if you have centroided a profile scan. The Xcalibur application
shows the results returned by the centroider.
Charge
Specify whether or not the data system displays charge information in the Spectrum List.
Charge is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.
Baseline
Specify whether or not the data system displays baseline information in the Spectrum List.
Baseline is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.
Noise
Specify whether or not the data system displays noise information in the Spectrum List.
Noise is a Label Stream parameter and is active if your raw file has Label Stream data. These
values are written by the instrument.
Centroid
Apply the same algorithm used in the firmware to convert from profile data to centroid.
When you select centroid, both the Resolution check box and the Choose Algorithm button
become active.
Centroid and Choose Algorithm are active when you have a profile scan.
Choose algorithm
Select a centroiding algorithm.
The Choose algorithm button is activated when you have a profile scan and select the
Centroid check box.
Order by
Mass
Order the Spectrum List in ascending m/z value order.
Sort by mass to ensure that the highest intensity peak (with relative intensity 100.00) is
always in the list, but not necessarily the first entry in the list.
Intensity
Order the Spectrum List in descending intensity order.
Sort by intensity to ensure that the highest intensity peak (with relative intensity 100.00) is
always the first entry in the list.
Precision
Decimals
Thermo Scientific
Specify the number of places after the decimal point that the Xcalibur application uses to
process MS data. Specify from 0 to 5 decimal places. The number of decimal places applies
to the MS data in the Qual Browser window.
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Global Mass Options Dialog Box
IMPORTANT Use the Global Mass Options dialog box to specify tolerance and precision
settings for the mass data displayed in the chromatogram, spectrum, map, and ion map
plots.
Specify the default values for tolerance and precision on the Mass Options page of the
Configuration dialog box.
Table 70. Global Mass Options dialog box parameters
Parameter
Description
Options
Apply To Current Cell
Apply the settings in this dialog box to the currently pinned cell.
Apply To All Cells In Current Window
Apply the settings in this dialog box to all cells in the current file window
in Qual Browser.
Apply To All Cells In All Windows
Apply the settings in this dialog box to all cells in all open file windows in
Qual Browser.
Set Mass Tolerance
Use User Defined
Specify a custom mass tolerance. If you do not specify a user defined
tolerance, Qual Browser will use tolerance values recorded by the mass
spectrometer in the raw file.
Mass Tolerance
Specify the value for mass tolerance. Enter a value in the range of 0.1 to
50,000, and then select units to apply to the value. The Xcalibur
application uses the tolerance value to create the limits of a range of masses.
Units
Specify the unit of measurement for processing your data. Select mmu
(millimass units) or ppm (parts per million).
Set Mass Precision
Decimals
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Specify the number of decimal places (mass precision) that the data system
uses to display mass values. You can specify from 0 to 5 decimal places.
The number of decimal places applies to the mass data in a window.
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Heading Editor Dialog Box
Use the Heading Editor dialog box to edit the heading above the raw data graphical views in
the Qual Browser window. The heading contains information about the raw file whose
chromatogram, mass spectrum, or map views are displayed. An example of a heading is shown
below:
Table 71. Heading Editor dialog box parameters (Sheet 1 of 5)
Parameter
Description
Heading table
Enter labels and values to be displayed above the graphical views.
The Xcalibur application arranges the heading information into one, two, or three columns
of label/value pairs (Label1, Value1; Label2, Value2; Label3, Value3).
Label columns
Type in a label or enter an asterisk (*) to accept the default label.
The Label column uses these default values:
File Name: File Name
Time Stamp: Created
Sample Name: Sample Name
Comment: Comment
Sequence Row: Sequence Row
Sample Type: Sample Type
Calibration Level: Cal Level
Sample ID: Sample ID
Instrument Method: Inst Meth
Processing Method: Proc Meth
Path: Path
Calibration File: Cal File
Position: Position
Injection Volume: Inj Vol
Sample Weight: Sample Weight
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Table 71. Heading Editor dialog box parameters (Sheet 2 of 5)
Parameter
Description
Sample Volume: Sample Volume
Internal Standard Amount: ISTD Amount
CD Factor: CD Factor
Bar Code: Bar Code
Bar Code Status: Bar Code Status
Tray Index: Tray Index
Vial Index: Vial Index
Vials Per Tray: Vials Per Tray
Vials Per Tray X: Vials Per TrayX
Vials Per Tray Y: Vials Per TrayY
Tray Shape: Tray Shape
Tray Name: Tray Name
Instrument Name: Inst Name
Instrument Model: Inst Model
Instrument Serial Number: Inst Serial #
Instrument Software Version: Inst Software Version
Instrument Hardware Version: Inst Hardware Version
Flags: Flags
User Text 1: Study
User Text 2: Client
User Text 3: Laboratory
User Text 4: Company
User Text 5: Phone
Mass Tolerance: Mass Tolerance
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Table 71. Heading Editor dialog box parameters (Sheet 3 of 5)
Parameter
Description
Value columns
Select the values from a drop down list. You display the drop down list by clicking a
Value field in the Label/Value grid.
For the Values column, you can choose from these values:
File Name: The name and path of the file storing the displayed data.
Time Stamp: The date and time the Xcalibur application acquired the displayed data.
Sample Name: The sample name specified in the Sample Name column in the sequence
row corresponding to the displayed data.
Comment: The comment specified in the Comment column in the sequence row
corresponding to the displayed data.
Sequence Row: The number of the sequence row corresponding to the displayed data.
Sample Type: The type of sample selected in the Sample Type column in the sequence row
corresponding to the displayed data.
Calibration Level: The calibration level specified in the Level column in the sequence row
corresponding to the displayed data.
Sample ID: The unique identification (ID) number specified in the Sample ID column in
Sequence Setup.
Instrument Method: The path and file name of the instrument method specified in the
Inst Method column in Sequence Setup.
Processing Method: The path and file name of the processing method specified in the Proc
Method column in Sequence Setup.
Path: The path where you had the Xcalibur application save the raw file(s) specified in the
Path column in Sequence Setup.
Calibration File: The path and file name of the Calibration File specified in the Calibration
File column in Sequence Setup.
Position: The position of the sample in the autosampler specified in the Position column in
Sequence Setup.
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Table 71. Heading Editor dialog box parameters (Sheet 4 of 5)
Parameter
Description
Injection Volume: The injection volume in microliters of sample specified in the Inj Vol
column in Sequence Setup.
Sample Weight: The amount of a component specified in the Sample Weight column in
Sequence Setup.
Sample Volume: The volume of a component specified in the Sample Vol column in
Sequence Setup.
Internal Standard Amount: The internal standard correction amount specified in the
ISTD Corr Amt column in Sequence Setup.
CD Factor: The concentration/dilution factor set in Sequence Setup.
Bar Code: The bar code information number from the autosampler.
Bar Code Status: Indicates whether the bar code has been read by the autosampler.
Tray Index: A combination of letters and numbers that identifies the autosampler tray.
Vial Index: A combination of letters and numbers that identifies the autosampler vial.
Vials Per Tray: The number of vials in the autosampler tray.
Vials Per Tray X: The number of vials across the autosampler tray.
Vials Per Tray Y: The number of vials that the autosampler is deep.
Tray Shape: The shape of the autosampler tray (for example, rectangular).
Tray Name: A name that identifies the type of autosampler tray.
Instrument Name: The name of the mass spectrometer series (for example, LCQ).
Instrument Model: The model name of the mass spectrometer (for example,
Deca XP Plus).
Instrument Serial Number: The serial number of the mass spectrometer.
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Table 71. Heading Editor dialog box parameters (Sheet 5 of 5)
Parameter
Description
Instrument Software Version: The version number of the Xcalibur software that is installed
on the system.
Instrument Hardware Version: The version number of the hardware components that are
installed on the mass spectrometer.
Flags: Additional information about the mass spectrometer.
User Text 1: The text that you entered in the Heading 1 column in the Sequence Setup
view.
User Text 2: The text that you entered in the Heading 2 column in the Sequence Setup
view.
User Text 3: The text that you entered in the Heading 3 column in the Sequence Setup
view.
User Text 4: The text that you entered in the Heading 4 column in the Sequence Setup
view.
User Text 5: The text that you entered in the Heading 5 column in the Sequence Setup
view.
Mass Tolerance: The upper and lower mass limits that the Xcalibur data system uses to
condense to a single mass value all the scans in the mass range.
Set Label Color
Open the Color dialog box to select the color that you want to use for all labels in the
heading.
Set Value Color
Open the Color dialog box to select the color that you want to use for all values in the
heading.
Column Position Editor
Column Position
Editor
Set the absolute horizontal position of the columns of labels and values in the header.
Auto Value Position
Determine the spacing between a label and its corresponding value automatically.
Label
Specify the absolute position of each column of labels.
The value must be between 0 and 2000. However, for a screen resolution of 1152 by 864,
position values larger than about 75 place the label off the screen.
Value
Specify the absolute position of each column of values. These settings are unavailable if you
select the Auto Value Position check box.
The value must be between 0 and 2000. However, for a screen resolution of 1152 by 864,
position values larger than about 75 place the value off the screen.
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Library Search Constraints Page (Qual View)
Use the Library Search Constraints page from the Qual view of the Processing Setup window
to define additional constraints on the search. For example, limit the search to only
compounds with names containing specified letters (such as ol for alcohols) or specify that
only certain elements can be present in the compound.
Constrain a library search to increase processing efficiency. For example, you might want to
exclude certain high intensity ions that appear in many compounds or that are present in the
spectrum background. You can target a search to a particular range of molecular weights or to
compounds containing certain elements. This view is available both in the Library Browser
and the Qual Browser.
Table 72. Library Search Constraints page (Qual view) parameters (Sheet 1 of 7)
Parameter
Description
Molecular Weight
Enable
Limit the library search to compounds with a specific molecular weight or molecular
weight range.
Range
Type a molecular weight or molecular weight range in the box (for example, 200–250).
During a search, the Xcalibur application only compares processed spectra with
reference data derived from compounds with a molecular weight within the specified
range.
Other Databases
Enable
Limit the library search to entries in the NIST library also featured other databases.
Each entry in the NIST library contains a list of other commercial databases containing
information about the compound.
The Xcalibur application reports search results featuring in one or more of the selected
databases (a search result does not have to feature in all the selected databases).
Fine
Report search results from reference compounds or spectra also to be found in a
commercially available Fine Chemical Index.
TSCA
Report search results from reference compounds or spectra also to be found in the Toxic
Substances Control Act Inventory (TSCA).
RTECS
Report search results from reference compounds or spectra also to be found in the
Registry of Toxic Effects of Chemical Substances (RTECS).
EPA
Report search results from reference compounds or spectra also to be found in the
Environmental Protection Agency (EPA) Environmental Monitoring Methods Index.
USP
Report search results from reference compounds or spectra also to be found in the US
Pharmacopoeia (USP)/U.S.A.N.
HODOC
Report search results from reference compounds or spectra also to be found in the CRC
Handbook of Data of Organic Compounds (HODOC).
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 2 of 7)
Parameter
Description
NIH
Report search results from reference compounds or spectra also to be found in the
NIH-NCI Inventory File.
EINECS
Report search results from reference compounds or spectra also to be found in the
European Index of Commercial Chemical Substances (EINECS).
IR
Report search results from reference compounds or spectra also to be found in the
NIST/EPA Gas Phase IR Database.
Clear All
Clear all check boxes in the Other Databases area.
Name Fragment
Enable
Limit the library search to compounds with a specific name or name fragment.
Name
Type a text string (up to 39 characters) to represent a fragment of a compound name;
for example, cyclo. During the library search, the Xcalibur application filters search
results and only returns those containing the specified text in their names. The entry is
not case sensitive, CYCLO returns compounds containing the fragments cyclo, Cyclo
and CYCLO.
Element Constraints
Enable
Limit the library search to compounds containing specific elements using the Individual
Element or Elements in Compound methods.
You can use the two types of elemental constraints together, but make sure there are no
contradictions. For example, you might put C=0 in the Individual Element group and
then list C in the Elements in Compound box. When a contradiction occurs, the
Xcalibur application displays a warning dialog box.
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 3 of 7)
Parameter
Description
Individual Element
Individual Element Table
Set specific criteria about the elements required in a library search result. Each row in
the table represents an element constraint. There are three parts to each constraint:
Element: a IUPAC approved abbreviation for an element, for example Cl for chlorine
Condition: a mathematical operator, < (less than), > (greater than) or = (equals)
Value: a numerical value representing the number of atoms of the specified element
required to satisfy the constraint
In the example shown here, the Xcalibur application would only return search results
for compounds that contain:
More than five fluorine atoms
Exactly three chlorine atoms
You do not need to provide a complete elemental profile. The library search returns
compounds if they satisfy all the specified criteria regardless of any other elements
present.
[Row Number]
Each numbered row represents an item in the table. The asterisk symbol indicates the
last unused row in the table. Use this row to enter a new item.
Element
Type the IUPAC approved abbreviation for the element you want to use an element
constraint. It is used in conjunction with the Condition list and Value box in the same
row within the Individual Element table.
To enter an element constraint, click the box and type the required abbreviation. For
example, to apply carbon as an element constraint, type C. The Xcalibur application
adds a new row to the table for further entries.
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 4 of 7)
Parameter
Description
Condition
Enter a condition for an element constraint. It is used in conjunction with the Element
box and Value box in the same row within the Individual Element table. Valid
conditions are:
< (less than)
> (greater than)
= (equals)
To type an element constraint condition, click the box to activate the list. Click the
down arrow and select the required abbreviation.
Value
Type a numerical value for an element constraint. The Xcalibur data system uses this
value in conjunction with the Condition list and Element box in the same row within
the Individual Element table. The value represents the number of atoms of the specified
element required by library compounds to satisfy the constraint.
To type an element constraint value, click the box and type the required number (the
valid range is 0 to 99).
Elements In Compound
Elements
Specify a list of elements that must be present in returned search results. To enter an
element list, click the box and type the IUPAC approved abbreviation for each element.
Separate each element in the list (of up to 30 characters) by a comma.
All
Specify that the data system should return search results containing all and only the
listed elements. For example C, H, O would return HCHO but not CO2, CH4, or
CH2Cl2. Compare with the Some option.
Some
Specify that the data system should return search results that contain at least one of the
specified elements and no elements that are unlisted. For example, C, H, O would
return CO2, CH4, HCHO but not CH2Cl2. Compare with the All option.
Clear
Delete the text in the Elements in Compounds box.
Mass Spectral Peak Constraints
Enable
Thermo Scientific
Build a profile of ions and ion abundances to be matched against library entries during
the search. The search algorithm only returns search results matching the specified
constraints.
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 5 of 7)
Parameter
Description
Mass Spectral Peak
Constraints Table
Set specific criteria about the mass spectral peaks required in a library search result.
Each row in the table represents an individual mass spectral peak constraint. There are
four components to each constraint represented by the table columns:
Type: Normal, Loss, Rank, or Maxmass
m/z: In a Normal, Rank or Maxmass type constraint, use this box to type the m/z value
of the mass spectral peak to be constrained. In a Loss type constraint, use this box to
type the value of a neutral loss.
From: In a Normal, Loss or Maxmass type constraint, use this box to type the
minimum abundance of the constrained mass spectral peak. In a Rank type constraint,
use this box to type the lowest position of the ion in an intensity ordered list of spectral
peaks.
To: In a Normal, Loss or Maxmass type constraint, use this box to type the maximum
abundance of the constrained mass spectral peak. In a Rank type constraint, use this
box to type the highest position of the ion in an intensity ordered list of spectral peaks.
[Row Number]
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Each numbered row represents an item in the table. The asterisk symbol indicates the
last unused row in the table. Use this row to enter a new item.
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 6 of 7)
Parameter
Description
Type
Specify the type of ion constraint.
Normal: This constraint applies to a specific ion represented by its m/z value. The
From and To values represent the abundance of the ion.
Loss: This constraint describes a neutral loss from a molecular ion. In this case, the
m/z value (limited to 64) represents the mass of the lost neutral group, for example, for
methyl m/z = 15. For this constraint to be matched, a library spectrum must contain:
• A fragment ion at an m/z value 15 less than the molecular ion
• An abundance in the specified From and To range
Rank: This constraint tests the order of an ion in the spectrum in terms of relative
abundance. Ions are ranked from the largest (the base peak) to the 16th. A compound
matches a Rank constraint if its library spectrum contains an mass spectral peak:
• At the specified m/z value
• Ranked between the specified From and To rank positions
If you specify the same number in both fields, the designated ion must have that rank in
the retrieved spectrum.
Maxmass: Sets a constraint on the m/z value of the most significant high mass ion.
Library search results must feature:
• An ion at the specified m/z value
• No significantly larger masses at higher m/z values
• An abundance in the specified From and To range
m/z
Type the m/z value of the mass spectral peak to be constrained in a Normal, Rank or
Maxmass type constraint. The application discards a library search result if it does not
contain a mass spectral peak at the specified m/z value.
Type the value of a neutral loss in a Loss type constraint. The application discards a
library search result if it does not feature a fragment ion at an m/z value appropriate to
the specified neutral loss (in relation to the molecular ion).
From
In a Normal, Loss or Maxmass type constraint, use this box to type the minimum
abundance of the constrained mass spectral peak. In a Rank type constraint, use this
box to type the lowest position of the ion in an intensity ordered list of spectral peaks.
You can specify the same number in both From and To boxes. In this case, The Xcalibur
application discards a library search result unless the designated mass spectral peak is
present in exactly the specified abundance or rank in the retrieved spectrum.
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Table 72. Library Search Constraints page (Qual view) parameters (Sheet 7 of 7)
Parameter
Description
To
In a Normal, Loss or Maxmass type constraint, type the maximum abundance of the
constrained mass spectral peak. In a Rank type constraint, type the highest position of
the ion in an intensity ordered list of spectral peaks.
You can specify the same number in both From and To boxes. In this case, the Xcalibur
application discards a library search result unless the designated mass spectral peak is
present in exactly the specified abundance or rank in the retrieved spectrum.
Absolute
Evaluate all table entries as a percentage of the base (largest) ion in the spectrum.
Values must be between 0 and 100%. For example, if you type 10 and 50 in the
From and To fields of a Normal type constraint, the Xcalibur application discards any
search results where the specified mass spectral peak is not present at an abundance of
between 10 and 50%.
Use the Absolute and Relative options to specify how the application applies the
From and To parameters in the Mass Spectral Peak Constraints table.
In the case of Normal and Loss type constraints, the abundance values can also be
Relative.
Relative
Treat the first entry as an absolute Normal or Loss type. The Xcalibur application
considers subsequent entries in the table relative to the first. In this example, library
search results must contain:
An ion at m/z 125 with an abundance between 10 and 50% of the base ion
An ion at m/z 250 with an intensity between 50 and 999% of the observed intensity of
the first ion in the list
Relative mode is not available for Rank or Maxmass types.
Use the Absolute and Relative options to specify how the application applies the
From and To parameters in the Mass Spectral Peak Constraints table.
Button
Save As Default
250
Validate and save the settings on the current page as default settings. The Xcalibur
application uses these settings for all new processing methods, overriding the previous
default values permanently.
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Peak Purity Dialog Box
Use the Peak Purity dialog box to specify the values of the peak purity parameters to be
applied to PDA raw data in an active chromatogram view.
The Peak Purity command in the Actions menu becomes active only when you open a raw file
that contains scan data (for example, PDA data) in Qual Browser and select the PDA
Detector Type from the Chromatogram Ranges Dialog Box.
Table 73. Peak Purity dialog box parameters
Parameter
Description
Enable
Turn on Peak Purity parameters for PDA chromatograms in an active chromatogram cell
and calculate peak purity results by selecting the Enable check box. Peak detection occurs
automatically before the peak purity calculation.
Scan Threshold
Specify a minimum value of intensity for wavelength scans in microabsorbance units (μAU).
Peak Purity computation using scan threshold starts with the scan at the apex of the peak
and collects wavelength data from scans on both sides of the apex until the scan threshold is
reached. Use scan threshold for either symmetrical or asymmetrical peaks.
The default value for scan threshold is 3000 μAU. The range of possible values is 0 to
1000000 μAU (or 1 AU). In a sample with high background or noise, you might start with
a value for scan threshold of 40000 μAU.
Peak Coverage
Specify a maximum percent value of the width of the integrated peak. Peak Purity
computation using peak coverage starts with the scan at the apex of the peak and collects
wavelength data from scans on both sides of the apex until the percent peak coverage is
reached. Use peak coverage for symmetrical peaks.
The default value for peak coverage is 95% of the integrated peak width.
Limit Scan Wavelength Activate the Wavelength Range box. Select this check box to limit the number of
wavelengths to include in the Peak Purity computation. Then, enter a range in the
Wavelength Range box.
Wavelength Range
Specify a range of UV scans (in nanometers) that include the wavelengths of your peak(s) of
interest. Peak Purity computation using wavelength range starts with the scan at the apex of
a peak; and then collects wavelength data from scans on both sides of the apex until all the
wavelengths in the range are included. Use wavelength range for either symmetrical or
asymmetrical peaks.
The default wavelength range is the full width of the scan. This box is available only if you
select the Limit Scan Wavelength check box.
Apply To All Traces
Thermo Scientific
Compute peak purity for all the peak traces in a cell. If the check box is empty, the Xcalibur
application computes peak purity for the selected trace only.
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Print Dialog Box
Use the Print dialog box in Qual Browser window to specify what to print and how to print it.
Table 74. Print dialog box parameters
Parameter
Description
Print What
All Cells In The Selected Window
Print all of the cells in the selected window. Before opening the Print dialog
box, select the window by clicking its title bar.
Selected Cell Only
Print a selected cell. Before opening the Print dialog box, select the cell by
clicking its cell pin icon,
.
Print How
One Page
Print cells on a single page.
To make sure the area selected for printing prints on only one page, this
option might delete some of the information contained in a cell or cells
displaying text. For example, the Xcalibur application might print only a
partial spectrum list or method.
Each Cell On A Separate Page
Print cells with each cell on a separate page. To print each cell on a separate
page, select the Each Cell On Separate Page option.
To make sure all information in all cells is printed, this option can print
more than one page per cell when one or more cells display text. For
example, a spectrum list or method can require multiple pages.
Ranges Dialog Boxes
Use the Ranges dialog boxes to define parameters for
• Chromatogram Ranges Dialog Box
• Spectrum Ranges Dialog Box
• Scan Filter Range Dialog Box
• Scan Header Range Dialog Box
• Spectrum List Ranges Dialog Box
• Status Log Range Dialog Box
• Tune Method Range Dialog Box
• Search Properties Dialog Box
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Chromatogram Ranges Dialog Box
Use the Chromatogram Ranges dialog box to view and edit the mass range, time range, and
other properties of a chromatogram plot:
• In Qual Browser, for all plots in the active chromatogram view.
• On the Home Page, for the active chromatogram plot in Real Time Plot mode.
You can also apply automatic processing options such as smoothing and background
subtraction.
The dialog box consists of two pages:
• Automatic Processing Page – Chromatogram Ranges Dialog Box
• Ranges Page – Spectrum Ranges Dialog Box
Automatic Processing Page – Chromatogram Ranges Dialog Box
Use the Automatic Processing page of the Chromatogram Ranges dialog box to apply
automatic processing options such as smoothing and baseline subtraction to all plots in the
active cell. You can also specify values for Mass Tolerance and Mass Precision that are applied
to the raw data display in the active chromatogram view.
Table 75. Automatic Processing page parameters – Chromatogram Ranges dialgo box (Sheet 1 of 3)
Parameter
Description
Smoothing
Smoothing
Apply smoothing to all chromatogram plots in the active view.
Enable
Turn on Xcalibur chromatogram smoothing for all the chromatograms in the active view.
Define the type of smoothing in the Chromatogram Smoothing Type list. Define the degree
of smoothing in the Smoothing Points box. To smooth all active chromatograms, select the
Enable Chromatogram Smoothing check box.
Type
View the current type of smoothing that the Xcalibur data system applies to the active
chromatogram. To make this list active, select the Chromatogram Smoothing Enable check
box. To change the current setting, click the arrow to display the list of smoothing type
options: Boxcar and Gaussian. Click one of the smoothing types. The data system displays
your new selection in the Chromatogram Smoothing Type list.
Points
View or change the number of points that the Xcalibur application uses for chromatogram
smoothing. The type of smoothing is defined in the Chromatogram Smoothing Type list.
This list is only active when you select the Chromatogram Smoothing Enable check box.
The valid range for smoothing points is 3 for minimum smoothing to 15 for maximum
smoothing. Select an odd number for the number of smoothing points. To change the
number of smoothing points, type the new number of points in the Points box.
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Table 75. Automatic Processing page parameters – Chromatogram Ranges dialgo box (Sheet 2 of 3)
Parameter
Description
Baseline Subtraction
Baseline Subtraction
Apply baseline subtraction to all chromatogram plots in the active view. This algorithm fits
a smooth curve through the noise in the chromatogram, then subtracts this curve from the
chromatogram, leaving the peaks on a flat baseline.
Enable
Activate Baseline Subtraction to chromatograms in the active cell. To turn on baseline
subtraction, select the Enable check box.
Polynomial Order
Specify the degrees of freedom allowed to the fitted curve. With polynomial order set to 0, a
horizontal straight line is fitted. With polynomial order set to 1, a sloping straight line is
fitted. The further the background is from a straight line, the higher you must set the
polynomial order control. Too high a value will cause the fitted curve to begin to follow the
peak shapes. Normal operating range for this parameter is 3 to 20.
With higher order polynomials, background subtract will sometimes have difficulty
converging on a solution. There is a pre-set upper limit of 300 iterations. If background
subtract does not seem to be making progress, press the Cancel button in the status box and
try again with a lower-order polynomial.
Below Curve
Move the background curve up and down in the noise. The curve fit is constrained to place
the specified percentage of data points beneath the fitted background curve. Normal
operating range for this parameter is 5% – 30%, depending on the abundance and width of
peaks in the chromatogram. For more or wider peaks, increase the value.
Tolerance
View the precision level for performing internal arithmetic. It should not normally be
altered from its default value of 0.01.
Flatten Edges
Select the Flatten Edges check box to apply the polynomial so that the beginning and end of
the chromatogram plot are horizontal.
Overlay Graph Of
Fitted Polynomial
Display the polynomial as an graphic overlay on the chromatogram plot.
Include Peaks
Include Peaks
Include or exclude the reference peaks (R) and exception peaks (E) for the MS data in a
Qual Browser window.
Reference And
Exception Peaks
Include or exclude the reference peaks (R) and exception peaks (E) for the MS data in a
Qual Browser window.
Mass Tolerance
Mass Tolerance
Specify a value for mass tolerance to affect the display of the MS data in a Qual Browser
window.
Use User Defined
Specify the values for mass tolerance and mass units for the MS data in a Qual Browser
window. To change the parameter values, select the Use User Defined check box. If you clear
the check box, the data system uses the values for mass tolerance and units that are stored in
the raw file.
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Table 75. Automatic Processing page parameters – Chromatogram Ranges dialgo box (Sheet 3 of 3)
Parameter
Description
Mass Tolerance
Specify the value for mass tolerance. Enter a value in the range from 0.1 to 50000 and select
units to apply to the value. For a mass range chromatogram, the Xcalibur application uses
the tolerance value to create the limits of a range of masses. The central mass of the range is
the one specified on the Ranges Page – Spectrum Ranges Dialog Box.
If a single mass is entered for a mass chromatogram, the data from each (filtered) scan is
analyzed in the chromatogram from mass-tolerance to mass+tolerance. If a range is masses is
entered, the limits are considered precise, and no tolerance is applied. Therefore, a
mass1–mass2 range causes data to be analyses between the exact masses entered. Use the
mass precision setting if more decimals are needed to specify masses. For base peak
chromatogram, the largest mass in the range is selected, and for mass chromatogram, the
data in the specified range is summed.
Units
Specify the default units that are used in processing MS data in the Qual Browser window.
To change the user-defined settings, select the Use User Defined check box. Select either the
mmu (millimass units) option or the ppm (parts per million) option. To turn off the
user-defined units, clear the Use User Defined check box.
Mass Precision
Mass Precision
Apply mass precision to the MS data in a Qual Browser window.
Decimals
Specify the number of decimal places (places after the decimal point) that the Xcalibur
application uses to process MS data. Specify from 0 to 5 decimal places. The number of
decimal places applies to the mass spectral data in a Qual Browser window.
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Ranges Page – Chromatogram Ranges Dialog Box
Use the Ranges page of the Chromatogram Ranges dialog box to view and edit the mass
range, time range and other properties of a chromatogram plot.
Table 76. Ranges page parameters – Chromatogram Ranges dialog box (Sheet 1 of 4)
Parameter
Description
Range
Time Range
View or change the time range in minutes for the active chromatogram. The valid range is
0.00 to 9999.00 minutes. To select a time range, type the lower and upper time limits in
minutes, separated by a dash (no spaces) in the Time Range box. For example, to select a
time range from 0.10 to 9.10 minutes, type 0.10–9.10.
Fixed Scale
Define the maximum range for the Y-axis of the active chromatogram by selecting the
Fixed Scale check box.
Plot Properties Table
Enable check boxes
View or hide the display of a chromatogram plot. The plot is defined by its position in the
list and is described by the settings in the Plot Properties box. Select the Type check box to
display the chromatogram.
Plot Properties
Raw File
View or change the path and filename of the raw file used to generate the highlighted plot in
the Ranges list on the Ranges page of the Chromatogram Ranges dialog box. Click the
arrow to see a list of all the files active in the current cell. You can change the source of the
active plot in one these ways:
• Select a file from the list.
• Click Browse adjacent to the combo box and browse to the required file.
• Type the full path and filename of the required file into the box.
Scan Filter
256
View the scan filter used for the active chromatogram. To select a filter, click the arrow on
the Filter combo box to display filter options that are stored in the raw file. Select the
desired filter. The Xcalibur application displays the selected filter. You can also use the scan
filter format to type a scan filter into the Filter combo box.
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Table 76. Ranges page parameters – Chromatogram Ranges dialog box (Sheet 2 of 4)
Parameter
Description
Plot Type
Specify the type of chromatogram you want to view in the active plot. You can select:
1. A basic chromatogram type, for example, TIC, from the first list.
2. A logical operator: + or – from the second list. Your selection of an operator activates.
3. The third list for you to select a second chromatogram type to add to, or subtract from,
the first type. For example, Mass Range. The list includes the valid remaining trace
types.
You can use trace combinations for subtracting contributions to a chromatogram from a
solvent or other noise. Combinations are limited to traces of the same type.
For MS scans, valid trace types are TIC, Mass Range and Base Peak.
For MS/MS scans, valid trace types are TIC, Mass Range, Base Peak, and Neutral Fragment.
For Analog data, up to four channels are supported (labeled Analog 1-4).
For data from an A/D Card, four channels are supported (labeled A/D Card Ch 1-4).
For PDA data, valid trace types are Wavelength Range, Total Scan, or Spectrum Maximum.
See below for valid trace types:
• MS Trace Combinations
• Analog Trace Combinations
• A/D Card Trace Combinations
• PDA Trace Combinations
• UV Trace Combinations
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Table 76. Ranges page parameters – Chromatogram Ranges dialog box (Sheet 3 of 4)
Parameter
Description
Range(s)
Specify the range of the selected chromatogram plot type.
For an MS detector type, the Ranges box displays the current mass range of the active
chromatogram if you select a Mass Range or Base Peak plot type. Two Ranges boxes are
displayed if you select one of these plot combinations:
• Mass Range ± Mass Range
• Base Peak ± Mass Range
• Mass Range ± Base Peak
Use the Ranges boxes to specify the ranges of the two plot types.
For a PDA detector type, the Ranges box displays the current wavelength range if you select
a Wavelength Range or plot type. Two Ranges boxes are displayed if you select one of these
plot combinations:
• Wavelength Range ± Wavelength Range
• Wavelength Range ± Spectrum Maximum
• Spectrum Maximum ± Wavelength Range
Use the Ranges boxes to specify the ranges of the two plot types.
For other detector types, the parameter is unavailable.
To change a range or to add a new range, type the range in the box.
The valid range is dependent upon the configured detector. The format is
Low Mass/Wavelength – High Mass/Wavelength. For example, for the range m/z 123
through 234, type the following:
123 – 234
To enter multiple ranges, separate each range with a comma, for example:
100–120, 130–150, 200–220, 300, 302–310
Mass
The neutral fragment mass.
This box is displayed only when you select the MS detector and Neutral Fragment plot type.
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Table 76. Ranges page parameters – Chromatogram Ranges dialog box (Sheet 4 of 4)
Parameter
Description
Detector
View the currently selected detector data type:
• MS
• Analog
• A/D Card
• PDA
• UV
 To change the detector data type
1. Click the arrow to display the list of detector types.
2. Click the required detector type. The Xcalibur application extracts the data type from
the raw file.
Peak Algorithm
Select one of the Xcalibur peak detection algorithms. The algorithm use is active for the
currently selected file. When you select an algorithm, the Xcalibur data system changes the
default parameters for peak detection and integration to those specific to that algorithm. If a
raw file is open, you can select a peak detection algorithm from the list and click OK to
recalculate the data using that algorithm.
Delay
View or change the delay time between a component mass peak detected by the liquid
chromatogram and the time that the same component is detected by the data system. The
valid time range is –5.0 to +5.0 minutes. To change the value, enter the new delay time in
the Delay box.
Fix Scale To
View or change the current maximum range for the Y-axis of the active chromatogram. This
box is only active when you select the Fixed Scale check box. The maximum Y-axis value
can range from 0.01 to 1010. To change the value, input the new maximum Y-axis value in
the Fix Scale To box.
See below for valid trace combinations.
MS Trace Combinations
This table lists the valid trace combinations available in the Trace lists. Your choice of
combination affects other controls on the page as described in the resulting controls column.
Table 77. MS trace combinations parameters (Sheet 1 of 2)
Thermo Scientific
Trace 1
Operator
Trace 2
Resulting Control
Mass Range
[blank]
[unavailable]
Mass (m/z) box
Mass Range
–
Mass Range
Mass1 (m/z) box
2 text box
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Table 77. MS trace combinations parameters (Sheet 2 of 2)
Trace 1
Operator
Trace 2
Resulting Control
Mass Range
+
Mass Range
Mass1 (m/z) box
2 text box
TIC
[blank]
[unavailable]
none
TIC
–
Mass Range
Mass (m/z) box
TIC
–
Base Peak
Mass (m/z) box
Base Peak
[blank]
[unavailable]
Mass (m/z) box
Base Peak
–
Mass Range
BP box MR text box
Base Peak
+
Mass Range
BP box MR text box
Neutral Fragment
(MS/MS data only)
[unavailable]
[unavailable]
Mass
Analog Trace Combinations
This table lists the valid trace combinations available in the Trace lists. The Mass
Range/Wavelength Range control is unavailable.
Table 78. Analog trace combinations parameters
Trace 1
Operator
Trace 2
Resulting Controls
Analog n
(1 ≤ n ≤ 4)
[blank]
[unavailable]
None
Analog n
(1 ≤ n ≤ 4)
–
Analog m
(1 ≤ m ≤ 4, m /= n)
None
Analog n
(1 ≤ n ≤ 4)
+
Analog m
(1 ≤ m ≤ 4, m /= n)
None
A/D Card Trace Combinations
This table lists the valid trace combinations available in the Trace lists when you have selected
an A/D Card detector type. The Mass Range/Wavelength Range control is unavailable.
Table 79. A/D card trace combinations parameters
260
Trace 1
Operator
Trace 2
Resulting Controls
A/D Card Channel n
(1 ≤ n ≤ 4)
[blank]
[unavailable]
None
A/D Card Channel n
(1 ≤ n ≤ 4)
–
A/D Card Channel m
(1 ≤ m ≤ 4, m /= n)
None
A/D Card Channel n
(1 ≤ n ≤ 4)
+
A/D Card Channel m
(1 ≤ m ≤ 4, m /= n)
None
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PDA Trace Combinations
This table lists the valid trace combinations available in the Trace lists when you have selected
a PDA detector type in the Type list on the Identification page of Qual or Quan views. Your
choice of combination affects other controls on the page as described in the Resulting
Controls column.
Table 80. PDA trace combinations parameters
Trace 1
Operator
Trace 2
Resulting Controls
Wavelength Range
[blank]
[unavailable]
Wavelength (nm) box
Wavelength Range
+
Wavelength Range
Wavelength1 (nm) box
2 text box
Wavelength Range
–
Wavelength Range
Wavelength1 (nm) box
2 text box
Wavelength Range
+
Spectrum Maximum
Wavelength1 (nm) box
2 text box
Wavelength Range
–
Spectrum Maximum
Wavelength1 (nm) box
2 text box
Total Scan
[blank]
[unavailable]
None
Total Scan
–
Wavelength Range
Wavelength (nm) box
Total Scan
–
Spectrum Maximum
Wavelength (nm) box
Spectrum Maximum
[blank]
[unavailable]
Wavelength (nm) box
Spectrum Maximum
+
Wavelength Range
Wavelength1 (nm) box
2 text box
Spectrum Maximum
–
Wavelength Range
Wavelength1 (nm) box
2 text box
UV Trace Combinations
This table lists the valid trace combinations available in the Trace lists for UV detectors. The
Mass Range/Wavelength Range control is unavailable.
Table 81. UV trace combinations parameters
Thermo Scientific
Trace 1
Operator
Trace 2
Resulting Controls
Channel n
(A ≤ n ≤ D)
[blank]
[unavailable]
None
Channel n
(A ≤ n ≤ D)
–
Channel m
(A ≤ m ≤ D, m /= n)
None
Channel n
(A ≤ n ≤ D)
+
Channel m
(A ≤ m ≤ D, m /= n)
None
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Spectrum Ranges Dialog Box
Use the Spectrum Ranges dialog box to view and edit the mass range, time, and other
properties of a spectrum plot:
• In Qual Browser, for all plots in the active spectrum view.
• On the Home Page, for the active spectrum plot in Real Time Plot mode.
You can also apply automatic processing options such as smoothing and background
subtraction. The dialog box consists of two pages:
• Ranges Page – Spectrum Ranges Dialog Box
• Automatic Processing Page – Chromatogram Ranges Dialog Box
Automatic Processing Page – Spectrum Ranges Dialog Box
Use the Automatic Processing page of the Spectrum Ranges dialog box to set spectrum
Smoothing or Refine enhancement parameters. These are applied to all spectra in the active
view.
Table 82. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 1 of 3)
Parameter
Description
Smoothing
Enable
Turn on the Xcalibur application chromatogram smoothing for all the chromatograms in
the active view. Define the type of smoothing in the Chromatogram Smoothing Type list.
Define the degree of smoothing in the Smoothing Points box. To smooth all active
chromatograms, select the Enable Chromatogram Smoothing check box.
Type
View the current type of smoothing that the data system applies to the active
chromatogram. To make this list active, select the Chromatogram Smoothing Enable check
box. To change the current setting, click the arrow to display the list of smoothing type
options: Boxcar and Gaussian. Click one of the smoothing types. The data system displays
your new selection in the Chromatogram Smoothing Type list.
Points
View or change the number of points that the Xcalibur data system uses for spectrum
smoothing. The type of smoothing is defined in the Spectrum Smoothing Type list. This list
is only active when you select the Enable Spectrum Smoothing check box. The valid range
for smoothing points is 3 for minimum smoothing to 15 for maximum smoothing. Select
an odd number for the number of smoothing points. To change the number of smoothing
points, type the new number of points in the [Spectrum Smoothing] Points box.
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Table 82. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 2 of 3)
Parameter
Description
Refine
Apply the Refine spectrum enhancement to all the spectra displayed in the active spectrum
view. Refine requires two parameters: Window Size (sec) and Noise Threshold.
The Refine algorithm examines the mass chromatogram of each ion contributing to a
chromatogram peak apex scan:
1. It discards masses without a peak maximum within ±1 scan of the defined
chromatogram peak apex.
2. It then searches for a minimum within the specified Window Size range either side of
the peak apex. These points define the peak start and peak end.
3. Using scans at and beyond the peak start and peak end, Refine measures the
background noise level in the mass chromatogram.
4. Refine uses extrapolation to estimate the contribution of noise to the scan at the peak
apex. Refine adjusts the mass intensity of the apex scan accordingly.
5. Finally, Refine uses the Noise Threshold parameter to determine whether the adjusted
intensity is significant in comparison to the background noise. If:
Adjusted Intensity < Noise Threshold × Background Noise
the mass is discarded from the final spectrum.
Enable
Turn on Refine spectrum enhancement for all the spectra in the active view. To apply Refine
to the active spectrum view, select the Enable check box.
Window Size
Enter a time window for the Refine spectrum enhancement method. The Refine algorithm
applies the window across a chromatogram peak apex and uses it to search for the peak start
and peak end and to estimate the background noise. Set this parameter to the peak width.
Noise Threshold
Enter a value for the Noise Threshold parameter. The Refine algorithm uses the Noise
Threshold parameter to determine whether adjusted ion intensities are significant in
comparison to the background noise. The parameter is actually a factor rather than a
threshold. For example, with a Noise Threshold value of 2, ions are discarded from the
enhanced spectrum unless their intensities are twice the measured background noise.
Include Peaks
Include or exclude the reference peaks (R) and exception peaks (E) for the MS data in a
Qual Browser window.
Reference and
Exception Peaks
Include or exclude the reference peaks (R) and exception peaks (E) for the mass data in a
Qual Browser window.
Mass Tolerance
Specify a value for mass tolerance to affect the display of the MS data in a Qual Browser
window.
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Table 82. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 3 of 3)
Parameter
Description
Use User Defined
Specify the values for mass tolerance and mass units for the MS data in a Qual Browser
window. To change the parameter values, select the Use User Defined check box. If you clear
the check box, the Xcalibur data system uses the values for mass tolerance and units that are
stored in the raw file.
Mass Tolerance
Specify the value for mass tolerance. Enter a value in the range of 0.1 to 50,000, and then
select units to apply to the value. The Xcalibur data system uses the tolerance value to create
the limits of a range of values. Specify up to eight spectral ranges on the Ranges Page –
Spectrum Ranges Dialog Box.
Units
Specify the default units that are used in processing MS data in the Qual Browser window.
To change the user-defined settings, select the Use User Defined check box. Select either the
mmu (millimass units) option or the ppm (parts per million) option. To turn off the
user-defined units, clear the Use User Defined check box.
Mass Precision
Apply mass precision to the MS data in a Qual Browser window.
Decimals
Specify the number of decimal places (places after the decimal point) that the data system
uses to display mass values. You can specify from 0 to 5 decimal places. The number of
decimal places applies to the MS data in a Qual Browser window.
Ranges Page – Spectrum Ranges Dialog Box
Use the Ranges page of the Spectrum Ranges dialog box to set the mass and time ranges and
other parameters for a spectrum plot.
Table 83. Ranges page parameters – Spectrum Ranges dialog box (Sheet 1 of 3)
Parameter
Description
Range
Mass/Wavelength
Range
• Detector = MS
View or change the current mass range of the active spectrum. To change the mass
range, input the first mass and last mass of the scan in the Mass Range box. The format
is First Mass – Last Mass. For example, to display mass/charge 100 through 200, type
100 – 200.
• Detector = PDA
View or change the current wavelength range in nanometers. To change the wavelength
range, input the short wavelength and long wavelength of the scan in the Wavelength
Range box. The format is Short Wavelength – Long Wavelength. For example, to display
a wavelength range of 195 through 795 nanometers, type 195 – 795.
Average
264
Turn on the Xcalibur application spectrum averaging. To average all scans defined by the
mass range, time range, and filter settings in the Spectrum Ranges dialog box, select the
Scan Average check box.
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Table 83. Ranges page parameters – Spectrum Ranges dialog box (Sheet 2 of 3)
Parameter
Description
Fix Scale
Turn on the fix scale setting displayed in the Spectrum Fix Scale box. To change the
maximum range for the Y-axis of the active spectrum, select the Spectrum Fix Scale check
box.
Plot Properties Table
Enable check boxes
Turn on the display of a spectrum plot. The plot is defined by its position in the list and is
described by the settings in the Plot Properties box. Select the Type check box to display the
chromatogram.
Plot Properties
Detector
View the currently selected detector data type:
• MS
• Analog
• A/D Card
• PDA
• UV
 To change the detector data type
1. Click the arrow to display the list of detector types.
2. Click the required detector type. Qual Browser extracts the data type from the raw file.
Time
View or change the time range in minutes for the active spectrum in minutes. The valid
range is 0.00 to 200.00 minutes. To select a time range, type the lower and upper time
limits in minutes, separated by a dash (no spaces) in the Time box. For example, to select a
time range from 0.10 to 9.10 minutes, type the following: 0.10–9.10.
Scan Filter or Scan
Filter Type
View the scan filter used for the active spectrum. To select a filter, click the arrow on the
Filter combo box to display filter options that are stored in the raw file. Select the desired
filter. The Xcalibur application displays the selected filter. You can also use the scan filter
format to type a scan filter into the Filter combo box.
Not all MSn detectors provide the MSn Browser feature.
If your MSn detector provides the MSn Browser feature, you can display either the scan
filters by selecting the Scan option or you can display the processing filters by selecting the
Process option. The processing filters display the average spectra and composite spectra
builds using the data in the file displayed in the Raw File list.
This combo box is available only for MS detectors.
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Table 83. Ranges page parameters – Spectrum Ranges dialog box (Sheet 3 of 3)
Parameter
Description
Raw File
View the path and filename of the current raw file. Click the arrow to see a list of all the
active files. To change the current raw file, choose one of these options:
• Select a file from the list.
• Click Browse adjacent to the combo box and browse to the required file.
• Type the full path and filename of the required file into the box.
Formula
Enter a formula to simulate.
This box is only available when you select the Simulation check box.
Background Subtraction
Time Range 1
View whether or not background subtraction has been performed for the active spectrum.
When the check box is selected, the Xcalibur application displays the first time range used
for background subtraction in the Time Range 1 box.
In Qual Browser, the Xcalibur application enters these settings automatically when you
perform a background subtraction using Actions > Subtract Spectra.
Time Range 2
View whether or not background subtraction has been performed for the active spectrum.
When the check box is selected, the Xcalibur application displays the second time range
used for background subtraction in the Time Range 2 box.
In Qual Browser, the Xcalibur application enters these settings automatically when you
perform a background subtraction using Actions > Subtract Spectra.
Simulation
266
View whether or not the selected plot contains simulated data.
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Map Ranges Dialog Box
The Map Ranges dialog box consists of two pages:
• Map Ranges Dialog Box (Ion Map)
• Map Ranges Dialog Box (Map)
Map Ranges Dialog Box (Ion Map)
Use the [Ion] Map Ranges dialog box to set the mass ranges for parent and product masses.
Table 84. Map Ranges dialog box (ion map) parameters
Parameter
Description
Parent Mass
View or change the parent mass coordinates for the Ion Map pane in the Parent Mass box.
To display the parent mass coordinates, drag the cursor in the Ion Map pane along the
Parent m/z axis. The Xcalibur application displays the parent mass coordinates in the Parent
Mass box. You can also enter the parent mass coordinates in the Parent Mass box. The valid
range is m/z 0.00 to 100000.00.
Product Mass
View or change the product mass coordinates for the Ion Map pane in the Product Mass
box. To display the product mass coordinates, drag the cursor in the Ion Map pane along
the Product m/z axis. The Xcalibur application displays the product mass coordinates in the
Product Mass box. You can also enter the product mass coordinates in the Product Mass
box. The valid range is m/z 0.00 to 100000.00.
Full Range
Click Full Range to reset the mass coordinates to the full range of the Ion Map.
Scan Filter
View the scan filters available for the data and edit the scan filters as text.
 To edit a scan filter
1. Click the arrow and display the list of filters.
2. Click one of the scan filters and edit the text.
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Map Ranges Dialog Box (Map)
Use the Map Ranges dialog box to set the mass and time range for a map.
Table 85. Map Ranges dialog box (map) parameters
Parameter
Description
Detector
View the currently selected detector data type:
• MS
• Analog
• A/D Card
• PDA
• UV
 To change the detector data type
1. Click the arrow to display the list of detector types.
2. Click the required detector type. Qual Browser extracts the data type from the raw file.
Mass
View or change the current mass range of the active map. To change the mass range,
input the first mass and last mass of the scan in the Mass Range box. The format is
First Mass – Last Mass. For example to display mass/charge 100 through 200, type
100 – 200.
Time
View or change the time range in minutes for the active map. The valid range is set by the
current data. To select a time range, type the lower and upper time limits in minutes,
separated by a dash (no spaces) in the Time box. For example, to select a time range from
0.10 to 9.10 minutes, type: 0.10–9.10.
Scan Filter
View the scan filter used for the active map. To select a filter, click the arrow on the Filter
combo box to display filter options that are stored in the raw file. Select the desired filter.
The Xcalibur application displays the selected filter. You can also use the scan filter format
to type a scan filter into the Filter combo box.
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Scan Filter Range Dialog Box
Use the Scan Filter Range dialog box to set the scan filter time.
Table 86. Scan Filter Range dialog box parameter
Parameter
Description
Time
View or change the time range in minutes for the active scan filter.
The valid range is 0.00 to 200.00 minutes. To select a time range,
type the lower and upper time limits in minutes, separated by a
dash (no spaces) in the Time box. For example, to select a time
range from 0.10 to 9.10 minutes, type: 0.10–9.10.
Scan Header Range Dialog Box
Use the Scan Header Range dialog box to set the scan header time.
Table 87. Scan Header Range dialog box parameter
Thermo Scientific
Parameter
Description
Time
View or change the time range in minutes for the active scan
header. The valid range is 0.00 to 200.00 minutes. To select a time
range, type the lower and upper time limits in minutes, separated
by a dash (no spaces) in the Time box. For example, to select a
time range from 0.10 to 9.10 minutes, type: 0.10–9.10.
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Spectrum List Ranges Dialog Box
Use the Spectrum List Ranges dialog box to set the mass range and time for a spectrum list.
Table 88. Spectrum List Ranges dialog box parameters (Sheet 1 of 3)
Parameter
Description
Mass
View or change the current mass range of the active spectrum list. To change the mass
range, input the first mass and last mass of the scan in the Mass Range box. The format is
First Mass – Last Mass. For example to display mass/charge 100 through 200, type
100 – 200.
Detector
This drop-down list displays the currently selected detector data type:
• MS
• Analog
• A/D Card
• PDA
• UV
 To change the detector data type
1. Click the arrow to display the list of detector types.
2. Click the required detector type. Qual Browser extracts the data type from the raw file.
Time
View or change the time range in minutes for the active spectrum list. The valid range is
0.00 to 200.00 minutes. To select a time range, type the lower and upper time limits in
minutes, separated by a dash (no spaces) in the Time box. For example, to select a time
range from 0.10 to 9.10 minutes, type: 0.10–9.10.
Scan Filter
View the scan filter used for the active spectrum list. To change the scan filter, use the scan
filter format to type a scan filter into the Filter combo box or click the arrow on the Filter
combo box to display filter options that are stored in the raw file and select the desired filter.
The Xcalibur application displays the selected filter.
Smoothing
Enable
Turn on Xcalibur chromatogram smoothing for all the chromatograms in the active view.
Define the type of smoothing in the Chromatogram Smoothing Type list. Define the degree
of smoothing in the Smoothing Points box. To smooth all active chromatograms, select the
Enable Chromatogram Smoothing check box.
Type
View the current type of smoothing that the Xcalibur data system applies to the active
chromatogram. To make this list active, select the Chromatogram Smoothing Enable check
box. To change the current setting, click the arrow to display the list of smoothing type
options: Boxcar and Gaussian. Click one of the smoothing types. The Xcalibur application
displays your new selection in the Chromatogram Smoothing Type list.
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Table 88. Spectrum List Ranges dialog box parameters (Sheet 2 of 3)
Parameter
Description
Points
View or change the number of points that the Xcalibur data system uses for spectrum list
smoothing. Define the type of smoothing in the Spectrum List Smoothing Type list. Select
the Enable Spectrum List Smoothing check box to turn on this list. The valid range for
smoothing points is 3 for minimum smoothing to 15 for maximum smoothing. Select an
odd number for the number of smoothing points. To change the number of smoothing
points, type the new number of points in the Points box.
Refine
Refine
Apply the Refine spectrum enhancement to the spectrum described in the spectrum list
view. Refine requires two parameters: Window Size (sec) and Noise Threshold.
The Refine algorithm examines the mass chromatogram of each ion contributing to a
chromatogram peak apex scan:
1. Refine discards masses without a peak maximum within ±1 scan of the defined
chromatogram peak apex.
2. Refine then searches for a minimum within the specified Window Size range either side
of the peak apex. These points define the peak start and peak end.
3. Using scans at and beyond the peak start and peak end, Refine measures the
background noise level in the mass chromatogram.
4. Refine uses extrapolation to estimate the contribution of noise to the scan at the peak
apex. Refine adjusts the mass intensity of the apex scan accordingly.
5. Finally, Refine uses the Noise Threshold parameter to determine whether the adjusted
intensity is significant in comparison to the background noise. If:
Adjusted Intensity < Noise Threshold × Background Noise
the mass is discarded from the final spectrum.
Enable
Turn on Refine spectrum enhancement for the spectrum listed in the active spectrum list
view. To apply Refine, select the Enable check box.
Window Size
Enter a time window for the Refine spectrum enhancement method. The Refine algorithm
applies the window across a chromatogram peak apex and uses it to search for the peak start
and peak end and to estimate the background noise. Set this parameter to the peak width.
Noise Threshold
Enter a value for the Noise Threshold parameter. The Refine algorithm uses the Noise
Threshold parameter to determine whether adjusted ion intensities are significant in
comparison to the background noise. The parameter is actually a factor rather than a
threshold. For example, with a Noise Threshold value of 2, ions are discarded from the
enhanced spectrum unless their intensities are twice the measured background noise.
Background Subtraction
Background
Subtraction
Thermo Scientific
These settings display the background subtraction time regions applied to the spectrum
described in the spectrum list view. You can adjust these values or type your own.
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Table 88. Spectrum List Ranges dialog box parameters (Sheet 3 of 3)
Parameter
Description
Time Range 1
View whether or not background subtraction has peen performed for the spectrum
described in the active spectrum list. When you select the check box, the Xcalibur
application displays the first time range used for background subtraction in the
Time Range 1 box.
The application enters these settings when you perform a background subtraction using the
Actions > Subtract Spectra from the Qual Browser window.
Time Range 2
View whether or not background subtraction has peen performed for the spectrum
described in the active spectrum list. When you select the check box, the Xcalibur
application displays the second time range used for background subtraction in the
Time Range 2 box.
The application enters these settings when you perform a background subtraction using the
Actions > Subtract Spectra from the Qual Browser window.
Mass Tolerance
Mass Tolerance
Specify a value for mass tolerance. Settings in this box affect the display of MS data in a
Qual Browser window.
Use User Defined
Specify the values for mass tolerance and mass units for the MS data in a Qual Browser
window. To change the parameter values, select the Use User Defined check box. If you clear
the check box, the Xcalibur application uses the values for mass tolerance and units that are
stored in the raw file.
Mass Tolerance
Specify the value for mass tolerance. Enter a value in the range from 0.1 to 50000, and then
select units to apply to the value. The Xcalibur application uses the tolerance value to create
the limits of a range of masses.
Units
Specify the default units that are used in processing MS data in the Qual Browser window.
To change the user-defined settings, select the Use User Defined check box. Select either the
mmu (millimass units) option or the ppm (parts per million) option. To turn off the
user-defined units, clear the Use User Defined check box.
Include Peaks
Reference And
Exception Peaks
Include or exclude the reference peaks (R) and exception peaks (E) for the mass data in a
Qual Browser window.
Mass Precision
Decimals
272
Specify the number of decimal places (places after the decimal point) that the Xcalibur data
system uses to process MS data. Specify from 0 to 5 decimal places. The number of decimal
places applies to the MS data in a Qual Browser window.
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Status Log Range Dialog Box
Use the Status Log Range dialog box to set the status log time range.
Table 89. Status Log Range dialog box parameters
Parameter
Description
Time
View or change the time range in minutes for the active status log view. The valid range is
0.00 to 200.00 minutes. To select a time range, type the lower and upper time limits in
minutes, separated by a dash (no spaces) in the Time box. For example, to select a time
range from 0.10 to 9.10 minutes, type: 0.10–9.10.
Detector
This drop-down list displays the currently selected detector data type:
• MS
• Analog
• A/D Card
• PDA
• UV
 To change the detector data type
1. Click the arrow to display the list of detector types.
2. Click the required detector type. Qual Browser extracts the data type from the raw file.
Tune Method Range Dialog Box
Use the Tune Method Range dialog box to select the tune method for a specific run segment.
Table 90. Tune Method Range dialog box parameter
Parameter
Description
Segment
View or change the current run segment. The active Qual Browser window cell displays the
tune method for that segment. To display the tune method of another run segment, enter
the segment number and click OK.
Search Properties Dialog Box
Use the Search Properties dialog box to select and order the libraries used during library
searching. You can also change the way that the search is carried out. The dialog box consists
of two pages:
• Search Properties Dialog Box
• Search Parameters Page – Search Properties Dialog Box
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Search Properties Dialog Box
Use the Search List page to select the libraries and search order for library searches of spectra
from Qual Browser.
Table 91. Search List page parameters – Search Properties dialog box
Parameter
Description
Library Lists
Available Libraries
View the libraries that are currently excluded from searching during processing. The Xcalibur
application regenerates this list when you open the dialog box.
Selected Libraries
View the libraries that are currently included in searches during processing. The order of the
libraries defines the order in which they are searched by the Xcalibur application.
Buttons
Add
Transfer a library from the Available Libraries list box to the Selected Libraries list box. This
appends the library in the search list.
Remove
Transfer a library from the Selected Libraries list box to the Available Libraries list box.
Top
Move a library in the Selected Libraries list box to the top of the list (first in the search order).
Up
Move a library in the Selected Libraries list box up one position (earlier in the search order).
Down
Move a library in the Selected Libraries list box down one position (later in the search order).
Bottom
Move a library in the Selected Libraries list box to the final position (last in the search order).
Search Parameters Page – Search Properties Dialog Box
The Search Parameters page of the Search Properties dialog box allows you to select the type
of library search, limit the search by a molecular weight constraint, and determine how the
results of the search are returned.
Table 92. Search Parameters page parameters – Search Properties dialog box (Sheet 1 of 3)
Parameter
Description
Search Type
Use the settings in this group box to choose the type of library search applied to spectra. There are two main options:
Identity and Similarity. The difference between the two search types is primarily in the weightings of the spectrum as
a function of mass.
Identity
Apply an Identity search algorithm for library matching of spectra. A Normal Identity
search is the default option.
Normal
Apply a Normal Identity search algorithm for library matching of spectra. This is the default
option. A Normal Identity search is suited to low quality or unusual spectra. The search
algorithm uses a standard pre-screen search filter.
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Table 92. Search Parameters page parameters – Search Properties dialog box (Sheet 2 of 3)
Parameter
Description
Quick
Apply a Quick Identity search algorithm for library matching of spectra. Use this option
when you are sure the spectrum or compound exists in the library. The search algorithm
uses a fast pre-screen search filter.
Penalize Rare
Compounds
Limit the impact of rare compounds by reducing the match factor. This option is effective
only when you have selected one or more of the NIST databases (such as MAINLIB). It has
no effect on spectra in user libraries or other commercial libraries.
Each reference spectrum in a NIST library contains a record of other commercial databases
containing information about the compound. A compound is considered 'rare' if it is
present in a limited number of these databases. If you select the Penalize Rare Compounds
option, hit compounds present in few, or no other databases other than the NIST libraries,
will have their match factors reduced (the maximum penalty is 50 out of 1000). This, in
effect, leads to a relative increase in the match factors of 'common' compounds, placing
them higher in the hit list than exotic isomers with near identical spectra. This roughly
adjusts for the so-called “a priori probabilities” of finding a compound in an analysis.
Similarity
Apply a Similarity search algorithm for library matching of spectra.
Simple
Select this option button if you want to apply a Simple Similarity search algorithm for
library matching of spectra. This option finds a large set of spectra to compare with the
submitted spectrum, and is generally slower than an Identity search.
A Simple Similarity search should be used if:
• You know that the unknown spectrum is not in the library
• The spectrum is of poor quality so that a reliable match is unlikely
Hybrid
Select this option button if you want to apply a Hybrid Similarity search algorithm for
library matching of spectra.
This option uses a combination of the Simple and Neutral Loss search strategies. As for the
neutral loss search, an estimate of the unknown’s molecular weight is required. If the
unknown compound contains chemical structures that generate both characteristic ions and
neutral loss patterns, these structures can be identified from the hit list produced by this
search.
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Table 92. Search Parameters page parameters – Search Properties dialog box (Sheet 3 of 3)
Parameter
Description
Neutral Loss
Select this option button if you want to apply a Neutral Loss Similarity search algorithm for
library matching of spectra.
The neutral losses in a spectrum are the mass differences between the molecular ion and
other major ions in the spectrum. For certain classes of compound, neutral losses can be
very characteristic spectral features.
In a Neutral Loss search, the Xcalibur application examines the submitted spectrum and
identifies the molecular ion. The application submits the mass value of the molecular ion to
the search along with the spectrum. The search algorithm calculates the significant neutral
losses and compares them with library data. Hits are returned according to matches of the
molecular ion and its neutral losses.
Options
Search With MW=
Select this check box if you want to restrict the search to library entries with a particular
molecular weight. Use the associated text box to enter the molecular weight.
Reverse Search
Select this check box to sort matching library spectra by the Reverse Search Match Factor.
By default, the Xcalibur application sorts matches by the Forward Match Factor.
Mass Defect
This group box contains the parameters used in library searches that allow you to correct for the differences between
the actual masses and the nominal integer masses of the atoms in a molecule. Assign a larger value (in millimass units)
for mass defect to larger molecules because, in general, they are composed of more atoms than smaller molecules;
larger molecules need a larger correction factor to approximate the linear function that the Xcalibur data system uses
to calculate masses.
When you enable mass defect, the Xcalibur application uses the parameters in library searches of spectra that you
export from the spectrum view of Qual Browser.
Enable
Include mass defect values for library searches in a processing method.
Defect
Specify values (in millimass units) for mass defect. Specify a smaller value for lower mass
ranges in the first text box, and specify a larger value for higher mass ranges in the second
text box.
At Mass
Specify the masses at which the Xcalibur data system applies specified mass defect values to
calculations of mass. Specify a smaller mass value in the first text box, and specify a larger
mass value in the second text box.
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Select Isotopes Dialog Box
Use the Select Isotopes dialog box to display the isotopes of each element and select one or
more isotopes to include in the calculation of chemical formulas.
Table 93. Select Isotopes dialog box parameters
Parameter
Description
Elements
View the chemical elements. Click an element in the Periodic Table to add it to the
Elements list. Click the element in the Elements list to display isotopes for that element.
The isotopes appear in the Isotopes list.
Isotopes
View the name and relative intensities of the isotopes for the current element you selected
from the Elements list. Select an isotope from the list. The Xcalibur application displays it
in the Selected Isotope box.
Selected Isotopes
View the isotope you select from the Isotopes list.
Min. Number
View or change the minimum number of occurrences of the selected isotope in the formula
that Qual Browser calculates. To change the minimum number of occurrences, enter a
number from 0 to 10000 in the box.
Max. Number
View or change the maximum number of occurrences of the selected isotope in the formula
that Qual Browser calculates. To change the maximum number of occurrences, enter a
number from 0 to 10000 in the box.
Periodic Table
Click an element in the Periodic Table to add that element to the Elements list.
 To change the color of the multi-isotopic or monoisotopic elements
1. Click the Multi Isotopic or the Mono Isotopic button in the lower left corner of the
periodic table. The Color dialog box opens.
2. Select a new color.
Buttons
Add to List
Add the isotopes listed in the Selected Isotopes list to the Elements in Use list of the
Elemental Composition Page.
Delete
Remove an element from the list. Select an element in the Elements list and click the Delete
button.
Close
Close the Select Isotopes dialog box.
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Specify Mixture for Simulation Dialog Box
Use the Specify Mixture for Simulation dialog box to specify the compounds and amounts to
include in the mixture so that the Xcalibur application can simulate a spectrum.
Table 94. Specify Mixture for Simulation dialog box parameters
Parameter
Description
Formula
Enter the chemical formula of a compound in the mixture in the Formula column.
You can enter both upper and lower case letters, however the Xcalibur application interprets
all lower case input as two-letter symbols. For example, the string inau will be parsed as
In Au. You can force other interpretations by being more specific in capitalization, namely
INAu or INaU. The application interprets all upper case input as single-letter element
names. For example, COSI is interpreted as C O S I.
You can specify a specific isotope by naming it in the following fashion: [13]C. (That is,
square brackets about the isotope mass number.)
You can specify mixtures of substances by using additional symbols + (addition) and
* (multiplication). Both will be required to specify a mixture. A valid mixture has the format
substance*quantity + substance* quantity, for example, C4H8*2+H2O*5.
Parentheses are allowed in the formula input edit field to specify repeating moieties such as
found in polymers, for example, HO(C2H4O)5H.
Amount
Enter the percentage of the compound in the mixture in the Amount column.
Color
Select one of 48 basic colors or 16 (maximum) preselected custom colors. The Color
column becomes active when you select the Also Show Separate Traces for Each Compound
check box.
Click a color in the Color column. The Color dialog box opens.
Also Show Separate
Traces for Each
Compound
278
Select one of 48 basic colors or 16 (maximum) preselected custom colors to display the
traces for each compound.
Click a color in the Color column. The Color dialog box opens.
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Subtract Background Dialog Box
Use the Subtract Background dialog box to subtract a raw file or a single scan from a raw file
from any other selected raw file. You can use this utility to subtract a background spectrum
from a raw file or deconvolute merged or overlapping component peaks.
Table 95. Subtract Background dialog box parameters (Sheet 1 of 2)
Parameter
Description
Input
File
View or change the pathname of the input raw file. You can change the source of
the input file in one of these ways:
• Click Browse adjacent to the box and browse to the required file
• Type the full path and filename of the required file into the box.
Scan Filter
View the selected scan filter to be applied to the input file. You can also use the scan
filter format to type a scan filter into the Filter combo box.
 To select a filter
1. Click the arrow on the Filter combo box to display filter options that are stored
in the raw file.
2. Select the desired filter. The Xcalibur application displays the selected filter.
All Detectors
Specify that all detector data sources should be used to produce the input
chromatogram. The check box is unavailable for single source raw files.
Single Detector
Select a data source for the input chromatogram from the chosen raw file. The box
lists the detector sources recorded in the raw file.
Negative Chromatographic
Subtraction Results Allowed
Background subtraction normally enforces a rule that chromatogram data cannot
be less than zero. Normally, if background subtraction results in a negative value, it
is set to zero. However, select this check box to prevent this action from happening.
Background
File
View or change the pathname of the raw file to be subtracted from the input file.
You can change the source of the background file in one of these ways:
• Click Browse adjacent to the box and browse to the required file
• Type the full path and filename of the required file into the box.
Scope
Subtract Whole File
Specify that the whole of the background file is to be subtracted from the input file.
Subtract Single Scan (RT)
Specify that a single scan from the background file is to be subtracted from each
scan of the input file. Type the number of the scan in the adjacent box.
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Table 95. Subtract Background dialog box parameters (Sheet 2 of 2)
Parameter
Description
Alignment Offset (RT)
Specify how much time, in minutes, to offset the background subtraction file.
A positive alignment offset implies that the peaks in the background subtraction
file have larger retention times than the peaks in the file it is subtracted from.
Scaling Factor
Specify a scaling factor for the subtract background file operation. Type the factor
you want to apply to the background file before its subtraction from the input file.
Output
Name
View the filename for the output file resulting from the subtraction of the
background file from the input file. The Xcalibur application uses the input
filename with a BG_ prefix.
Folder
View or change the folder to store the output file after the subtract background file
operation. You can change the folder in one of these ways:
• Click the Folder button adjacent to the box and browse to the required folder
• Type the full path of the folder into the box.
Buttons
Proceed
Start the Subtract Background file operation using the settings in the dialog box.
Exit
Exit the dialog box and stop the Subtract Background file operation.
Toolbars Dialog Box
Use the Toolbars dialog box to show or hide the Main and Amplify toolbars. You can also
choose to display ToolTips and determine whether the toolbars display large or small buttons.
Table 96. Toolbars dialog box parameters
Parameter
Description
Main and Amplify check boxes
List the toolbars available in Qual Browser: Main and Amplify. To display a toolbar,
select its check box. To hide the toolbar, clear its check box.
Show ToolTips
Show or hide ToolTips. To display ToolTips, select the ToolTips check box. If you
do not want to display ToolTips, clear the ToolTips check box.
Large Buttons
Display the toolbars with large or small buttons. To display large buttons on
the toolbar, select the Large Buttons check box. To display small buttons on the
toolbar, clear the Large Buttons check box.
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Index
A
A/D Card detector type 260
adductions 4
amplification factor, specifying 117, 207
analog trace combinations 260
audit trail 109
autofilter 64
automatic peak detection 72
avalon peak detection settings 178
axis options
chromatogram view 66
map view 79
overview 225
B
background, subtracting 279
band width, changing 83, 221
baseline subtraction 62, 254
baselines 72
C
cell
active view 23
copying to clipboard 211
creating 23
deleting 24
expanding 110
reducing 111
size, adjusting 25, 110, 209
Cell Information page
chromatogram 36
overview 35, 167
spectrum 37
cell information, viewing 35
cell view, changing 30
centroiding algorithm 210
chemical formulas, displaying 233
Thermo Scientific
chemical ionization 4
chromatogram view
automatic processing 60
axis options 66, 213
background, subtracting 99
baseline subtraction 62, 254
color options 67, 216
heading 239
icons for 36
label options 68, 216
mass data settings 238
mass precision 63
mass tolerance 63
normalization 69, 218
overview 128
peak detection, all chromatogram plots 72
peak detection, selected chromatogram plot 72
peaks 62
plots, inserting and deleting 58
printing 252
ranges, setting 58, 253, 256
reference 128
smoothing 61, 253
style options 70, 219
trace combinations 259
viewing 57
color
chromatogram view 67
map view 80
options 211
column, grouping 113, 124
cursor actions 14
D
data files, opening 16
dataset name 109
display options, overview 226
double bonds 171
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Index: E
E
M
elemental compositions, displaying 168, 233
error log, viewing 115, 133
manual peak detection 73
map view
axis options 79
band width 221
color options 80, 222
display options 220, 224
heading 239
mass data settings 238
normalization 223
overview 75, 144
printing 252
ranges 268
ranges, setting 76
scan filter 269
scan header time 269
style options 78
viewing 75
mass precision, chromatogram view 63
mass tolerance, chromatogram view 63
mass, chromatograms 6
MSn experimental data, analyzing and displaying 173
F
fragmentation patterns 3
G
genesis peak detection settings 184
graphics, adding 198
grid lines 110, 113, 124
H
heading, editing 239
Help menu 113
I
ICIS peak detection settings 182
Info Bar pages 166
Info Bar tabs 12
instrument method view 135
instrument method, viewing 115
Ion Map view
band width 221
color options 222
display options 220, 224
mass settings 238
normalization 223
ranges 267
reference 138
ionization modes 3
isotopes, selecting 277
L
labels
chromatogram view 68
overview 228
spectrum view 98
layout
applying 34
creating 33
opening saved 33
saving 33
summary information, displaying 34
library search
constraints, setting 244
search list 274
search parameters 274
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neutral loss 2
Nitrogen Rule 170
noise region 104, 126
normalization, chromatogram view 69
P
PDA detector type 261
peak detection
automatic 72
manual 72–73
settings, changing 73
peak properties 22
peak purity 104
peak purity parameters, setting 251
peaks
adding 72
baseline 72
chromatogram view 62
detection 72
plot
adding 115
graphics, adding 27
graphics, removing 29
point, selecting 40
regions, amplifying 26
regions, expanding 56
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Index: Q
scaling 32
scan filter view 53
text, adding 26, 201
text, removing 29
plot range
one-dimensional 43
two-dimensional 47
plots, chromatogram 58
polynomial order, setting 254
preview, activating 14
printing 252
Q
Qual Browser window
overview 7
toolbar 9
R
ranges, spectrum view 94
raw data file
opening 16
peaks 71
reagent gas 4
result file information 187
result file, viewing 20, 146
ring equivalents 171
row, grouping 112, 123
S
sample information view 146
scan filter format 50
scan filter view 149
scan filter, selecting 208
scan filter, using 49
scan header view 151
selected ion monitoring 5
sequence file, opening 18
sequence information, viewing 19, 188
simulated isotopic distribution spectrum, creating 189
simulations 278
smoothing, chromatogram 61
spectra, overview 1
spectrum list view 154
spectrum normalization, overview 231
spectrum view
color options 87
display options 236
header information 157
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heading 239
icons for 37
labels 98
mass data settings 238
normalization 235
overview 157
printing 252
ranges 264, 270
smoothing 262
style options 90
spectrum, viewing 142
status log
time range, setting 273
viewing 115, 160
style options
chromatogram view 70
map view 78
overview 232
spectrum view 90
T
text, adding to plot 201
theoretical mass, displaying 233
tool
adding 11
button, repositioning 12
removing 11
toolbar
customizing 10, 280
displaying or hiding 10
Tools menu
adding programs to 200
adding tools to 207
overview 114
trace analysis 6
trace combinations 259
tune method
selecting 273
viewing 114
tune method view 164
U
UV detectors 261
V
view
changing 30
display options 212
opening 30
selecting 114
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Index: W
W
window menu, working with 116
X
Xcalibur Library Browser 4
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