Xcalibur 3.0 Qual Browser User Guide Version A

Xcalibur 3.0 Qual Browser User Guide Version A
Thermo
Xcalibur Qual Browser
Reviewing Qualitative Data
User Guide
Software Version 3.0
XCALI-97553 Revision A
June 2013
© 2013 Thermo Fisher Scientific Inc. All rights reserved.
Xcalibur and Q Exactive are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
Microsoft, Windows, 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.
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, June 2013
Software version: Xcalibur 3.0 and later
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
About This Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Understanding Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Base Peak. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Neutral Losses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Effect of Ionization Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Adduct Formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Effect of Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Analysis Modes for the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Full Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Selected Ion Monitoring (SIM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
MS/MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Using the Qual Browser Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Opening the Qual Browser Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Using the Qual Browser Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Displaying Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Customizing the Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Using the Info Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Working with Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Identifying Inactive, Active, and Pinned Cells . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Changing the Cell State. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Using the Cursor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Viewing Data Files in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Opening Single Raw Files in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Opening a Sequence Set of Raw Data Files in Qual Browser . . . . . . . . . . . . . 24
Opening and Viewing Result Files in Qual Browser . . . . . . . . . . . . . . . . . . . 26
Xcalibur Qualitative Analysis User Guide
iii
Contents
Working with Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Making a View Active . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Inserting and Deleting Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Adjusting Cell Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Amplifying Regions of a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Adding Text to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Adding Graphics to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Removing Text and Graphics from a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Opening or Changing Views in Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Scaling a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Managing Layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Creating and Saving a Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Opening and Applying a Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Displaying Layout Summary Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Using the Cell Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chromatogram Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Spectrum Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
iv
Chapter 3
Using Views Interactively . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Selecting a Point on a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Selecting a Point on a Plot: Example 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Selecting a Point on a Plot: Example 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Selecting a Point on a Plot: Example 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Selecting a One-Dimensional Range on a Plot. . . . . . . . . . . . . . . . . . . . . . . . . . 54
Selecting a One-Dimensional Range: Example 1 . . . . . . . . . . . . . . . . . . . . . . 56
Selecting a One-Dimensional Range: Example 2 . . . . . . . . . . . . . . . . . . . . . . 57
Selecting a Two-Dimensional Range on a Plot . . . . . . . . . . . . . . . . . . . . . . . . . 58
Using Scan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Scan Filter Format. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Applying a Scan Filter to a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Displaying Multiple Magnifications of a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Chapter 4
Working with a Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Inserting and Deleting Chromatogram Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Setting the Chromatogram Ranges and Processing Options . . . . . . . . . . . . . . . 73
Setting Chromatogram Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Setting Automatic Processing Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Adding Plots to a Chromatogram View with the Autofilter Command . . . . . . . 79
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
Contents
Setting the Chromatogram Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Setting the Chromatogram Axis Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Setting the Chromatogram Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Setting the Chromatogram Label Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Setting the Chromatogram Normalization Options. . . . . . . . . . . . . . . . . . . . 84
Setting the Chromatogram Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Detecting Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Automatic Detection of One Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Automatic Detection of All Plots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Manual Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Reviewing the Effect of Different Peak Detection Settings . . . . . . . . . . . . . . . . 90
Thermo Scientific
Chapter 5
Working with a Map View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Setting Map Ranges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Setting Map Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Setting the Map Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Setting the Map Axis Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Setting the Map Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Setting the Map Normalization Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Setting the Band Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Chapter 6
Working with a Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Setting Spectrum Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Setting the Spectrum Axis Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Setting the Spectrum Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Setting the Spectrum Label Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Setting the Spectrum Normalization Options . . . . . . . . . . . . . . . . . . . . . . . 110
Setting the Spectrum Style Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Setting Spectrum List Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Setting the Spectrum List Normalization Options . . . . . . . . . . . . . . . . . . . . 113
Setting the Spectrum List Style Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Setting Up Spectrum Plot Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Setting Spectrum Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Setting Spectrum Automatic Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Specifying Spectrum Composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Subtracting Background Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Xcalibur Qualitative Analysis User Guide
v
Contents
Appendix A Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
Qual Browser Menus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Actions Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Display Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Edit Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
File Menu– Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Grid Menu – Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Help Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Tools Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
View Menu – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Window Menu – Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Qual Browser Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Amplify Toolbar – Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Main Toolbar – Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Qual Browser Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Error Log View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Instrument Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Ion Map View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Map View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Sample Information View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Scan Filter View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Scan Header View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Spectrum List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Status Log View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Tune Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Qual Browser Info Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Cell Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Elemental Composition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
MSn Browser Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Avalon Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
ICIS Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Genesis Peak Detection Settings Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Result File Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Sequence Information Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Spectrum Simulation Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
vi
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
Contents
Qual Browser Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Add Graphics Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Add Text Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Amplify by Other Factor Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Average Filter Selection Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Cell Size Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
Choose Centroiding Algorithm Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . 224
Color Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Copy to Clipboard Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Display Options Dialog Box in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 226
Global Mass Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Heading Editor Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Peak Purity Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Print Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
Ranges Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Search Properties Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Select Isotopes Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
Specify Mixture for Simulation Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 289
Toolbars Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Subtract Background Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Qual Browser Result File Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .295
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
vii
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 your Thermo Scientific mass spectrometer so that you are
familiar with the basic features of the Xcalibur data system, such as the Home Page and the
Instrument Setup view.
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:
• Use the Qual Browser window of the Xcalibur data system to review raw data.
• Submit spectra to library searches.
For information about acquiring data with the Xcalibur data system, refer to the Xcalibur
Data Acquisition and Processing User Guide. For information about setting up personal user
libraries of reference spectra, refer to the Xcalibur Library Browser Creating and Searching Mass
Spectral Libraries User Guide.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
ix
Preface
Related Documentation
Thermo Fisher Scientific provides the following documentation for the Xcalibur data system:
• Xcalibur Quantitative Analysis Getting Started Guide
• Xcalibur Data Acquisition and Processing User Guide
• Xcalibur Quan Browser User Guide
• Xcalibur Qual Browser User Guide
• Xcalibur Library Browser User Guide
• XReport User Guide
• Help from within the software
To access the Xcalibur manual set from the computer taskbar, choose Start > All Programs
(or Programs) > Thermo Xcalibur > Manuals > Xcalibur.
To open the Help topic or section of interest, do the following:
• To open the Xcalibur Help to the Welcome topic, choose Help > Xcalibur Help from the
menu bar.
• To open the Xcalibur Help section for the Qual Browser window, choose Help > Qual
Browser Help from the menu bar in the Qual Browser window.
• To open the Help topic for a specific dialog box or page, click Help (button located at the
bottom of the page or dialog box) or press the F1 key.
x
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
Preface
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
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
xi
Preface
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
 To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
 To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
 To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
 To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[email protected]
xii
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
1
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 focuses on solving two analysis problems:
• The identification of unknown compounds
• Trace analysis and the confirmation of target compounds
Contents
• Understanding Spectra
• Analysis Modes for the Mass Spectrometer
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 mass-to-charge (m/z) ratios.
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 chemical substances, a mass spectrum can be a characteristic
molecular fingerprint.
These topics describe some common features of mass spectra:
• Base Peak
• Neutral Losses
• Effect of Ionization Modes
• Adduct Formation
• Effect of Isotopes
1
Thermo Scientific
In the majority of cases z=1 and the x axis becomes equivalent to mass, m.
Xcalibur Qualitative Analysis User Guide
1
1
Introduction
Understanding Spectra
Base Peak
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 data system can compare
spectra directly.
Figure 1 is an example of a simple library spectrum showing the fragmentation of acetone
C3H6O (molecular weight = 58 Da) in an electron ionization (EI) ion source. The most
abundant ions have been labeled with their mass-to-charge ratios. In this example, the
molecular ion (58 Da) is not the most abundant. The base peak is actually 43 Da because of
the acetyl ion.
Figure 1.
70 eV electron ionization (EI) mass spectrum of acetone
Neutral Losses
You can use fragmentation patterns like the pattern in Figure 1 to determine molecular
structure. For example, the neutral loss of 15 Da from the molecular ion of acetone indicates
the presence of a methyl group in the original molecule. A subsequent loss of 28 Da
corresponds to the loss of CO. Table 1 lists commonly observed neutral losses, measured by
the molecular weight of the compound. 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.
2
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
1 Introduction
Understanding Spectra
Table 1. Common neutral losses
Loss
Fragment
15
CH3
18
H2O
19
F
28
CO
29
C2H5 or CHO
35
Cl
46
NO2
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.
Effect of Ionization Modes
The ionization mode affects the spectrum characteristics of a compound.These topics describe
the common ionization modes for LC/MS (liquid chromatograph/mass spectrometer) and
GC/MS (gas chromatograph/mass spectrometer) instruments:
• 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 [M + H]+. These can be
analyzed in positive ion detection mode, giving an ion peak at the m/z value 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 mode as ion peaks at the
m/z value M–1.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
3
1
Introduction
Understanding Spectra
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 that use EI can produce virtually
identical spectra as long as the electron energy is the same.
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.
4
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
1 Introduction
Understanding Spectra
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).
Figure 2.
Mass spectrum showing sodium and acetonitrile adducts
Table 2 lists common adducts for the positive and negative ESI modes.
Table 2. Common adduct ions
Cationized adducts (positive mode)
]+
Anionized adducts (negative mode)
[M + NH4
M + 18
[M + OAc]–
M + 18
[M + Na]+
M + 23
[M + Na]–
M + 21
[M + CH3OH + H]+ M + 33
[M + Cl]–
M + 35
[M + K]+
[M + K]–
[M + CH3CN + H]
M + 39
+
M + 42
M + 37
–
[M + HCOO]
M + 59
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
5
1
Introduction
Analysis Modes for the Mass Spectrometer
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 for the Mass Spectrometer
A Thermo Scientific mass spectrometer has these analysis modes:
• Full Scan
• Selected Ion Monitoring (SIM)
• MS/MS
Full Scan
In full-scan operation, the MS detector scans repetitively over a wide mass range throughout
the analysis and sends the data to the data system computer.
With the Xcalibur data system, you can display the chromatograms (measured intensity versus
analysis time) for full-scan MS data in these ways (plot types):
• As a total ion current (TIC) chromatogram. A TIC chromatogram represents the
summed intensities of all the ions in the scanned mass range (mass spectrum) plotted
against the chromatographic retention time. Each peak in the TIC represents one or
more eluting compounds, which can be identified from the mass spectra recorded across
the peak.
• As a mass chromatogram for a range of masses within the scan range. Mass
chromatograms show the ion intensities of selected mass-to-charge ratios (m/z). The
Xcalibur data system extracts these mass spectra from each stored scan and plots them
against the analysis 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.
• As a base peak chromatogram. Base peak chromatograms show the ion intensities of the
most intense ions for each time point in the chromatogram.
The full-scan mode is suited to the identification of unknowns and can also be used for trace
analysis when sensitivity is not important.
6
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
1 Introduction
Analysis Modes for the Mass Spectrometer
Selected Ion Monitoring (SIM)
In the selected ion monitoring (SIM) mode, the MS detector monitors a limited number of
m/z values that are characteristic of a targeted compound or compounds. During an analytical
run, the mass analyzer repeatedly switches between the selected m/z values and monitors each
m/z value for a programmed dwell time before averaging the measured ion intensities and
moving on to the next value.
SIM generates mass chromatograms only of the monitored m/z values, not complete mass
spectra as in the full-scan mode. Without a complete mass spectrum, you cannot perform a
library search to identify an unknown.
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 an MS/MS experiment, an ion from the mass spectrum is selected for fragmentation while
all other masses are discarded. The selected ion, called a precursor (parent) ion, is then
collided with a neutral background gas. As a result of the collisions, the precursor ion is
broken into fragments called product ions. An ion trap mass spectrometer (a mass
spectrometer with an ion trap type of mass analyzer) can perform additional stages of MS
(called MSn), up to MS10.
The MS detector can monitor the product ions in either the full-scan mode or the SIM mode.
When you set up the MS detector to monitor a specific product ion of a specific precursor
(parent) ion, the scan type is called selective reaction monitoring (SRM).
You can create your own libraries of full-scan MS/MS data to use for matching.
You can display the chromatograms for full-scan MS/MS data in these plot types: TIC, mass
range, base peak, or neutral fragment. With the neutral fragment plot type, you must specify
the neutral fragment.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
7
2
Using the Qual Browser Window
Thermo Xcalibur Qual Browser is a powerful and versatile utility for viewing chromatograms
and spectra from raw files or result files.
Note Raw files contain unprocessed data and result files contain data that has been
processed with a processing method. When you view raw files in Qual Browser, the data
system applies default integration settings to the chromatograms.
For information about the Qual Browser window, toolbars, menus, dialog boxes, and so on,
see “Qual Browser” on page 123.
These procedures describe how to use some of the basic features of the Qual Browser window.
Contents
• Opening the Qual Browser Window
• Using the Qual Browser Toolbars
• Using the Info Bar
• Working with Windows
• Identifying Inactive, Active, and Pinned Cells
• Changing the Cell State
• Using the Cursor
• Viewing Data Files in Qual Browser
• Working with Cells
• Managing Layouts
• Using the Cell Information Page
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
9
2
Using the Qual Browser Window
Opening the Qual Browser Window
Opening the Qual Browser Window
You can open the Qual Browser window from the Home Page, Processing Setup, and Quan
Browser windows.
 To open the Qual Browser window
Depending where you are in the Xcalibur data system, do one of the following:
• From the Home Page – Road Map view, click the Qual Browser icon,
.
• From any view in the Home Page window, choose GoTo > Qual Browser
from the menu bar.
• From the Home Page, Processing Setup, and Quan Browser windows, choose GoTo >
Qual Browser from the menu bar.
• From the Instrument Setup window, click the Home Page icon,
Then in the Home Page window, choose GoTo > Qual Browser.
, in the toolbar.
Figure 3 shows the Info bar on the left side of the Qual Browser window and a single data
window with two cells on the right side of the Qual Browser window. The top cell in the data
window contains a chromatogram view with a TIC chromatogram. The bottom cell contains
a spectrum view with a mass spectrum extracted from the 1.94 minute time point.
Figure 3.
Qual Browser window
Info Bar
Pin
Chromatogram
view
Info
pages
Spectrum
view
10
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Using the Qual Browser Toolbars
The tasks that you can carry out in the Qual Browser window include the following:
• Generate a variety of chromatogram plots and determine suitable peak detection
parameters for subsequent automated analyses that use a processing method.
• Optimize the spectrum for the apex of a chromatographic peak by averaging the scans
across the peak apex and subtracting other scans averaged from the baseline on either side
of the peak.
• Determine the elemental composition of the peaks in the mass 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 a qualitative data analysis and the library results.
Using the Qual Browser Toolbars
In the Qual Browser window, the buttons (for typical Windows features such as Open File
and Print) and icons are divided into two toolbars: Main and Amplify.
Use the icons and buttons on the Main toolbar to load, save, and print files, and to scale plots,
manipulate cells, detect peaks, change views, and arrange windows (Figure 4).
Figure 4.
Main toolbar with the default icons and buttons displayed
File buttons
Edit buttons
Display icons
View icons
Grid icons
Actions icons
Help
button
Use the icons on the Amplify toolbar to adjust the normalization in specific sections of a
chromatogram, spectrum, or map plot (Figure 5).
Figure 5.
Thermo Scientific
Amplify toolbar
Xcalibur Qualitative Analysis User Guide
11
2
Using the Qual Browser Window
Using the Qual Browser Toolbars
By default these two toolbars 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 by
using the Toolbars dialog box (see Figure 6). You can also use the Toolbars dialog box for these
tasks:
• Viewing or hiding the display of ToolTips
• Choosing between large or small icons in the toolbar
To open the Toolbar dialog box, choose View > Toolbars.
Figure 6.
Toolbars dialog box
For more information about displaying and customizing the toolbars in the Qual Browser
window, see these topics:
• Displaying Toolbars
• Customizing the Toolbar
Displaying Toolbars
Use the Toolbars dialog box to display or hide the Main, Amplify, or both of these Qual
Browser toolbars. You can also use the Toolbars dialog box to turn off the tooltips and to
enlarge the toolbar icons and buttons.
 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.
12
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Using the Qual Browser Toolbars
4. Select a button size option.
• To display large buttons (icons) in the toolbar, select the Large Buttons check box.
• To display small buttons (icons) in 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.
You can then launch any added program by double-clicking the added Tool menu command.
Application programs have an .exe extension.
• Adding, Removing, and Repositioning Standard Toolbar Buttons
• Adding a Program to the Tools Menu
• Removing a Program from the Tools Menu
Adding, Removing, and Repositioning Standard Toolbar Buttons
The default toolbar in the Qual Browser window does not display all of the available toolbar
buttons (and icons).
 To add or remove buttons (and icons) in the toolbar
1. Choose View > Customize Toolbar.
The Customize Toolbar dialog box opens (Figure 7). The toolbar commands (buttons or
icons) are organized into categories. When you select a category in the Categories list, a
different set of commands (buttons or icons) appears in the Commands list.
Figure 7.
Customize Toolbar dialog box
2. To add a button (or icon), do the following:
a. In the Categories list, select the appropriate category.
The commands (buttons) for the selected category appear in the Commands list.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
13
2
Using the Qual Browser Window
Using the Qual Browser Toolbars
b. In the Commands list, select the command (button) that you want to add to the
toolbar and drag it onto the toolbar.
When the cursor reaches the toolbar, a vertical bar and a + sign appear.
c. Release the mouse button when the vertical bar is in the appropriate location.
3. To remove a button (icon), drag it from the toolbar and into the Commands list.
4. Click Close to accept the changes and close the Customize Toolbar dialog box.
 To reposition a button in the Main toolbar
1. Open the Customize Toolbar dialog box.
2. Drag the button (or icon) in the Main toolbar to its new position.
Tip 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.
Adding a Program to the Tools Menu
 To add a program to the Tools menu
1. Choose Tools > Add Tools from the Qual Browser window or the 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.
14
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Using the Qual Browser Toolbars
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 data system adds the filename without the extension at the bottom of the Menu
Contents box and the Menu Text box. The 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 data system 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 a Program from the Tools Menu
For information about the parameters in the Add Programs To Tool Menu dialog box, see
“Add Programs to Tool Menu Dialog Box” on page 402.
 To remove a program from the Tools 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
15
2
Using the Qual Browser Window
Using the Info Bar
Using the Info Bar
The Info Bar initially is located on the left side of the Qual Browser window (see Figure 3 on
page 10).
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.
16
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Working with Windows
Working with Windows
The Qual Browser main window displays raw files, interactive library search results, and
qualitative processing. You can view raw files in the same window 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, with 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 view.
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 42.
You can apply various automatic processing options as follows.
Thermo Scientific
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
Xcalibur Qualitative Analysis User Guide
17
2
Using the Qual Browser Window
Identifying Inactive, Active, and Pinned Cells
Identifying Inactive, Active, and Pinned Cells
There are three hierarchical states for a cell in the grid: active and pinned, active, and inactive.
In the cell grid, one cell is active, while all of the other cells are inactive. When you pin the
active cell, it remains active when you click another cell in the grid. If no cell is pinned, the
active cell is the last cell acted on by a mouse action.
Table 3 describes the three cell states.
Table 3. Cell states
Cell state
Active and pinned
Description
You can identify the active and pinned cell by its light gray border and the green
background behind its pinned pin icon. A pinned cell is an active cell that cannot be
made inactive by clicking another cell. Instead, actions performed in the inactive cells
affect the pinned cell.
Green background and
pinned pin
Gray border
Active
You can identify the active (but unpinned) cell by its gray border and the light gray
background behind its unpinned pin icon. Menu commands, toolbar buttons (icons),
and cursor actions affect the active cell.
Light gray background
and unpinned pin
Gray border
Inactive
You can identify inactive cells by the absence of a gray border and the dark gray
background behind its unpinned pin icon. Menu commands, toolbar buttons (icons),
and cursor actions do not affect inactive cells.
Dark gray background
and unpinned pin
18
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Changing the Cell State
Changing the Cell State
A cell can be inactive, active, or active and pinned (see “Identifying Inactive, Active, and
Pinned Cells” on page 18).
 To make a cell active or active and pinned
Tip Clicking a cell’s pin icon is the only action required to make a cell active and
pinned. Making a cell active (but unpinned) can take up to two actions. If another
cell in the grid is active and pinned, you must first unpin it, and then click the target
cell to make it active (but unpinned).
Because you can work both directly and interactively with an active and pinned cell,
there is no advantage to making a cell active rather than active and pinned. So for
practical reasons, make the cell that you want to modify an active and pinned cell by
clicking its pin icon.
Do one of the following:
• If the current active view is pinned, click its pin icon to unpin it. Then, click
anywhere in the cell that you want to make active.
The selected cell is active (but unpinned). You can modify its contents by using a
menu bar command, shortcut menu command, or toolbar button (icon).
–or–
• Click the pin icon of the cell that you want to make active.
The selected cell is active and pinned. You can modify its contents by using a menu
bar command, shortcut menu command, or toolbar button (icon). You can also
modify its contents by working interactively in other views.
 To access the active cell’s shortcut menu
Right-click in the active cell.
 To select a plot in a multi-plot cell
When a chromatogram or spectrum view contains more than one plot, menu operations
target the active plot, which is indicated by a shaded background.
To select an individual plot in a multi-plot cell, click it.
For more information about working interactively with views, see the next topic and “Using
Views Interactively” on page 49.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
19
2
Using the Qual Browser Window
Using the Cursor
Using the Cursor
Within the chromatogram and spectrum views, use the cursor in three ways:
• To select a point on the view, 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.
When you place the cursor 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. For example,
in a spectrum view the status bar shows the cursor position in terms of the mass-to-charge
ratio and intensity.
The effect of clicking or dragging the cursor in a view depends on the cell state and whether
another cell in the grid is pinned.
Cursor actions in an active cell (or active and pinned cell) scale the view according to the
dimensions of the dragged line or area (see Table 4).
Table 4. Effect of cursor actions in an active or active and pinned cell
Cursor action in active
or active and pinned cell
Effect
Drag parallel to x axis
Rescale graph showing selected x-axis range only, same y-axis range. The y-axis
range might rescale depending on the selected Normalization display options.
Drag parallel to y axis
Rescale graph showing selected y-axis range only, same x-axis range.
Drag diagonally over x and y axes
Rescale graph showing both the selected x- and y-axis ranges.
20
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Using the Cursor
When the grid contains an active and pinned cell, the same actions in an inactive cell have a
very different effect. Rather than making the inactive cell active, the action affects the active
and pinned cell (see Table 5). Qual Browser displays a plot or information in the active and
pinned cell using data appropriate to the selected point, range, or ranges.
Table 5. Effect of a cursor action in an inactive cell on the active and pinned cell
Active and
pinned cell
Inactive cell
Cursor action in inactive cell
Effect on active and pinned cell
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 198.4–299.7.
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 100–200 with a
m/z 100 to 200.
time range of 0.5 to 1 min.
The preceding table illustrates only a few of the possible effects of the interactive behavior in
Qual Browser. To get expected results, remember these actions:
• Pin the target view to keep it active.
• Within an active cell, use the cursor to rescale the view.
• Use the coordinates in the Status bar to select ranges precisely.
• To correct mistakes, choose Edit > Undo.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
21
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
Viewing Data Files in Qual Browser
View data files in Qual Browser by following any of these procedures:
• Opening Single Raw Files in Qual Browser
• Opening a Sequence Set of Raw Data Files in Qual Browser.
• Opening and Viewing Result Files in Qual Browser.
Raw files are unprocessed data files from a single injection or a sequence set of injections. Raw
files have a .raw file extension and sequence files have a seq file extension. Result files are the
product of processing raw data files with a processing method. Result files have an .rst file
extension. After you run a sequence and acquire data files, the data files are associated with the
sequence.
Opening Single Raw Files in Qual Browser
 To open a single raw data file
1. Choose File > Open or click
in the toolbar.
The Open Raw File dialog box opens (Figure 8).
Figure 8.
22
Xcalibur Qualitative Analysis User Guide
Open Raw File dialog box
Thermo Scientific
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
2. Browse to the file that you want to open.
3. Select a Replace option as follows:
• 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 as follows:
• 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
23
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
Opening a Sequence Set of Raw Data Files in Qual Browser
After you acquire a set of data files with a sequence, the data files are associated with the
sequence.
 To open a sequence file containing raw data files in the Qual Browser window
1. Choose File > Open Sequence or click
in the toolbar.
The Open Sequence dialog box opens.
2. Browse to the sequence (.sld) that you want to open and click Open.
The list of data files associated with the sequence appears on the Sequence Information
page of the Info Bar (see Figure 9).
Figure 9.
Sequence Information page showing the shortcut menu
Sequence
Information
page
24
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
 To display one or more data files in the Qual Browser window
Do one of the following:
• To replace the data in the current window, double-click the name of the file on the
Sequence Information 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.
 To open the result file that is associated with the selected raw data file
On the Sequence Information page of the Info Bar, right-click the data file name and
choose Open Result File.
 To view the sample properties for the raw data file
1. On the Sequence Information page of the Info Bar, right-click the data file name and
choose Properties.
The Sample Properties dialog box opens (Figure 10), showing basic information about
the selected sample. This information includes the row, filename, sample ID, name,
sample type, and result filename.
Figure 10. Sample Properties dialog box
When the Sample Properties dialog box is unpinned, it closes when you click outside
of it.
2. To keep the Sample Properties dialog box open while you review its contents, click the
pin icon.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
25
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
3. To close the pinned Sample Properties dialog box, do one of the following:
• Click the close box icon.
–or–
• Unpin the dialog box by clicking the pin icon again. Then click anywhere outside the
dialog box.
Opening and Viewing Result Files in Qual Browser
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 11). 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 “Working with a Chromatogram View” on page 71
and “Working with a Spectrum View” on page 105, respectively.
 To open a result file and view the information
1. Click
in the toolbar or choose File > Open Result File.
The Open Result file dialog box opens.
2. Browse to select the result file (.rst) that you want to open.
3. Click Open.
 To open a result file for a file in an opened sequence
Right-click the filename on the Sequence Information 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 data system grays the
menu command.
26
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
Figure 11 shows the Information page for a result file.
Figure 11. Result File view showing the Result File Information page in the Info Bar
Chromatogram
view
Spectrum
view
Information page of the Info Bar
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 Xcalibur 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.
 To view result file information
In the Info Bar, click the Result File Information tab
Information page.
to open the Result File
This page shows the following basic information about all detected peaks in the result file:
• Retention times at the peak start (left), peak apex, and peak end (right)
• The peak area and height
For information about the peak, including flags, open the Peak Properties dialog box.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
27
2
Using the Qual Browser Window
Viewing Data Files in Qual Browser
 To view the peak properties
1. Right-click the peak identifier in the Peak list.
2. Choose Properties from the shortcut menu.
The Peak Properties dialog box opens (Figure 12).
Figure 12. Peak Properties dialog box
The unpinned Peak Properties dialog box closes when you click outside of it.
3. To keep the Peak Properties dialog box open while you review its content, click the
pin icon.
4. To close the pinned Peak Properties dialog box, do one of the following:
• Click the close box icon.
–or–
• Unpin the dialog box by clicking the pin icon again. Then click anywhere outside the
dialog box.
28
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
Working with Cells
Qual Browser displays chromatograms and spectra in a grid of cells. These topics describe the
commands used to manipulate cells:
• Making a View Active
• Inserting 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
Note You can work directly within an active but unpinned cell. However, because there is
no advantage to making a cell active rather than active and pinned, the procedures in this
section instruct you to select the active cell by clicking its pin icon.
Making a View Active
The active cell contains the active view. There can only be one active view at a time. The
active view can be active (but unpinned) or active and pinned.
Tip There is no advantage to making cells active rather than active and pinned. So to
make a cell active, click its pin icon. The cell becomes active and pinned.
 To make a view active or active and pinned
Do one of the following:
• If the current active view is pinned, click its pin icon to unpin it. Then, click
anywhere in the cell that you want to make active.
The selected cell is active (but unpinned). You can modify its contents by using a
menu bar command, shortcut menu command, or toolbar button (icon).
–or–
• Click the pin icon of the cell that you want to make active.
The selected cell is active and pinned. You can modify its contents by using a menu
bar command, shortcut menu command, or toolbar button (icon). You can also
modify its contents by working interactively in other views.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
29
2
Using the Qual Browser Window
Working with Cells
 To make one of the cell plots active
Click the plot within the view.
To show the plot is active, the data system shades the background of the plot.
Figure 13 shows a cell with a chromatogram view and two plots. The chromatogram and
spectrum views can contain up to eight plots.
Figure 13. Cell with two chromatogram plots (TIC and base peak)
 To pin an active but unpinned cell
Click its pin icon.
Inserting and Deleting Cells
When a raw file is open, Qual Browser displays one or more cells according to the selected
layout.
Note In the following procedure, the active cell does not have to be pinned.
 To insert 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 pin icon for the active (and pinned) cell changes from
30
Xcalibur Qualitative Analysis User Guide
to
.
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
2. To add additional cells, select from these options:
in 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 data
system 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
in the toolbar or
choose Grid > Insert Cells > Right. If the active cell is in a column of cells, the data
system 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
in the toolbar or choose Grid > Insert Cells > Above. If the active cell is in a row of
cells, the data system inserts a duplicate row of cells above the row containing the
active cell.
• To insert a duplicate row of cells below the row containing the active cell, click
in the toolbar or choose Grid > Insert Cells > Below. If the active cell is in a row of
cells, the data system 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.
in the toolbar or
in the toolbar or
in the toolbar or choose
Note As you delete excess cells, the cell size of the remaining cells becomes larger.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
31
2
Using the Qual Browser Window
Working with Cells
Adjusting Cell Size
Use the Cell Size dialog box to adjust the size of the active cell in the grid. 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.
 To adjust the cell size
1. To make a cell the active and pinned cell or the active cell in the Qual Browser window so
that you can adjust its size, click the pin in the upper right corner of the cell or click the
cell if no other cell is pinned.
2. Choose Grid > Cell Size.
The Cell Size Dialog Box opens (Figure 14).
Figure 14. 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.
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.
32
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
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 (icons) 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 data
system 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 data system amplifies the region, places a label above the
amplified region like the following: ------x5------, and displays the original cursor.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
33
2
Using the Qual Browser Window
Working with Cells
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 in Qual Browser.
For information about the Add Text dialog box, see “Add Text Dialog Box” on page 216.
 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 (Figure 15), do one of the following:
• From the menu bar, choose Display > Annotate > Add Text.
–or–
• Click
in the toolbar.
Figure 15. Add Text dialog box
3. Type one or more lines of annotation text in the Annotation Text text box.
Press the ENTER key to enter multiple lines.
34
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
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), select the Left option.
• To align lines in the center (center justification), select the Center option.
• To align lines to the right (right justification), select the Right option.
The data system 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, select the Just Above Graph option.
• To place the text above where you position the cursor pointer on the plot, select the
Above Marked Position option.
• To place the text below where you position the cursor pointer on the plot, select the
Below Marked Position option.
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, select the Left
option.
• To place the text in the center of the cursor pointer position on the graph, select the
Center option.
• To place the text to the right of the cursor pointer position on the graph, select the
Right option.
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.
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 data system saves
your previous text and settings.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
35
2
Using the Qual Browser Window
Working with Cells
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.
Use the Add Graphics dialog box to specify the appearance of these graphic objects. For more
information about the Add Graphics dialog box, see “Add Text Dialog Box” on page 216.
 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. To specify the appearance of the graphic object, do the following:
a. Open the Add Graphics dialog box (Figure 16) by doing one of the following:
• Click the Add Graphics icon,
, in the toolbar
–or–
• Choose Display > Annotate > Add Graphics from the menu bar.
Figure 16. Add Graphics dialog box
b. To specify the style of the graphic to be added, select one of the following options:
• To add a horizontal line, select the Horizontal Line option. Go to step 2c.
• To add a vertical line, select the Vertical Line option. Go to step 2c.
• To add a diagonal line, select the Diagonal Line option. Go to step 2c.
• To add a rectangular box, select the Box option. Go to step 2c.
36
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
• To add a filled box, select the Filled Box option.
–
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 2d.
Behind graph
Not behind graph
c. 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.
d. 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.
e. To close the Add Graphics dialog box, click OK so that you can draw the graphic on
the plot.
3. To draw the graphic on the plot, do one of the following:
• 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.
• 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
37
2
Using the Qual Browser Window
Working with Cells
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 in Qual Browser.
 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. Do one of the following:
• To select and remove previously added annotation text or graphics, go to step 3.
• To remove all previously added annotation text and graphics from a plot, go to step 4.
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
38
Xcalibur Qualitative Analysis User Guide
or choose
in the toolbar or choose Edit > Undo.
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
Opening or Changing Views in Cells
A cell can contain one of eleven views.
 To open views in cells
1. To choose a cell to hold the view, click the pin icon of the cell.
The Xcalibur data system changes the cell pin icon from
to
to indicate that it is
the active and pinned cell. 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 6.
 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
selected (see Table 6 for options).
Table 6 lists the eleven possible views and how to open them.
Table 6. Opening views in cells (Sheet 1 of 2)
View
Chromatogram View
Select one of these options to open the view
• Choose View > Chromatogram.
• Right-click the cell and choose View > Chromatogram from the shortcut menu.
• Click
Spectrum View
in the toolbar.
• Choose View > Spectrum.
• Right-click the cell and choose View > Spectrum from the shortcut menu.
• Click
Map View
in the toolbar.
• Choose View > Map.
• Right-click the cell and choose View > Map from the shortcut menu.
• Click
Spectrum List View
in the toolbar.
• Choose View > Spectrum List.
• Right-click the cell and choose View > Spectrum List from the shortcut menu.
• Click
Thermo Scientific
in the toolbar.
Xcalibur Qualitative Analysis User Guide
39
2
Using the Qual Browser Window
Working with Cells
Table 6. Opening views in cells (Sheet 2 of 2)
View
Select one of these options to open the view
Scan Header View
• Choose View > Scan Header.
• Right-click the cell and choose View > Scan Header from the shortcut menu.
• Click
Scan Filter View
in the toolbar.
• Choose View > Scan Filters.
• Right-click the cell and choose View > Scan Filters from the shortcut menu.
• Click
Tune Method View
in 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
in 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
in 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
in 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
in the toolbar.
• Choose View > Report > Error Log.
• Right-click the cell and choose View > Report > Error Log from the shortcut
menu.
• Click
40
Xcalibur Qualitative Analysis User Guide
in the toolbar.
Thermo Scientific
2
Using the Qual Browser Window
Working with Cells
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 (see Table 7).
Table 7. Zoom and Pan menu commands
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 icon in the toolbar to pan across a zoomed plot by dragging it to the
left or right with the mouse.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
41
2
Using the Qual Browser Window
Managing Layouts
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 and Applying a Layout
• Displaying Layout Summary Information
Creating and Saving a Layout
You can create and save customized layouts for the Qual Browser window.
 To create and save a layout
1. To create the desired arrangement of cells for the data displays, choose Grid > Insert
Cells to insert cells and Grid > Delete to delete cells.
2. To create the desired arrangement of views, do the following for each cell:
a. Pin the cell.
b. Right-click the pinned cell and choose View > Desired View from the shortcut
menu. Or, choose the view from the list of views in the View menu
3. To add multiple plots to a cell and change the arrangement of the plots, do the following:
a. Pin the cell.
b. Right-click the plot of interest and choose one of the following:
• To insert a plot below the selected plot, choose Plot > Insert from the shortcut
menu.
• To delete the selected plot, choose Plot > Delete from the shortcut menu.
• To move the selected plot, choose Plot > Move Up or Plot > Move Down from
the shortcut menu.
42
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Managing Layouts
You can change the display options for a chromatogram, spectrum, map, ion map, or
spectrum list view.
4. To select the display options for a cell, do the following:
a. Pin the cell.
b. Right-click the pinned cell and choose Display > Display Options from the shortcut
menu.
The Display Options dialog box opens. For information about the display options for
the selected view, see “Display Options Dialog Box in Qual Browser” on page 226.
5. To save the layout, do one of the following:
• To save a modified layout with the current name, click the Save icon,
toolbar or choose File > Layout > Save from the menu bar.
, in the
• To assign a file name and save a new layout, do the following:
a. Click the Save As icon,
from the menu bar.
, in the toolbar or choose File > Layout > Save As
The Save Layout dialog box opens.
b. In the Save In box, browse to the folder where you want to store the layout file.
c. In the File Name box, type a name for the file. Then, click Save.
• To save the current layout as the new default layout, click the Save As Default
, in the toolbar or choose File > Layout > Save As Default.
Layout icon,
For additional information, see “Using Views Interactively” on page 49.
Opening and Applying a Layout
You can open and apply a custom layout file or apply the default layout file to the current
Qual Browser window.
 To open and apply a custom layout
1. To open a custom layout file, do one of the following:
• Choose File > Layout > Apply from the menu bar.
–or–
• Click the Apply Layout icon,
, in the toolbar.
The Open Layout File dialog box opens.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
43
2
Using the Qual Browser Window
Managing Layouts
2. Browse to the folder where you stored the layout file and select the layout file (.lyt) of
interest.
3. Click Open.
The data system applies the stored layout to the current raw file.
 To apply the default layout
Do one of the following:
• Choose File > Layout > Apply Default from the menu bar.
–or–
• Click the Apply Default Layout icon,
, in the toolbar.
 To restore the factory layout
From the menu bar, choose File > Layout > Restore Factory Layout.
Displaying Layout Summary Information
Choose File > Layout > Summary Info to display this file’s information.
44
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
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
(Figure 17). Its contents depends on whether the plot is a chromatogram or a spectrum.
Figure 17. Cell Information page showing chromatogram cell information
Cell information page for the chromatogram cell
 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 the Chromatogram Ranges and Processing
Options” on page 73 and “Setting Up Spectrum Plot Ranges” on page 115). 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
45
2
Using the Qual Browser Window
Using the Cell Information Page
These topics describe the chromatogram and spectrum information pages:
• Chromatogram Information
• Spectrum Information
Chromatogram Information
For a chromatogram plot (see Figure 18), 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 18. Cell Information for a chromatogram plot
46
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
2
Using the Qual Browser Window
Using the Cell Information Page
Spectrum Information
For a spectrum plot, the Cell Information page shows these icons (Figure 19).
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 19. Cell Information for a spectrum plot
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
47
3
Using Views Interactively
These procedures describe how to work interactively with the Qual Browser views.
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
• Scan Filter Format
• Applying a Scan Filter to a Plot
• Displaying Multiple Magnifications of a Plot
Use the Qual Browser window to open a raw file (.raw), a sequence (.sld), or a result file (.rst).
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.
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. Many of Qual Browser's features are not available for use with a result
file because the raw file is not available for processing.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
49
3
Using Views Interactively
Selecting a Point on a Plot
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.
Selecting a Point on a Plot
The following procedure describes how to work interactively with an inactive view and an
active and pinned view to display a point of interest in the active and pinned view. For
example, you can use this procedure to display the spectrum in the active and pinned view for
a particular time point in a chromatogram (inactive view).
Note Working interactively with views requires pinning the view that you want to modify.
 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 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.
50
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3
Using Views Interactively
Selecting a Point on a Plot
3. To select a point in an inactive view to apply to the active and pinned view (or the active
plot in an active and pinned view), click a point in one of the inactive views.
A red vertical marker, , indicates the point selected.
When you click any other cell, the red vertical marker disappears.
You can apply these coordinate values from an inactive chromatogram view to the
following active views:
• Spectrum: Scan Number and
Retention Time
• Tune Method: Segment Number
• Map: Retention Time and Mass
Range
• Instrument Method: No effect
• Spectrum List: Scan Number and
Retention Time
• Sample Information: No effect
• Scan Header: Scan Number and
Retention Time
• Status Log: Scan Number and Status
Log Time (RT)
• Scan Filter: Scan Number
• Error Log: No effect
See these examples of selecting a point on a plot:
• Selecting a Point on a Plot: Example 1
• Selecting a Point on a Plot: Example 2
• Selecting a Point on a Plot: Example 3
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
51
3
Using Views Interactively
Selecting a Point on a Plot
Selecting a Point on a Plot: Example 1
In the following example, the spectrum view is the active and pinned view and the
chromatogram view is the inactive view.
• Active and pinned view: spectrum
• Inactive view: chromatogram
When you click the time point at 1.98 minutes in the inactive chromatogram view, the active
spectrum view displays the mass spectrum for this time point.
Inactive
chromatogram view
Active and pinned
spectrum view
52
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3
Using Views Interactively
Selecting a Point on a Plot
Selecting a Point on a Plot: Example 2
In the following example, the status log view is the pinned view and the chromatogram view is
the inactive view.
• Pinned view: status log
• Inactive view: chromatogram
When you click the time point at 3.16 minutes in the inactive chromatogram view, the
pinned status log view displays the status log for this time point in the run.
Selecting a Point on a Plot: Example 3
In the following example, the scan filter view is the pinned view and the chromatogram view
is the inactive view.
• Pinned view: scan filter
• Inactive view: chromatogram
When you click the time point at 1.36 minutes in the inactive chromatogram view, the active
scan filter view displays the scan filter used at this time point.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
53
3
Using Views Interactively
Selecting a One-Dimensional Range on a Plot
Selecting a One-Dimensional Range on a Plot
You can select a one-dimensional range in an active plot by dragging the cursor horizontally or
vertically across the plot. However, to interactively change the range displayed in one view by
selecting a point or range in another view, you must pin the view that you want to modify.
 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, and then drag the
cursor to the end of the range.
Figure 20 and Figure 21 demonstrate this selection process.
Figure 20. Position the cross-hair
54
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3 Using Views Interactively
Selecting a One-Dimensional Range on a Plot
Figure 21. Drag the cursor
A black horizontal line defines the selection range. When you release the mouse button,
the line disappears and the data system replots the active plot using the new range
(see Figure 22).
Use this procedure with the x axis or y axis of the chromatogram, spectrum, and map
views.
Figure 22. Xcalibur data system redraws the active plot
3. To use the cursor to apply a different range of values for the active plot, do the following:
a. Pin the active plot so that it remains active when you click another cell.
b. Drag the cursor across an axis of a plot in an inactive view to apply the selected range
to the active and pinned cell.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
55
3
Using Views Interactively
Selecting a One-Dimensional Range on a Plot
See these examples of selecting a one-dimensional range on a plot:
• Selecting a One-Dimensional Range: Example 1
• Selecting a One-Dimensional Range: Example 2
Selecting a One-Dimensional Range: Example 1
In the following example, the spectrum view is the pinned view and the chromatogram view is
the inactive view.
• Pinned view: spectrum
• Inactive view: chromatogram
When you drag the cursor across a peak of interest in the inactive chromatogram view,
a red horizontal marker (
) defines the selection range, and the pinned spectrum view
displays a spectrum that is the average of the scans during the selected time range of
1.78 to 2.35 minutes.
Selected time range
of 1.78 to 2.35 minutes
Averaged spectrum of the
scans from scan #150–201.
56
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3 Using Views Interactively
Selecting a One-Dimensional Range on a Plot
Selecting a One-Dimensional Range: Example 2
In the following example, the chromatogram view is the active and pinned view and the
spectrum view is the inactive view.
• Active and pinned view: chromatogram
• Inactive view: spectrum
 To add a plot to the chromatogram view
1. Click the Add or Replace Plot icon,
, on the toolbar.
2. In the inactive spectrum view, drag the cursor from m/z 198.4 through 299.7.
In the inactive spectrum view, a red horizontal marker (
) defines the selection
range. In the pinned chromatogram view, a second chromatogram appears below the
original chromatogram.
In the following figure, the chromatogram for the selected mass range appears below the
original TIC chromatogram.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
57
3
Using Views Interactively
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 data system 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 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 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, and then drag the cursor to
the opposite corner of the area. To include the axis, extend the selected area over the axis.
Figure 23. Position the cross-hair
58
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3 Using Views Interactively
Selecting a Two-Dimensional Range on a Plot
Figure 24. Drag the cursor to define the area of interest
The data system displays a black outline to indicate the area selected. When you release
the mouse button, the data system replots the selected area of the active view.
Use this procedure with the x axis or y axis of the chromatogram, spectrum, and map
views.
Figure 25. Xcalibur data system replots the area of interest in the active plot
3. If you do not obtain the desired result, click the Zoom Reset icon,
restore the active plot, and then repeat step 2.
Thermo Scientific
, in the toolbar to
Xcalibur Qualitative Analysis User Guide
59
3
Using Views Interactively
Using Scan Filters
Using Scan Filters
You can use a scan filter to specify that data 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 Setup, Instrument Setup, Quan Browser, and Qual Browser
windows. You can either select a scan filter from the list of filters that the data system creates
from the instrument method settings for your mass spectrometer, 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 (Scan Filter list or Filter list) in one of the following windows:
Instrument Setup, Qual Browser, Processing Setup, Quan Browser, or Home Page.
2. Check the current filter.
The data system displays the current scan filter in the Scan Filter list (see Figure 26). To
view other scan filters available in the raw file, click the down arrow to display the list.
Figure 26. Example of the scan filter list (Qual Browser window)
60
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3
Using Views Interactively
Using Scan Filters
3. Do one of the following:
• To edit the current scan filter, type the change in the Scan Filter box and go to step 6.
• To modify a different filter in the list, go to step 4.
• To manually enter a new scan filter, go to step 5.
4. 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.
Edit the selected scan filter to create a new scan filter, as required. Go to step 6.
5. Type a new scan filter in the Scan Filter list.
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 masses
• Product mass range
• TurboScan
• Constant neutral gain
• Constant neutral loss
6. Continue to enter other settings.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
61
3
Using Views Interactively
Scan Filter Format
Scan Filter Format
The data system 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 8. Scan filter format (Sheet 1 of 3)
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
Source CID
sid, !sid
Include Source CID scans, Exclude Source CID scans
(Source CID scans are scans for ions produced by source
induced dissociation.)
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
62
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3
Using Views Interactively
Scan Filter Format
Table 8. Scan filter format (Sheet 2 of 3)
Feature
Option
Interpretation
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.
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, AME
Include accurate mass scans, Exclude accurate mass scans,
Include accurate mass internal, Include accurate mass external
Ultra
u, !u
Include ultra scans, Exclude ultra scans
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
63
3
Using Views Interactively
Scan Filter Format
Table 8. Scan filter format (Sheet 3 of 3)
Feature
Option
Interpretation
Sector
BSCAN
Include magnetic sector scans
ESCAN
Include electric sector scans
LOCK
lock, !lock
Include lock scans, Exclude lock scans
Multiplex
msx, !msx
Include multiplexing scans, Exclude multiplexing scans
Synchronous
Precursor Selection
sps
Rapid scan rate
r
rapid scan rate ion trap scan
Electron Capture
Dissociation
ecd, !ecd
Include electron capture dissociation, Exclude electron capture
dissociation
Multi Photo
Dissociation
mpd, !mpd
Include photo dissociation, Exclude photo dissociation
Electron Transfer
Dissociation
etd, !etd
Include electron transfer dissociation scans, Exclude electron
transfer dissociation scans
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
(Source SID scans are surface induced scans.)
Free Region
64
ffr1, ffr2
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3
Using Views Interactively
Applying a Scan Filter to a Plot
Applying a Scan Filter to a Plot
This procedure demonstrates the interactive use of a scan filter view. For the routine
application of scan filters to the 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.
 To familiarize yourself with the scan filter view
1. Open the chromatogram view by clicking the View Chromatogram icon,
toolbar or by choosing View > Chromatogram.
, in the
The Chromatogram View appears in the cell.
2. To display the entire time range for the chromatogram, choose
Display > Zoom > Display All.
3. To display the entire chromatogram, choose Display > Zoom > Reset.
4. If a filter has been applied to the chromatogram view, remove it as follows:
a. Choose Display > Ranges.
The Chromatogram Ranges Dialog Box opens.
b. Select the scan filter in the Scan Filter box.
c. Press the DELETE key and then click OK to remove the filter.
5. To open the scan filter view, select another cell and choose View > Scan Filter.
The Scan Filter View opens in that cell.
6. To display all of the scan filters used in the sample, drag the cursor in the chromatogram
view parallel to the x axis.
7. 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 54 for more
information.
The data system displays all of the scan filters used for the sample run in the scan filter
view.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
65
3
Using Views Interactively
Applying a Scan Filter to a Plot
8. To select and apply a scan filter to a plot in the active chromatogram view, drag the scan
filter to the active view. Release the mouse button to apply the filter.
Figure 27, Figure 28, and Figure 29 demonstrate this process.
Select a scan filter in the scan filter view. The cursor changes to the page cursor.
Figure 27. Select a scan filter
TIC chromatogram trace
without a scan filter.
Selected scan filter
and page cursor
As you drag the scan filter into the active chromatogram view, the cursor changes to the
add page cursor, if the scan filter is compatible with the view. Or, the cursor changes to
the not allowed cursor, , if the scan filter is incompatible with the view.
Figure 28. Drag the scan filter to a plot in another view
Cursor for the
compatible scan filter
66
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3 Using Views Interactively
Displaying Multiple Magnifications of a Plot
When you release the mouse button, the data system applies the scan filter, redraws the
plot, and makes the view that contains the plot with the applied filter the active view.
Figure 29. Xcalibur data system applies the scan filter and redraws the plot
Filtered chromatogram
If you do not obtain the desired result, click the Undo button,
restore the previous plot and repeat step 4.
, in the toolbar to
Displaying Multiple Magnifications of a Plot
You can magnify a region of an active plot by dragging the cursor across the region of interest.
However, to view the original plot after you magnify a region of interest, or to select a
different region of the plot, you must first reset the magnification.
The following procedure describes how to repeatedly magnify different sections of a plot
without first resetting the magnification.
 To display multiple magnifications of a plot
1. Open a data file in the Qual Browser window.
Figure 30 shows the default layout for the steroids14.raw example file when you open the
raw file in a new window. The window contains two cells. The upper cell is inactive and
displays a chromatogram view with a TIC plot. The lower cell is pinned and displays a
spectrum view with the mass spectrum from the beginning of the run (RT = 0).
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
67
3
Using Views Interactively
Displaying Multiple Magnifications of a Plot
Figure 30. Default layout for the steroids14 example data file
2. Click the pin icon of the target cell.
A gray border appears around the target cell, the background behind the pin turns green,
and the pin turns to the pinned position (see Figure 31).
Note To add a copy of the active cell to the grid, you can make the cell active or active
and pinned.
68
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
3 Using Views Interactively
Displaying Multiple Magnifications of a Plot
Figure 31. Active and pinned chromatogram view and inactive spectrum view
3. To make a copy of the active cell in a new cell below the current cell, choose Grid > Insert
Cells > Below.
An inactive copy of the cell appears below the active cell (see Figure 32).
Figure 32. Cell grid with a copy of the original cell
Note You can magnify a section of an active cell. However, after you modify the
display range, you cannot select a range outside this range without first resetting the
magnification.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
69
3
Using Views Interactively
Displaying Multiple Magnifications of a Plot
4. In the inactive copy of the cell that you want to modify, select the region of interest as
follows:
• For a chromatogram view or a spectrum view, drag the cursor in the plot parallel to
the x axis or y axis (see “Selecting a One-Dimensional Range on a Plot” on page 54).
• For a map view, 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 58.
The selected region appears in the active and pinned cell. The inactive cells are
unaffected.
Note To work interactively with cells, the active cell must be pinned.
Figure 33 shows the red horizontal marker that defines the selected region in the inactive
cell and the magnified region in the active and pinned cell.
Figure 33. Cell grid with the original chromatogram plot and the magnified section of the plot
5. Repeat step 4 until you are satisfied with the selection.
70
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4
Working with a Chromatogram View
A chromatogram view shows the intensities of one or more masses as a function of time.
These procedures describe how to manipulate chromatograms.
Contents
• Inserting and Deleting Chromatogram Plots
• Setting the Chromatogram Ranges and Processing Options
• Adding Plots to a Chromatogram View with the Autofilter Command
• Setting the Chromatogram Display Options
• Detecting Peaks
• Reviewing the Effect of Different Peak Detection Settings
Figure 34 shows a chromatogram view with the chromatogram shortcut menu displayed.
For the y axis, the label is from the detector, the intensity is normalized to the largest peak in
the selected time range, and the units are set to relative.
Figure 34. Chromatogram view with the chromatogram shortcut menu displayed
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
71
4
Working with a Chromatogram View
Inserting and Deleting Chromatogram Plots
 To view a chromatogram
To view a chromatogram in the active cell, do one of the following:
• Click the View Chromatogram icon,
, in the toolbar.
• Right-click the cell and choose View > Chromatogram from the shortcut menu.
–or–
• From the menu bar, choose View > Chromatogram.
Inserting and Deleting Chromatogram Plots
You can display up to eight plots within a chromatogram view.
 To insert a plot in a cell with a chromatogram view
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 from a multi-plot chromatogram view
1. Select the cell containing the view.
2. Right-click the plot that you want to delete.
3. Choose Plot > Delete from the shortcut menu.
You can also use the Ranges dialog box to add, delete, or enable plots.
72
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4 Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
Setting the Chromatogram Ranges and Processing Options
Use these procedures to select the chromatograms that you want to display and the automatic
processing options for the chromatograms:
• 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 view.
 To set the mass range and time range for a chromatogram
1. Make the chromatogram view the active view.
2. To open the Chromatogram Ranges Dialog Box (Figure 35), do one of the following:
• Click the Ranges icon,
, in the Qual Browser toolbar.
• Right-click a chromatogram plot in the cell and choose Ranges from the shortcut
menu.
–or–
• Choose Display > Ranges.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
73
4
Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
Figure 35. Ranges page of the Chromatogram Ranges dialog box
3. 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.
4. To view or hide the chromatogram, select (or clear) the Type check box.
A row of settings in the Chromatogram Ranges dialog box describes the chromatogram.
5. To change the source of the active plot, select a raw data file by doing one of the
following:
• Select a file from the Raw File list.
The list contains all of the currently selected raw data files. When you open another
raw data file, it appears in the list.
• Click Browse adjacent to the list to open the Open dialog box. Then, browse to the
required file or type the full path and filename of the required file.
6. To specify the scan filter, select a scan filter from the Scan Filter list.
The Scan Filter list displays the scan filters stored in the .raw file.
74
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4 Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
7. 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.
8. 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).
9. In the Plot Properties area, select a detector type and specify a peak algorithm type.
10. Specify the delay time between when a component peak is detected by the MS detector
and the same peak is detected by a UV detector or other type of analog detector. To
change the value, enter the new delay time in the Delay box. The valid time range is –5.0
to +5.0 minutes.
11. To turn on, change, or turn off the fixed scale setting, do the following:
• 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 fixed scale setting, clear the Fixed Scale check box.
12. To save the settings and close the dialog box, click OK.
Setting Automatic Processing Options
Use the Automatic Processing page (Figure 36) to apply smoothing or baseline subtraction to
all the plots in the active chromatogram view. You can also use this page to set the mass
tolerance and precision for the current data file.
Tip You can set default values for mass tolerance and precision on the Mass Options page
of the Xcalibur Configuration dialog box. The settings on the Mass Options page affect
the display of all the mass data in the Xcalibur data system. You can also set default values
in the Global Mass Options dialog box. Settings in this dialog box affect the display of all
the mass data in the Qual Browser window.
Use the Mass tolerance and Mass precision areas of the Automatic Processing page to set
new values for the current data file.
Follow these procedures to set up the parameters on the Automatic Processing page:
• Setting Smoothing Area Options
• Setting Baseline Subtraction Area Options
• Setting Include Peaks Area Options
• Setting Mass Tolerance Area Options
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
75
4
Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
• Setting Mass Precision Area Options
 To open the Automatic Processing page for the 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 36), do one of the following:
• Click the Ranges icon,
, in the Qual Browser toolbar.
• Right-click a chromatogram plot in the cell and choose Ranges from the shortcut
menu.
–or–
• Choose Display > Ranges.
3. Click the Automatic Processing tab.
The Automatic Processing page opens. The default values in the Mass tolerance and Mass
precision areas are set in the Global Mass Options dialog. You can override these default
values by setting new values on the Automatic Processing page.
Figure 36. Automatic Processing page of the Chromatogram Ranges dialog box
76
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4 Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
Setting Smoothing Area Options
Use the Smoothing area parameters to smooth all scans defined by the mass range, time range,
and filter settings in the Spectrum Ranges dialog box.
 To set the smoothing parameters
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 an integer in the
Points box.
The valid range for smoothing points includes the odd integers from 3 (minimum
smoothing) to 15 (maximum smoothing).
Setting Baseline Subtraction Area Options
Use the Baseline subtraction parameters 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 specify the polynomial order, type or select an order for the baseline curve in the
Polynomial order box.
The normal range is 3 to 20. For complex chromatograms, use a high polynomial order.
3. To specify the Below curve (%) value, which moves the baseline up or down in the
chromatogram noise, type or select a value in the Below Curve (%) box.
The typical range for this parameter is 5 to 30%, depending on the number and width of
peaks in the chromatogram. Increase this value as the number of peaks or the peak width
increases. The valid range is from 1 to 99.
4. To specify the algorithm’s precision, type or select a value in the Tolerance box.
The valid range is from 0.001 to 0.2.
5. To specify how the algorithm fits the beginning and end of the chromatogram, select or
clear 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
77
4
Working with a Chromatogram View
Setting the Chromatogram Ranges and Processing Options
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.
Setting Mass Tolerance Area Options
Use the Mass Tolerance area of the Automatic Processing page of the Chromatogram Ranges
dialog box to specify a mass tolerance for the current data file.
Tip You can set a default value for mass tolerance on the Mass Options page of the
Xcalibur Configuration dialog box. Settings on this page affect the display of all the mass
data in the Xcalibur data system. You can also set a default value for mass tolerance in the
Global Mass Options dialog box. Settings in this dialog box 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.
Setting Mass Precision Area Options
Use the Mass precision area of the Automatic Processing page of the Chromatogram Ranges
dialog box to specify a mass precision for the current data file.
Tip You can set a default value for mass precision on the Mass Options page of the
Xcalibur Configuration dialog box. Settings on this page affect the display of all the mass
data in the Xcalibur data system. You can also set a default value for mass precision in the
Global Mass Options dialog box. Settings in this dialog box affect the display of all the
mass data in the Qual Browser window.
 To set Mass precision area settings
1. Specify the number of places after the decimal point that display in mass values in the
Decimals box.
78
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4 Working with a Chromatogram View
Adding Plots to a Chromatogram View with the Autofilter Command
2. To save the settings and close the dialog box, click OK.
Adding Plots to a Chromatogram View with the Autofilter Command
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 automatically add plots for all of the scan filters to a chromatogram view
1. Pin the chromatogram view.
2. Do one the following:
• Choose Actions > Autofilter from the menu bar.
• Right-click the cell and choose Autofilter from the shortcut menu.
–or–
• Click the Autofilter icon,
, in the toolbar.
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. Figure 37 shows the result of the Autofilter command on the
drugX_03.raw data file (Xcalibur\examples\data).
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
79
4
Working with a Chromatogram View
Setting the Chromatogram Display Options
Figure 37. Chromatogram view for a data file with two scan filters and a TIC
Setting the 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
Setting the Chromatogram Axis Options
For more information, see “Chromatogram View – Display Options Dialog Box – Axis Page”
on page 227.
80
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4
Working with a Chromatogram View
Setting the Chromatogram Display 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Axis tab.
The Chromatogram View – Display Options Dialog Box – Axis Page opens.
Figure 38. Axis page for a Chromatogram 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, do one of the following:
• To split the time scale, select the Split Time Range check box. Then, 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
81
4
Working with a Chromatogram View
Setting the Chromatogram Display Options
Setting the Chromatogram Color Options
For more information see “Chromatogram View – Display Options Dialog Box – Color Page”
on page 229.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Color tab.
The Color page opens.
Figure 39. 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 data system 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 data system 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.
82
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4
Working with a Chromatogram View
Setting the Chromatogram Display Options
Setting the Chromatogram Label Options
For more information, see “Chromatogram View – Display Options Dialog Box – Labels
Page” on page 230.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Labels tab.
The Labels page opens.
Figure 40. Labels page for a Chromatogram view in the Display Options dialog box
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
83
4
Working with a Chromatogram View
Setting the Chromatogram Display Options
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.
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 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 Chromatogram Normalization Options
For more information, see “Chromatogram View – Display Options Dialog Box –
Normalization Page” on page 232.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Select the Normalization tab.
The Normalization page opens.
84
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4
Working with a Chromatogram View
Setting the Chromatogram Display Options
Figure 41. Normalization page for a Chromatogram view in the Display Options dialog box
4. To specify the normalization method, select one of 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
For more information, see “Chromatogram View – Display Options Dialog Box – Style Page”
on page 233.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
85
4
Working with a Chromatogram View
Setting the Chromatogram Display 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
Figure 42. Style page for a chromatogram view in the Display Options dialog box
3. Select the Style tab.
4. To specify the graphic style, select 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, select 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), select 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.
86
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4
Working with a Chromatogram View
Detecting Peaks
Detecting Peaks
Qual Browser provides several ways for detecting the chromatographic peaks in a
chromatogram view. These topics describe the three most common ways to detect peaks:
• Automatic Detection of One Plot
• Automatic Detection of All Plots
• Manual Detection
The detect peak icons on the Main toolbar and the detect peak menu commands are active
only when a raw file is open in the Qual Browser window and a chromatogram view is the
active view.
Icon
Command
Actions > Peak Detection > Toggle Peak Detection in This Plot
Actions > Peak Detection > Toggle Peak Detection in All Plots
Actions > Peak Detection > Add Peaks
Actions > Peak Detection > Delete Peaks
 To open a raw data file in the Qual Browser window
1. Choose File > Open from the menu bar or click the Open icon,
, in the toolbar.
The Open Raw File dialog box appears.
2. Select a raw data file and click Open.
The raw data file appears in the Qual Browser window.
 To display the Main toolbar
1. From the menu bar, choose View > Toolbars.
The Toolbars dialog box opens.
2. Select the Main check box and click OK to accept the setting and close the dialog box.
Automatic Detection of One Plot
Use the Toggle Peak Detection in This Plot icon or menu command to detect and integrate
the chromatographic peaks in the selected plot of a multi-plot chromatogram view. The data
system integrates the peaks using the current peak detection and integration settings.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
87
4
Working with a Chromatogram View
Detecting Peaks
 To detect and integrate all peaks in a selected chromatogram plot
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
in the
toolbar or choose Actions > Peak Detection > Toggle Detection in This Plot from the
Qual Browser menu bar.
This option uses the current peak detection and integration settings.
3. To undo the peak detection, click the icon in the toolbar a second time or choose
Actions > Peak Detection > Toggle Detection in This Plot from the menu bar.
Automatic Detection of All Plots
Use the Toggle Peak Detection in All Plots icon or menu command to detect and integrate the
chromatographic peaks in all of the plots in a multi-plot chromatogram view. The data system
integrates the peaks using the current peak detection and integration settings.
 To detect and integrate all peaks in all chromatogram plots in the active cell
1. Click
in the toolbar or choose Actions > Peak Detection >
Toggle Detection in All Plots from the Qual Browser menu bar.
2. To undo all detected peaks, click the icon in 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 icons in the toolbar.
• Adding Peaks
• Deleting Peaks
Adding Peaks
Use the Add Peaks icon or menu command to manually detect one or more chromatographic
peaks.
 To add a peak to a chromatogram plot
1. To detect and integrate any peak in the selected cell, click
in the toolbar or choose
Actions > Peak Detection > Add Peaks from the Qual Browser menu bar.
The data system changes the cursor to the Add Peaks
88
Xcalibur Qualitative Analysis User Guide
cursor.
Thermo Scientific
4
Working with a Chromatogram View
Detecting Peaks
2. Drag the Add Peaks cursor horizontally across the peak to detect and integrate the peak.
The data system marks the added peak with a blue baseline and integrates the peak.
3. To adjust the beginning and ending points of the integrated peak, drag the baseline
markers.
4. To restore the default cursor, click the Add Peaks icon in the toolbar a second time, or
choose Actions > Peak Detection > Add Peaks from the menu bar.
Deleting Peaks
The active cell must have one or more peaks detected (as indicated by
) for the Delete
Peaks icon in the toolbar and the Delete Peaks menu command to be active. For information
about displaying the Qual Browser toolbars, see “To display the Main toolbar” on page 87.
 To delete peaks in a raw file
1. To open the raw file containing the peaks that you want to delete, click
File > Open from the Qual Browser window.
or choose
The Open Raw File dialog box opens.
2. Select a raw file and click OK.
The data system displays the raw file in the Qual Browser window.
3. To delete specific peaks in an active cell, click
.
The cursor changes to the delete peaks cursor
.
4. To delete a specific peak, click within the peak’s boundary, indicated by the
blue baseline
.
a second time,
5. To return the delete peaks cursor to the default cursor, click
choose Actions > Peak Detection > Delete Peaks from the Qual Browser menu bar, or
right-click the plot and select Peak Detection > Delete Peaks from the shortcut menu.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
89
4
Working with a Chromatogram View
Reviewing the Effect of Different Peak Detection Settings
Reviewing the Effect of Different Peak Detection Settings
Use the Peak Detection Settings page on the Info Bar of the Qual Browser window to test the
effect of changing the peak detection settings (Figure 43).
Figure 43. Peak Detection Settings page in Qual Browser
Peak Detection Settings page
 To display the Peak Detection Settings page on the Info Bar
1. Pin the chromatogram view of interest.
2. To add the Peak Detection Settings page to the Info Bar, right-click the pinned
chromatogram view and choose Peak Detection > Set Peak Detection Algorithm and
Detect in This Plot or Peak Detection > Set Peak Detection in All Plots from the
shortcut menu, and choose the appropriate algorithm (ICIS, Avalon, or Genesis).
90
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
4 Working with a Chromatogram View
Reviewing the Effect of Different Peak Detection Settings
3. To display the Peak Detection Settings page, do one of the following:
• Click the Peak Detection Settings tab,
, on the Info Bar.
• 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.
 To change the peak detection settings and apply the new settings
1. Change the settings as appropriate.
For information about the settings on the Peak Detection Settings page, refer to the
Xcalibur Qual Browser 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.
2. Do one of the following:
• 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.
3. To apply the settings, click Apply.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
91
5
Working with 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 44). 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.
These procedures describe how to set the ranges and display options for a map view.
Contents
• Setting Map Ranges
• Setting Map Display Options
The Map view consists of a time point (x axis) versus an m/z value (y axis) versus a relative
abundance value (z axis) map plot. An example of a map view is shown below (see Figure 44).
Figure 44. Map view
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
93
5
Working with a Map View
Setting Map Ranges
 To view a map
Do one of the following:
• Right-click the cell and choose View > Map from the shortcut menu (see Figure 45).
• From the menu bar, choose View > Map.
• Click
in the toolbar.
Figure 45. 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 (Figure 46), right-click the map view and choose
Ranges from the shortcut menu.
Figure 46. 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 as follows:
First Mass (Range 1) – Last Mass (Range 1) + First Mass (Range 2) – Last Mass (Range 2).
94
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
5
Working with a Map View
Setting Map Display Options
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.
Setting Map Display Options
Use the Display Options dialog box to set up the display options for a map view.
 To open the Display Options dialog box for 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 (see Figure 47). 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 47. Style page for a Map view in the Display Options dialog box
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
95
5
Working with a Map View
Setting Map Display Options
Follow one or more of these procedures to set up the 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
Setting the Map Style Options
For information about the map style options, see “Map or Ion Map View – Display Options
Dialog Box – Style Page” on page 248.
 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 47).
The Style page opens.
4. To specify the arrangement style, select one of 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.
The 3D area becomes available.
• 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, do the following in the 3D area:
• 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.
96
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
5
Working with a Map View
Setting Map Display Options
Setting the Map Axis Options
For information about the map axis options, see “Map or Ion Map View – Display Options
Dialog Box – Axis Page” on page 244.
 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 Axis page opens (see Figure 48).
Figure 48. 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.
For the y axis, first select the Custom option in the Source area.
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, do the following:
• To split the time scale, select the Split Time Range check box. Then, to specify the
number of time range subsections, type a number in the Divisions (time) box.
• To display only one time range, clear the Split Time Range check box.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
97
5
Working with a Map View
Setting Map Display Options
8. To save the settings and close the dialog box, click OK.
Setting the Map Color Options
For information about the map color options, see “Map or Ion Map View – Display Options
Dialog Box – Color Page” on page 246.
 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 Color page opens.
Figure 49. 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.
98
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
5
Working with a Map View
Setting Map Display Options
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, do one of the following:
• To plot the map in grayscale, select the Grayscale check box.
• To plot the map in color, clear the Grayscale check box.
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, do the following:
• 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
For information about the map normalization options, see “Map or Ion Map View – Display
Options Dialog Box – Normalization Page” on page 247.
 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 Normalization page opens (see Figure 50).
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
99
5
Working with a Map View
Setting Map Display Options
Figure 50. Normalization page for a Map view in the Display Options dialog box
\
4. To specify the mass grouping, select 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, do one of the following:
• 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. Then
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.
100
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
5
Working with a Map View
Setting Map Display Options
6. To specify a peak to normalize the y-axis maximum, 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 (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, select 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
101
5
Working with a Map View
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 Bandwidth page opens (see Figure 51).
Figure 51. 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.
102
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
5
Working with a Map View
Setting Map Display Options
The map view reflects the chosen band size (see Figure 52).
Figure 52. Map view with changed band width
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
103
6
Working with a Spectrum View
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
For information about setting up the options on the Composition page of the Display
Options dialog box, see “Specifying Spectrum Composition” on page 120.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
105
6
Working with a Spectrum View
Setting Spectrum Display Options
Setting the Spectrum Axis Options
For information about the spectrum axis options, see “Spectrum View – Display Options
Dialog Box – Axis Page” on page 234.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Axis tab.
The Axis page opens (see Figure 53).
Figure 53. 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.
106
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Spectrum Display Options
7. To set up mass range splitting, choose from these options:
• To display only one mass range, clear the Split range check box.
• To split the mass range, select the Split range check box. Then type the new number
in the Divisions box to specify the number of divisions (subsections) for the split
range.
8. To save the settings and close the dialog box, click OK.
Setting the Spectrum Color Options
For information about the spectrum color options, see “Spectrum View – Display Options
Dialog Box – Color Page” on page 235.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Color tab.
The Color page opens (see Figure 54).
Figure 54. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
107
6
Working with a Spectrum View
Setting Spectrum Display Options
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.
Setting the Spectrum Label Options
For information about the spectrum label options, see “Spectrum View – Display Options
Dialog Box – Labels Page” on page 237.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Labels tab.
The Labels page opens.
108
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Spectrum Display Options
Figure 55. Labels page for a Spectrum view in the Display Options dialog box
4. To define the spectrum labels, do the following:
• To display an m/z label over spectrum peaks, select the Mass check box. In the
Decimals box, type a value from 0 to 5 to specify the number of digits to be displayed
to the right of the decimal. 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, select 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, do the following:
• 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.
• 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
109
6
Working with a Spectrum View
Setting Spectrum Display Options
Setting the Spectrum Normalization Options
For information about the spectrum normalization options, see “Spectrum View – Display
Options Dialog Box – Normalization Page” on page 240.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Normalization tab.
The Normalization page opens.
Figure 56. 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.
5. To specify the spectrum 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 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.
110
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Spectrum Display Options
6. To specify the multiple scan normalization option, select 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
For information about the spectrum style options, see “Spectrum View – Display Options
Dialog Box – Style Page” on page 241.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Style tab.
The Spectrum View – Display Options Dialog Box – Style Page opens (see Figure 57).
Figure 57. Style page in the Spectrum view in the Display Options dialog box
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
111
6
Working with a Spectrum View
Setting Spectrum List Display Options
4. To specify the graphic style, select 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, select one of these options in the Arrangement area:
• 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
For information about the Composition page parameters for the spectrum list view, see
“Spectrum List View – Display Options Dialog Box – Composition Page” on page 252.
112
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Spectrum List Display Options
Setting the Spectrum List Normalization Options
For information about the normalization options for the spectrum list, see “Spectrum List
View – Display Options Dialog Box – Normalization Page” on page 249.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Normalization tab.
The Normalization page opens (see Figure 58).
Figure 58. 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, do one of the following:
• 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.
–or–
• 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
113
6
Working with a Spectrum View
Setting Spectrum List Display Options
Setting the Spectrum List Style Options
For information about the style options for the spectrum list view, see Spectrum List View –
Display Options Dialog Box – Style Page.
 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 in Qual Browser, choose Display > Display
Options or right-click the cell and choose Display Options from the shortcut menu.
3. Click the Style tab.
The Style page opens (see Figure 59).
Figure 59. 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 values, 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.
114
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Up Spectrum Plot Ranges
5. To specify peak order, choose one of these options in the Order by area:
• To order the spectrum list by m/z value (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.
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 60).
For more information about the Ranges page, see “Ranges Page – Spectrum Ranges Dialog
Box” on page 274.
 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, do one of the following:
• Right-click a spectrum plot in the cell and choose Ranges from the shortcut menu.
• Choose Display > Ranges.
–or–
• Click
on the Qual Browser toolbar.
3. Click the Ranges tab.
The Ranges page of the Spectrum Ranges dialog box opens (see Figure 60).
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
115
6
Working with a Spectrum View
Setting Up Spectrum Plot Ranges
Figure 60. 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 as follows:
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 as follows:
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.
116
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Up Spectrum Plot Ranges
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:
• 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
117
6
Working with a Spectrum View
Setting Up Spectrum Plot Ranges
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 (see Figure 61).
Figure 61. 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.
118
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Setting Up Spectrum Plot Ranges
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.
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 data system
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
119
6
Working with a Spectrum View
Specifying Spectrum Composition
Specifying Spectrum Composition
Use the Composition page of the Display Options dialog box for the spectrum view
(Figure 62) 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.
For information about the Composition page, see Spectrum View – Display Options Dialog
Box – Composition Page.
 To specify the spectrum composition
1. Open a spectrum view in the Qual Browser window and make it active.
2. To open the Display Options Dialog Box in Qual Browser, 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 (see
Figure 62).
Figure 62. Spectrum Composition page for a Spectrum view in the Display Options dialog box
4. To display the chemical formula labels at the top of spectrum peaks, select the Elemental
Comp. check box.
The data system determines which chemical formulas have a m/z value most like that of
the spectrum peaks. The Theo. Mass, RDB Equiv., and Delta check boxes and the
Formulae box become available.
120
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
6
Working with a Spectrum View
Subtracting Background Spectra
5. Do the following:
• To specify how many of the most likely chemical formulas you want the data system
to display at the top of spectrum peaks, type a number in the Formulae box.
• To display the theoretical m/z values of the chemical formulas that the data system
determines, select the Theo. Mass check box.
The data system displays the theoretical m/z values to the right of the formula
separated by an equal sign (=).
• 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 data system 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.
• To label the peak with the difference between the theoretical and experimental
m/z values, select the Delta check box. Then, to specify the units to use when
calculating the difference between the theoretical and experimental m/z values, select
amu, mmu, or ppm in the Delta units area.
6. To save the settings and close the dialog box, click OK.
Subtracting Background Spectra
Use a chromatogram view to interactively subtract background ions from a spectrum view,
subtract background ions 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 cell grid.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
121
6
Working with a Spectrum View
Subtracting Background Spectra
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.
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.
122
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A
Qual Browser
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
• Subtract Background Window
• Qual Browser Result File Window
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
123
A
Qual Browser
Qual Browser Menus
Qual Browser Menus
This figure shows the Qual Browser menu bar when a raw file (.raw) or a result file (.rst)
is displayed in the window.
For information about the Qual Browser menus, see these topics:
• “Actions Menu – Qual Browser” on page 124
• “Display Menu – Qual Browser” on page 125
• “Edit Menu – Qual Browser” on page 131
• “File Menu– Qual Browser” on page 131
• “Grid Menu – Qual Browser” on page 133
• “Help Menu – Qual Browser” on page 136
• “Tools Menu – Qual Browser” on page 137
• “View Menu – Qual Browser” on page 137
• “Window Menu – Qual Browser” on page 139
Actions Menu – Qual Browser
Table 9 lists the Actions menu commands for the Qual Browser window.
124
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Display Menu – Qual Browser
Table 9. Actions menu (Sheet 1 of 3)
Icon
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 121.
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 121.
Clear
Remove all subtract spectra modifications to the spectrum view. The data system
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 data system 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 data
system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
125
A
Qual Browser
Qual Browser Menus
Table 9. Actions menu (Sheet 2 of 3)
Icon
Command
Description
Set Peak Detection
Algorithm and Detect
In This Plot
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 in Qual
Browser 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.
126
Xcalibur Qualitative Analysis User Guide
.
) for this command
Thermo Scientific
A Qual Browser
Qual Browser Menus
Table 9. Actions menu (Sheet 3 of 3)
Icon
Command
Description
Manual Noise Region
Selection
Choose this command and drag the cursor horizontally across the region of the
chromatogram that you want to select as the noise region. The data system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
127
A
Qual Browser
Qual Browser Menus
Table 10 lists the Display menu commands for the Qual Browser window.
Table 10. Display menu (Sheet 1 of 3)
Icon
Command
Description
Ranges
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 View
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
128
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Table 10. Display menu (Sheet 2 of 3)
Icon
Command
Description
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.
Zoom
Pan
Thermo Scientific
so that you can drag the cursor to the left or right to pan
Xcalibur Qualitative Analysis User Guide
129
A
Qual Browser
Qual Browser Menus
Table 10. Display menu (Sheet 3 of 3)
Icon
Command
Description
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.
Amplify
When you click OK, the data system 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 data system 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 data system 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.
130
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Edit Menu – Qual Browser
Table 11 lists the Edit menu commands for the Qual Browser window.
Table 11. Edit menu
Button
Command
Description
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. This command is often
used after a Copy Cell command or after choosing the Copy Cell button.
Copy View
Copy the active window to the clipboard. You can then use the Paste command of
another application, such as Microsoft Word™ or Microsoft Excel™, to copy the
window object to a document or spreadsheet. To edit the window object after it is
pasted, return to the Xcalibur data system to edit the window 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– Qual Browser
Table 12 lists the File menu commands in the Qual Browser window.
Table 12. File menu (Sheet 1 of 2)
Button
Command
Description
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 data system displays a warning message if your selected result
file does not contain any qualitative data.
Open
To view the result file for a raw file in an opened sequence, right-click the file name
on the Sequence Information page of the Info Bar. Then, choose Open Result File
from the popup context menu. The result file is displayed in the Qual Browser
workspace and the Result File Information page of the Info Bar.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
131
A
Qual Browser
Qual Browser Menus
Table 12. File menu (Sheet 2 of 2)
Button
Command
Description
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 data system applies the .lyt layout file extension.
Save As
Save the current layout with a new name. The data system 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.
Layout
Other Commands
132
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.
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 data system 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.
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Grid Menu – Qual Browser
Table 13 lists the Grid menu commands in the Qual Browser window.
Table 13. Grid menu (Sheet 1 of 4)
Icon
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
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
133
A
Qual Browser
Qual Browser Menus
Table 13. Grid menu (Sheet 2 of 4)
Icon
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
134
Xcalibur Qualitative Analysis User Guide
in the toolbar.
Thermo Scientific
A Qual Browser
Qual Browser Menus
Table 13. Grid menu (Sheet 3 of 4)
Icon
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 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 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 data system makes the grouped row cells active, indicated by a gray border
around the grouped row cells and deactivates most menu commands and buttons in
the toolbar.
For example, consider the following view:
Chromatogram
Spectrum
Mass List
If your 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
135
A
Qual Browser
Qual Browser Menus
Table 13. Grid menu (Sheet 4 of 4)
Icon
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 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 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 in 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 – Qual Browser
Table 14 lists the Help menu commands in the Qual Browser window.
Table 14. 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.
136
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Tools Menu – Qual Browser
Table 15 lists the Tools menu commands in the Qual Browser window.
Table 15. 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 data
system displays the added programs as menu commands when you choose the Tools
menu from the Qual Browser window.
View Menu – Qual Browser
Table 16 lists the View menu commands in the Qual Browser window.
Table 16. View menu (Sheet 1 of 2)
Icon
Command
Description
Chromatogram
View one or more chromatograms in the active cell. The data system 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.
Views
Reports
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
137
A
Qual Browser
Qual Browser Menus
Table 16. View menu (Sheet 2 of 2)
Icon
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 in 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.
138
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 in 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 in 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 data system 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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Menus
Window Menu – Qual Browser
Table 17 lists the Window menu commands in the Qual Browser window.
Table 17. Window menu
Icon
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
139
A
Qual Browser
Qual Browser Toolbars
Qual Browser Toolbars
The Qual Browser window provides these toolbars:
• Amplify Toolbar – Qual Browser
• Main Toolbar – Qual Browser
Amplify Toolbar – Qual Browser
Use the Qual Browser window Amplify toolbar to amplify a region of a plot.
Table 18 describes the buttons on the Amplify toolbar.
Table 18. 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 data system 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 data system
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.
140
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Toolbars
Main Toolbar – Qual Browser
You can customize the Qual Browser window Main toolbar to display buttons for most menu
commands. The Amplify Toolbar – Qual Browser 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.
For information about customizing the Main toolbar, see “Customizing the Toolbar” on
page 13.
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 in the toolbar are also
arranged in this manner in the Customize Toolbar dialog box.
Table 19 describes the buttons and icons on the Main toolbar.
Table 19. Qual Browser Main toolbar (Sheet 1 of 10)
Button/
Icon
Command
Description
File
Open
Find and open a file that already exists.
Open Sequence
Select a sequence file (.sld).
Open Result File
Select a result file (.rst).
Apply
Select a layout file (lyt).
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
141
A
Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 2 of 10)
Button/
Icon
Command
Description
Print
Select print range and print quality.
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.
Edit
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.
View
142
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 3 of 10)
Button/
Icon
Command
Description
Error Log
Change the view in the active cell to an error log view.
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 in 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 data system 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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
143
A
Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 4 of 10)
Button/
Icon
Command
Description
Display Options
Select the style, color, label [chromatogram and spectrum only], axis,
normalization, and smoothing [chromatogram only] options for your
chromatogram, spectrum, or map.
Add Text
Add text to the active plot.
Add Graphics
Add simple graphic objects such as lines or boxes to the active plot.
Clear
Activates the
cursor so that you can selectively remove text or graphics
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 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 in the toolbar.
144
Clear All
Remove all text and graphics annotation entries in the active cell. To remove
annotations one at a time, use the Clear button in 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 xis.
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 5 of 10)
Button/
Icon
Command
Drag With Cursor
Description
Move (pan) the active plot horizontally left and right along the x axis by
dragging the cursor. The data system changes the cursor to
.
Click
again to turn off
.
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.
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.
Grid
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
145
A
Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 6 of 10)
Button/
Icon
Command
Reduce Cell
Description
Temporarily reduces the grid column size of the active cell to 20% of the
original size. The data system 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.
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.
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 in 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.
146
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 7 of 10)
Button/
Icon
Command
Group Column
Description
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 data system makes the grouped column cells active, draws a blue border
around the grouped cells, and deactivates most menu commands and buttons
in 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 121.
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 121.
Actions
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
147
A
Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 8 of 10)
Button/
Icon
Command
Description
Clear
Remove all subtract spectra modifications to the spectrum view. The data
system 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
in Qual Browser 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.
148
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 9 of 10)
Button/
Icon
Command
Delete Peaks
Description
Delete selected peak(s) in the active cell. The data system 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
cursor.
a second time to return the delete peaks cursor to the default
One or more peaks must be detected (as indicated by
button to be active.
Add Manual Noise Region
) for this
Select an area as the noise region. Click
and drag the cursor horizontally
across the chromatogram region you want to select. The data system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
149
A
Qual Browser
Qual Browser Toolbars
Table 19. Qual Browser Main toolbar (Sheet 10 of 10)
Button/
Icon
Command
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
150
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Qual Browser Views
The Qual Browser window contains a grid of cells. A cell displays only one view; however, you
can change the view displayed by a cell to any of the following views.
• “Chromatogram View” on page 153
• “Error Log View” on page 157
• “Instrument Method View” on page 157
• “Ion Map View” on page 160
• “Map View” on page 164
• “Sample Information View” on page 166
• “Scan Filter View” on page 168
• “Scan Header View” on page 169
• “Spectrum List View” on page 171
• “Spectrum View” on page 173
• “Status Log View” on page 176
• “Tune Method View” on page 180
Each of these views has a shortcut menu. Use the View command in the short cut menu to
change the view. Figure 63 shows the shortcut menu for the chromatogram view and the
expanded View menu. Table 63 describes the views that you can open with the View menu
commands.
Figure 63. Chromatogram view shortcut menu and View menu commands
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
151
A
Qual Browser
Qual Browser Views
Table 20. View menu (Sheet 1 of 2)
Command
Description
View
View > Chromatogram
Changes the view in the active cell to the chromatogram view. The data
system displays any chromatograms defined by the settings in the
Chromatogram Ranges Dialog Box.
View > Spectrum
Changes the view in the active cell to the spectrum view. The data system
displays the spectrum defined by the settings in the Spectrum Ranges
Dialog Box.
View > Map
Changes the view in the active cell to a three-dimensional x, y, z map of the
parameters time, relative peak height, and m/z value. The data system
displays the map defined by the settings in the Map Ranges Dialog Box.
View > Ion Map
Changes the view in the active cell to a three-dimensional x, y, z map of the
parameters time, relative peak height, and m/z value. The data system
displays the map defined by the settings in the Map Ranges Dialog Box.
View > Spectrum List
Changes the view in the active cell to the instrument method view. 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
Changes the view in the active cell to the scan header view. The data
system displays the scan header for the scan that is closest to the time set in
the Scan Header Range Dialog Box.
View > Scan Filters
Changes the view in the active cell to the scan filter view where you can
view all of the scan filters used in all scans of the active raw file. The data
system 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
Changes the view in the active cell to the tune method view where you can
view the tune parameters stored in the active raw file.
View > Reports > Instrument Method
Changes the view in the active cell to the instrument method view where
you can view the instrument method parameters stored in the active raw
file. If the instrument method controls more than one device,
click the right and left arrows
located in the toolbar to browse to
the through the pages of the instrument method for each device.
These right and left arrow buttons are not active for raw files that contain
only one device; for example, only a mass spectrometer.
View > Reports > Sample Information
152
Xcalibur Qualitative Analysis User Guide
Changes the view in the active cell to the sample information view where
you can view the sample list information stored in the active raw file.
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 20. View menu (Sheet 2 of 2)
Command
Description
View > Reports > Status Log
Changes the view in the active cell to the status log view where you can
view the status log stored with the active raw file.
View > Reports > Error Log
Changes the view in the active cell to the error log view where you can view
the error log stored with the active raw file.
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.
For information about the view header and the shortcut menu, see these topics:
• View Header Information
• Chromatogram View Shortcut Menu
View Header Information
Thermo Scientific
• RT
• Analog UV 1
• NL
• Analog UV 2
• m/z [Mass Range]
• Analog UV 3
• TIC
• Analog UV 4
• Base Peak
• Scan Filter
Xcalibur Qualitative Analysis User Guide
153
A
Qual Browser
Qual Browser Views
Chromatogram View Shortcut Menu
Right-click the chromatogram view to display the shortcut menu commands.
Table 21. Chromatogram view shortcut menu commands (Sheet 1 of 3)
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
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 data system 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 data system 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.
154
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 21. Chromatogram view shortcut menu commands (Sheet 2 of 3)
Command
Description
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.
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 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 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 in Qual Browser opens.
2. Click the Label tab, and 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.
Peak Detection > Delete Peaks
Delete selected peaks in the active cell. The data system 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.
Thermo Scientific
) for this
Xcalibur Qualitative Analysis User Guide
155
A
Qual Browser
Qual Browser Views
Table 21. Chromatogram view shortcut menu commands (Sheet 3 of 3)
Command
Description
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 data system 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
Export the time versus 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. For more information, see “Adding Plots to a
Chromatogram View with the Autofilter Command” on page 79.
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 more information, see the
“Scan Filter View” on page 168.
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
156
Xcalibur Qualitative Analysis User Guide
Select the Style, Color, Labels, Axis, and Normalization settings.
Thermo Scientific
A Qual Browser
Qual Browser Views
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 22. Error view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
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, click the show previous and show next buttons
located in 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.
The following example shows the method parameters in a raw data file that a
Thermo Fisher Scientific application chemist acquired with an LC/MS system made up of an
Accela™ Open AS, an Accela 1250 Pump, and a Q Exactive™ mass spectrometer.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
157
A
Qual Browser
Qual Browser Views
Figure 64. Instrument method view for an LC/MS instrument
Autosampler
section
Click the Show Next icon,
.
LC pump
section
Click the Show Next icon,
.
Mass
spectrometer
section
158
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
View Header Information
• Instrument Method: Drive:\Path
• Created
Instrument Method Information
• Creator
• Last Modified
• Summary
• MS Run Time
Instrument Method Settings
For an LC/MS instrument, the instrument method settings for the autosampler, LC pump,
and mass spectrometer are listed on separate pages.
Example parameters for the mass spectrometer:
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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
159
A
Qual Browser
Qual Browser Views
Instrument Method View Shortcut Menu
Right-click in the instrument method view to open the Instrument Method view shortcut
menu.
Table 23. Instrument Method view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ion Map View
Use the Ion Map view to analyze the parent, product, and neutral loss of MSn data. The Ion
Map view consist of three panes. The Map pane on the top, the Control pane on the right
side, and the Spectrum pane on the bottom. For information about the Ion Map view see
these topics:
• 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.
160
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 24. Map pane shortcut menu
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ranges
Ranges
Opens the Map Ranges dialog box where you can set the parent mass
range, product mass range, and scan filter for an ion map.
Display Options
Display Options
Opens the Display Options dialog box. Select the style, color, axis, and
normalization settings.
Toggle Neutral Loss
Toggle Neutral Loss
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 25. 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 data system 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 100 000.00.
This box is only active when you select the Product Spectrum option.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
161
A
Qual Browser
Qual Browser Views
Table 25. Control pane parameters (Sheet 2 of 3)
Parameter
Description
Parent Map
Produce a parent map consisting of parents that decompose to form the specified product
mass. When you select this option, the Product Mass box becomes available.
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 make this box available.
Drag the cursor in the Map pane along the Product axis. The data system 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 100 000.00.
Neutral Loss Map
Neutral Loss
When you select this option, the Neutral Loss box becomes available so that you can create
a neutral loss map consisting of parents that lose the specified neutral loss mass.
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 becomes available when you select the Neutral Loss option.
Drag the cursor in the Map pane along the diagonal neutral loss axis. The data system
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 –100 000.00 to 100 000.00.
Tolerance
Select the window where the data system selects either product masses or neutral loss masses,
depending upon which option you select.
• When 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
• When 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.
162
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 25. 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)
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
163
A
Qual Browser
Qual Browser Views
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 Spectrum pane to open the shortcut menu.
Table 26. Spectrum pane shortcut menu
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ranges
Ranges
Opens the Spectrum Ranges dialog box.
Display Options
Display Options
Opens the Display Options dialog box. Select the style, color, labels, axis,
and normalization settings.
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) versus m/z (y axis) versus relative abundance (z axis)
map plot. An example of a map view is shown below.
164
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
View Header Information
• RT:
• Mass:
• NL:
• T:
• F:
Map View Shortcut Menu
Right-click the map view to open the Map view shortcut menu.
Table 27. Map view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ranges
Ranges
Opens the Map Ranges dialog box where you can set the mass and time
range and scan filter for a map.
Display Options
Display Options
Thermo Scientific
Opens the Display Options dialog box where you can select the style,
color, axis, normalization, and bandwidth settings.
Xcalibur Qualitative Analysis User Guide
165
A
Qual Browser
Qual Browser Views
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
Table 28. Sample information view parameters (Sheet 1 of 2)
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.
166
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 28. Sample information view parameters (Sheet 2 of 2)
Parameter
Description
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
View the dilution factor that was used to prepare the sample.
Sample Information View Shortcut Menu
Right-click the sample information view to open the Sample Information view shortcut
menu.
Table 29. Sample Information view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
167
A
Qual Browser
Qual Browser Views
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
Scan Filter View Shortcut Menu
Right-click the scan filter view to open the Scan Filter view shortcut menu
Table 30. Scan Filter view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ranges
Ranges
168
Xcalibur Qualitative Analysis User Guide
Opens the Scan Filter Range dialog box where you can set the scan filter
time.
Thermo Scientific
A Qual Browser
Qual Browser Views
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
169
A
Qual Browser
Qual Browser Views
Display Header Information
• S#:
• RT:
Scan Header Information
The master scan number is an integer value assigned to the precursor scan for the current
data-dependent scan. This value is listed in the scan header of the data-dependent scan.
• Total Ion Current
• Elapsed Scan Time
• Scan Low Mass
• API Source CID Energy
• Scan Start Time
• Resolution
• Scan End Time
• Data Type
• Scan Number
• Polarity
• Master Scan Number (for some
mass spectrometers)
• Average Scan by Inst.
• Micro Scan Count
• Base Peak Intensity
• Base Peak Mass
• Ion Injection Time
• Scan Mode
• Backgd Subtracted by Instrument
• Charge State
• Number of Data Packets
• MS Order
• Parent Mass(es)
• Isolation Width(s)
• Scan Segment
• Collision Energy(s)
• Scan Event
Scan Header View Shortcut Menu
Right-click the scan header view to open the Scan Header view shortcut menu.
Table 31. Scan Header view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
Ranges
Ranges
170
Xcalibur Qualitative Analysis User Guide
Opens the Scan Header Range dialog box where you can set the scan
header time.
Thermo Scientific
A Qual Browser
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.
View Header Information
Thermo Scientific
• 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
Xcalibur Qualitative Analysis User Guide
171
A
Qual Browser
Qual Browser Views
Spectrum List View Shortcut Menu
To open the spectrum list view shortcut menu, right-click the spectrum list view.
Table 32. Spectrum List view shortcut menu commands
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
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 121.
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 121.
Export
Export > Clipboard
(Exact Mass)
Export the exact m/z versus intensity values of the spectrum to the clipboard. The
data system 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 versus 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
172
Change the appearance of your spectrum list.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
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 contains a scan header and a plot of the relative abundance versus
mass-to-charge (m/z) ratio of an ion. From left to right, the first line of the scan header lists
the file name, scan number, retention time, number of averaged scans, and the normalized
level of the scan. The second line lists the scan filter.
Figure 65 shows a spectrum view with a data-dependent MS/MS product ion scan (#61) that
has been selected from the TIC MS chromatogram at a retention time of 0.68 minutes.
Figure 65. Spectrum view (top cell) and chromatogram view (bottom cell)
Scan
number
Retention
time
Number of averaged scans
Normalized level
File
name
Scan
filter
Spectrum
view
Chromatogram
view
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
173
A
Qual Browser
Qual Browser Views
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
Normalized level
• T
Scan type
• F
Scan filter
Spectrum View Shortcut Menu
To open the spectrum view shortcut menu, right-click the spectrum view.
Table 33. Spectrum view shortcut menu commands (Sheet 1 of 3)
Command
Description
View
Use the commands on the View menu to change the view in the active cell. For a brief description of each view, see
Table 16 on page 137.
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.
174
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
Table 33. Spectrum view shortcut menu commands (Sheet 2 of 3)
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 121.
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 121.
Subtract Spectra > Clear
Remove all subtract spectra modifications to the spectrum view. The data
system 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 versus intensity values of the spectrum to the
clipboard. The data system 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 versus 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
175
A
Qual Browser
Qual Browser Views
Table 33. Spectrum view shortcut menu commands (Sheet 3 of 3)
Command
Description
Elemental Composition
Determine which chemical formulas have m/z values most like that of the
spectrum peaks. The data system 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.
For a list of the available views, see “Qual Browser Views” on page 151.
An example of a status log view is shown below.
View Header Information
• S#:
176
Xcalibur Qualitative Analysis User Guide
• Status Log Time
Thermo Scientific
A Qual Browser
Qual Browser Views
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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
177
A
Qual Browser
Qual Browser Views
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
178
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Views
LC Pump
• Status
• Pump Pressure [Minimum]
• Run Time
• Solvent Composition
• Flow Rate
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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
179
A
Qual Browser
Qual Browser Views
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.
For a list of the available cell views, see “Qual Browser Views” on page 151.
An example of a Tune method view is shown below.
View Header Information
• Segment
Tune Method Information
180
• Capillary Temp
• Tube Lens Offset (API)
• Data Type
• APCI Vaporizer Temp
• Octapole RF Amplifier
• Source Type
• Source Voltage (APCI)
• Octapole 1 Offset
• Polarity
• Source Voltage (API)
• Octapole 2 Offset
• Zoom Micro Scans
• Source Current (APCI)
• InterOctapole Lens Voltage
• Zoom AGC Target
• Source Current (API)
• Trap DC Offset Voltage
• Full Micro Scans
• Sheath Gas Flow
• Multiplier Voltage
• Full AGC Target
• Aux Gas Flow
• Maximum Ion Time
• MSn Micro Scans
• Capillary Voltage (API)
• Ion Time
• MSn AGC Target
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
181
A
Qual Browser
Qual Browser Info Bar
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 34. 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 data system 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
182
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 data system 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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 34. Cell Information page parameters (Sheet 2 of 2)
Parameter
Description
Detector Delay
View the time difference in minutes between data acquisition for the UV
or analog detector and the mass spectrometer. To align the
chromatographic information from two detectors, the data system corrects
for the delay time between the detectors.
The delay time is a user-specified value.
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 35. Cell Information page shortcut menu commands
Thermo Scientific
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.
Xcalibur Qualitative Analysis User Guide
183
A
Qual Browser
Qual Browser Info Bar
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 36. Elemental Composition page parameters (Sheet 1 of 4)
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 185 for more information.
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.
Mass
View or change the mass you want the data system 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
184
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 36. Elemental Composition page parameters (Sheet 2 of 4)
Parameter
Description
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.
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.”
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
185
A
Qual Browser
Qual Browser Info Bar
Table 36. Elemental Composition page parameters (Sheet 3 of 4)
Parameter
Description
Mass Tolerance
Specify a mass tolerance to restrict the number possible elemental
compositions. The data system 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.
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+).
186
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 36. Elemental Composition page parameters (Sheet 4 of 4)
Parameter
Description
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.
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
Thermo Scientific
Apply the Elemental Composition box settings to the spectrum.
Xcalibur Qualitative Analysis User Guide
187
A
Qual Browser
Qual Browser Info Bar
MSn Browser Information Page
Use the MSn Browser Information page of the Info Bar to display and analyze MSn
experimental data.
Figure 66. Information page – MSn Browser
Note The MSn Browser Information page is not available for all mass spectrometers.
These tables describe the parameters on the MSn Browser Information page and the shortcut
menu commands for this page.
• MSn Browser Information page parameters
• MSn Browser Information page shortcut menu commands
188
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 37. 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
Thermo Scientific
icon of interest.
Xcalibur Qualitative Analysis User Guide
189
A
Qual Browser
Qual Browser Info Bar
Table 37. MSn Browser Information page parameters (Sheet 2 of 4)
Parameter
Description
Composite Spectrum 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]
190
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 37. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
191
A
Qual Browser
Qual Browser Info Bar
Table 37. 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
Normalize the composite spectrum displayed in the spectrum view (View >
Composite Spectrum 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.
192
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 38. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
193
A
Qual Browser
Qual Browser Info Bar
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.
 To calculate values for initial value events
1. Open a raw file and make the chromatogram view active.
2. Click Auto Calculate Initial Events.
 To modify the settings for events in the event list
1. Select the row that you want to modify.
2. Enter the revised settings in the boxes below the list. Type values in the Time and Value
boxes.
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.
3. Click Change to automatically update both the event list and the chromatogram display.
 To add an event to the event list
1. Type values in the Time (Min) box and the Value box and select an event in the Event list.
2. Click Add.
 To delete an event
1. Select the row that you want to delete.
2. Click Delete.
This table describes the parameters on the Avalon Peak Detection Settings page of the
Info Bar.
194
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 39. Avalon Peak Detection Settings page parameters (Sheet 1 of 2)
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 Table
There are seven initial value 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.
Use the Time and Value boxes and the Event list below the table to modify the list of events.
Event column
Displays the integration events.
Time column
Displays the time for each event. You cannot change the time value for an Initial Value
event; however, you can add the same event with a non-zero time value to the table.
Value column
Displays the values associated with each event. The range of factors allowed for each value is
specific to each event.
Time box
Use this box to change the time for existing timed events or to specify the time for new
events. You cannot change the time value for an initial value event, but you can add these
events as events with non-zero time values to the table.
Event list
Use this list to add new events to the table.
Value box
Use this box to change the event values.
Events
There are seven initial value events: Start/End Threshold, Bunch Factor, Area Threshold, P-P Threshold, Negative
Peaks, Tension, and Tangent Skim. Of the seven initial value events, the Threshold and Bunch Factor parameters are
the most important ones in controlling peak detection. The data system provides the following 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 Threshold
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
195
A
Qual Browser
Qual Browser Info Bar
Table 39. Avalon Peak Detection Settings page parameters (Sheet 2 of 2)
Parameter
Description
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.
These events are not required.
Shoulders On
Turns on the detection of shoulders.
Shoulders Off
Shoulders Off Turns off the detection of shoulders.
Force Cluster On
Turns on the grouping of peaks into a single peak.
Force Cluster Off
Turns off the grouping of peaks into a single peak.
Disable Cluster On
Enables the grouping effect in the specified time range.
Disable Cluster Off
Disables the grouping effect in the specified time range.
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.
196
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
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 data system applies to the active raw file displayed in the Qual
Browser window.
Table 40. 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
Thermo Scientific
Specify advanced criteria to detect your chromatographic peak. The data system
provides these advanced settings: Manual Noise Region, INCOS Noise, Repetitive
Noise, RMS, Minimum Peak Width, Multiplet Resolution, Area Tail Extension,
and Area Scan Window.
Xcalibur Qualitative Analysis User Guide
197
A
Qual Browser
Qual Browser Info Bar
Table 40. 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
198
Apply the settings displayed in the dialog box.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 40. 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 41. 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 data system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
199
A
Qual Browser
Qual Browser Info Bar
Table 41. 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 data system 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 data system 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
200
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 41. 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 data system 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 data system 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
Thermo Scientific
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
data system applies the new baseline parameter.
Xcalibur Qualitative Analysis User Guide
201
A
Qual Browser
Qual Browser Info Bar
Table 41. 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 42. Result File Information page parameters
202
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
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 43. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
203
A
Qual Browser
Qual Browser Info Bar
Spectrum Simulation Page
Use the Spectrum Simulation page to create a simulated isotopic distribution spectrum of a
chemical formula.
To open the Spectrum Simulation page, click the tab,
, on the Info Bar.
These tables describe the following:
• Spectrum Simulation page parameters
• Common one- and three-letter abbreviations
• Less common three-letter abbreviations
Table 44. 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.
204
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 44. Spectrum Simulation page parameters (Sheet 2 of 5)
Parameter
Description
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.
See “List of Common One- and Three-Letter Abbreviations” on page 209.
See “List of Less Common Three-Letter Abbreviations” on page 210.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
205
A
Qual Browser
Qual Browser Info Bar
Table 44. Spectrum Simulation page parameters (Sheet 3 of 5)
Parameter
Description
Identity
Select the adduct for the simulated spectrum. Choose from H, K, or Na.
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 data system calculates the masses
accordingly. The range will be –99 to +99, and the default value is +1.
206
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 44. 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 data system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
207
A
Qual Browser
Qual Browser Info Bar
Table 44. 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 data system 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.
208
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
List of Common One- and Three-Letter Abbreviations
Use these abbreviations to enter the peptide/protein formula for the simulated spectrum
(see “Peptide/Protein” on page 205).
Table 45. Common one- and three-letter abbreviations
Thermo Scientific
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
Xcalibur Qualitative Analysis User Guide
209
A
Qual Browser
Qual Browser Info Bar
List of Less Common Three-Letter Abbreviations
Use these abbreviations to enter the peptide/protein formula for the simulated spectrum
(see “Peptide/Protein” on page 205).
Table 46. 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
Hse
210
C12H22N2O6
Xcalibur Qualitative Analysis User Guide
C6H7NO5
C5H5NO2
Homoserine
C4H7NO2
Thermo Scientific
A Qual Browser
Qual Browser Info Bar
Table 46. Less common three-letter abbreviations (Sheet 2 of 3)
Thermo Scientific
Three letter
Name
Formula
Hsl
Homoserine lactone
C4H5NO
Hya
Beta-hydroxyaspartate
C4H5NO4
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
C5H9NO2S
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
Xcalibur Qualitative Analysis User Guide
211
A
Qual Browser
Qual Browser Dialog Boxes
Table 46. Less common three-letter abbreviations (Sheet 3 of 3)
Three letter
Name
Sas
Formula
C8H8NO5
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” on page 213
• “Add Text Dialog Box” on page 216
• “Amplify by Other Factor Dialog Box” on page 222
• “Average Filter Selection Dialog Box” on page 222
• “Cell Size Dialog Box” on page 223
• “Choose Centroiding Algorithm Dialog Box” on page 224
• “Color Dialog Box” on page 225
• “Copy to Clipboard Dialog Box” on page 225
• “Display Options Dialog Box in Qual Browser” on page 226
• “Global Mass Options Dialog Box” on page 255
• “Heading Editor Dialog Box” on page 256
• “Peak Purity Dialog Box” on page 261
• “Print Dialog Box” on page 262
• “Ranges Dialog Boxes” on page 263
• “Search Properties Dialog Box” on page 284
• “Select Isotopes Dialog Box” on page 288
• “Specify Mixture for Simulation Dialog Box” on page 289
• “Toolbars Dialog Box” on page 290
For information about the Add Programs To Tool Menu and Add Tool dialog boxes, refer to
the reference section of the Xcalibur Getting Started Guide.
212
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Add Graphics Dialog Box
Use the Add Graphics dialog box to add graphic elements to a spectrum, chromatogram, or
map.
Table 47. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
213
A
Qual Browser
Qual Browser Dialog Boxes
Table 47. 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 data system 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.
214
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 47. 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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
215
A
Qual Browser
Qual Browser Dialog Boxes
Add Text Dialog Box
Use the Add Text dialog box to type, format, and position text on a spectrum, chromatogram,
or map plot.
For information about adding annotations, see “Adding Text to a Plot” on page 34.
Table 48. 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.
216
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 48. 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
217
A
Qual Browser
Qual Browser Dialog Boxes
Table 48. 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 data system 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 data system 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.
218
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 48. 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 data
system 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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
219
A
Qual Browser
Qual Browser Dialog Boxes
Table 48. 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.
220
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 48. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
221
A
Qual Browser
Qual Browser Dialog Boxes
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 data system changes the cursor to
so that you can drag the cursor horizontally to amplify a region of the active graph or type
a value into the Amplify Factor combo box.
Table 49. Amplify by Other Factor dialog box parameters
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.
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 50. 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 data system 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
222
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Cell Size Dialog Box
Use the Cell Size dialog box to define the size of a cell.
Table 51. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
223
A
Qual Browser
Qual Browser Dialog Boxes
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 52. 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 data system 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.
224
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Color Dialog Box
Use the Color dialog box to select one of 48 basic colors or 16 (maximum) preselected custom
colors.
Click Define Custom Colors to open the Color Space Spectrum box where you can 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 data system 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 53. 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.
 To open the Copy to Clipboard dialog box
In the Qual Browser menu bar, choose Edit > Copy Special.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
225
A
Qual Browser
Qual Browser Dialog Boxes
Display Options Dialog Box in Qual Browser
Use the pages of the Display Options dialog box to select Style, Color, Labels, Axis,
Band Width, Normalization, and Composition settings. The available parameters on these
pages depend on whether the view in the active cell is a chromatogram, spectrum, map, ion
map, or spectrum list.
View
Pages
Chromatogram
“Chromatogram View – Display Options Dialog Box – Axis Page” on page 227
“Chromatogram View – Display Options Dialog Box – Color Page” on page 229
“Chromatogram View – Display Options Dialog Box – Labels Page” on page 230
“Chromatogram View – Display Options Dialog Box – Normalization Page” on page 232
“Chromatogram View – Display Options Dialog Box – Style Page” on page 233
Spectrum
“Spectrum View – Display Options Dialog Box – Axis Page” on page 234
“Spectrum View – Display Options Dialog Box – Color Page” on page 235
“Spectrum View – Display Options Dialog Box – Labels Page” on page 237
“Spectrum View – Display Options Dialog Box – Normalization Page” on page 240
“Spectrum View – Display Options Dialog Box – Style Page” on page 241
“Spectrum View – Display Options Dialog Box – Composition Page” on page 242
Map and Ion Map
“Map or Ion Map View – Display Options Dialog Box – Axis Page” on page 244
“Map or Ion Map View – Display Options Dialog Box – Bandwidth Page” on page 245
“Map or Ion Map View – Display Options Dialog Box – Color Page” on page 246
“Map or Ion Map View – Display Options Dialog Box – Normalization Page” on page 247
“Map or Ion Map View – Display Options Dialog Box – Style Page” on page 248
Spectrum List
“Spectrum List View – Display Options Dialog Box – Normalization Page” on page 249
“Spectrum List View – Display Options Dialog Box – Style Page” on page 250
“Spectrum List View – Display Options Dialog Box – Composition Page” on page 252
226
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Chromatogram View – Display Options Dialog Box – Axis Page
Use the Axis page of the Display Options dialog box to modify the appearance of your
chromatogram. The data system displays the results of the current settings in the graphic on
the right side of the page.
Table 54. Chromatogram Axis page parameters (Sheet 1 of 2)
Parameter
Description
X
Name (X)
View or change the current x-axis name, as appropriate for the active chromatogram,
spectrum, or map. To change the x-axis name, type the new name in the Name box. The
data system displays the results of the current settings in the adjacent graphic.
The default x-axis name is Time (min).
Show name (X or Y)
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 data system 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 (X)
Set the location for the displayed plot a specified distance from the x axis.
The x-axis offset moves the y axis slightly above the x axis so that you can see baseline details.
Split time range (X)
Thermo Scientific
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 data system activates the divisions box so
that you can select the number of divisions.
Xcalibur Qualitative Analysis User Guide
227
A
Qual Browser
Qual Browser Dialog Boxes
Table 54. Chromatogram Axis page parameters (Sheet 2 of 2)
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
This box is available when the chromatogram view contains two or more plots. 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 data system
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 data system apply either a custom (user-defined) label or a label from the
detector to the y axis of a chromatogram plot.
When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file or the Name box. If you are using the default layout file, 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.
Name
The default y-axis name is Relative Abundance.
View or change the current y-axis name, as appropriate for the active chromatogram. To
change the y-axis name, select the Custom option in the Source area, and then type the new
name in the Name box. The data system displays the results of the current settings in the
adjacent graphic.
Show name
See the x-axis description.
Offset (Y)
Set the location for the displayed plot a specified distance from the y axis.
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.
228
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Chromatogram View – Display Options Dialog Box – Color Page
Use the Color page of the Display Options dialog box to modify the appearance of a
chromatogram view. The data system displays the results of the current settings in the graphic
on the right side of the page.
For information about the Color dialog box, see “Color Dialog Box” on page 225.
Table 55. 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 on the Color page 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 data
system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
229
A
Qual Browser
Qual Browser Dialog Boxes
Chromatogram View – Display Options Dialog Box – Labels Page
Use the Labels page of the Display Options dialog box to modify the appearance of your
chromatogram. The data system displays the results of the current settings in the graphic on
the right side of the page.
Table 56. Chromatogram Labels page parameters (Sheet 1 of 2)
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
View or change the number of decimal places in the retention time label. The range is
0 to 5.
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 data
system 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.
230
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 56. Chromatogram Labels page parameters (Sheet 2 of 2)
Parameter
Description
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
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.
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%.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
231
A
Qual Browser
Qual Browser Dialog Boxes
Chromatogram View – Display Options Dialog Box – Normalization Page
Use the Normalization page of the Display Options dialog box to modify the appearance of
your chromatogram. The data system displays the results of the current settings in the graphic
on the right side of the page.
Table 57. Chromatogram Normalization page parameters
Parameter
Description
Normalize method
Auto range
Select the auto range normalization method for chromatograms. The data
system 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.
232
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Chromatogram View – Display Options Dialog Box – Style Page
Use the Style page of the Display Options dialog box to modify the appearance of a
chromatogram view. The data system displays the results of the current settings in the graphic
on the right side of the page.
Table 58. 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 data system 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
Thermo Scientific
Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.
Xcalibur Qualitative Analysis User Guide
233
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum View – Display Options Dialog Box – Axis Page
Use the Axis page of the Display Options dialog box to modify the appearance of your
spectrum. The data system displays results of the current settings in the graphic on the right
side of the page.
Table 59. Spectrum Axis page parameters (Sheet 1 of 2)
Parameter
Description
X, Y, Z
View or change the current axis names for the x, y, and z axes, as appropriate for the active
spectrum view. To change an x- or z-axis name, type the new name in the Name box. The
data system displays results of the current settings in the adjacent graphic.
Name
The default axis names are as follows:
• X: m/z
• Y: Relative Abundance
• Z: Scan
Show name (X, Y, Z)
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 data system 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.
234
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 59. Spectrum Axis page parameters (Sheet 2 of 2)
Parameter
Description
Split time range (X)
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 data system displays the multiple spectra in the adjacent graphic.
Y
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 spectrum plot.
When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If you are using the data system’s default layout file, the application
retrieves the parameters from the default values you specified on the Labeling and Scaling
page of the Xcalibur Configuration dialog box.
Name
View or change the y-axis name.
To change the y-axis name, select the Custom option in the Source area, and then type the
new name in the Name box. The data system displays results of the current settings in the
adjacent graphic.
Spectrum View – Display Options Dialog Box – Color Page
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 60. 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 data system 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
235
A
Qual Browser
Qual Browser Dialog Boxes
Table 60. 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 data system 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 data system 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 View
– Display Options Dialog Box – Style Page.
236
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Spectrum View – Display Options Dialog Box – Labels Page
Use the Labels page of the Display Options dialog box to modify the appearance of your
spectrum. The data system displays the results of the current settings in the graphic on the
right side of the page.
Table 61. 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 data system 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 data system centroid the data after acquisition by selecting the
centroid check box. This action turns on the Resolution check box.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
237
A
Qual Browser
Qual Browser Dialog Boxes
Table 61. 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
238
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 activated when you select the Offset check
box. The valid range is 0.1 to 15.0. The default value is 2.0.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 61. 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 data
system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
239
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum View – Display Options Dialog Box – Normalization Page
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 data
system displays the results of the current settings in the graphic on the right side of the page.
Table 62. Spectrum Normalization page parameters
Parameter
Description
Normalize method
Auto range
Select the auto range normalization method for chromatograms. The data system
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 data system 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.
240
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Spectrum View – Display Options Dialog Box – Style Page
Use the Spectrum Style page of the Display Options dialog box to modify the appearance of a
Spectrum view. The data system displays the results of the current settings in the graphic on
the right side of the page.
Table 63. 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 data system 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 data system displays the current angle setting below the scroll box.
Draw Backdrop
Thermo Scientific
Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.
Xcalibur Qualitative Analysis User Guide
241
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum View – Display Options Dialog Box – Composition Page
Use the Spectrum Composition page of the Display Options dialog box to calculate elemental
compositions and to add columns containing the results to your Spectrum List. The data
system determines which chemical formulas have a m/z value most like that of the
experimental spectrum peaks. It displays a preview of the results for the current settings in the
graphic on the right side of the page.
Table 64. Spectrum Composition page parameters (Sheet 1 of 2)
Parameter
Description
Label with
Elemental comp.
Select whether the data system 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 data system 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 data system determines. The
application displays the theoretical m/z to the right of the formula separated by =.
242
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 64. Spectrum Composition page parameters (Sheet 2 of 2)
Parameter
Description
RDB equiv.
View the value of the ring and double-bond equivalents that the data system 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+).
Delta
Label the peak with the difference between the theoretical and experimental m/z.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
243
A
Qual Browser
Qual Browser Dialog Boxes
Map or Ion Map View – Display Options Dialog Box – Axis Page
Use the Axis page of the Display Options dialog box to modify the appearance of your Map or
Ion Map view. The data system displays the results of the current settings in the graphic on
the right side of the page.
Table 65. 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 data system 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 data system 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.
244
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 65. Map or Ion Map Axis page parameters (Sheet 2 of 2)
Parameter
Description
Y
Source
Specify that the data 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 map 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 divisions box becomes available 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 map plot 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 (m/z) box. The data system displays the multiple map plots in the adjacent
graphic.
Map or Ion Map View – Display Options Dialog Box – Bandwidth Page
Use the Bandwidth 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 bandwidth in amu units.
Table 66. 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 bandwidth.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
245
A
Qual Browser
Qual Browser Dialog Boxes
Map or Ion Map View – Display Options Dialog Box – Color Page
Use the Color page of the Display Options dialog box to modify the appearance of a Map or
Ion Map view. The data system displays the results of the current settings in the graphic on
the right side of the page.
Table 67. 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 data system 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 data system 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
data system 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 %
246
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Map or Ion Map View – Display Options Dialog Box – Normalization Page
Use the Normalization page of the Display Options dialog box to modify the appearance of a
Map or Ion Map view. The data system displays the results of the current settings in the
graphic on the right side of the page.
Table 68. 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 data system
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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
247
A
Qual Browser
Qual Browser Dialog Boxes
Table 68. 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 View – Display Options Dialog Box – Style Page
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 69. 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 data system 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.
248
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Spectrum List View – Display Options Dialog Box – Normalization Page
Use the Spectrum List Normalization page of the Display Options dialog box to modify the
appearance of your Spectrum List. The data system displays the results of the current settings
in the graphic on the right side of the page.
Table 70. 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 data system 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
249
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum List View – Display Options Dialog Box – Style Page
Use the Spectrum List Style page of the Display Options dialog box to modify the appearance
of a Spectrum view. The data system displays the results of the current settings in the graphic
on the right side of the page.
Table 71. 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 data system 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 data system 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
250
Fragmented peaks are peaks separated into multiple peaks by the centroiding activity.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 71. 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 data system 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 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 the Qual Browser window.
Xcalibur Qualitative Analysis User Guide
251
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum List View – Display Options Dialog Box – Composition Page
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
data system determines which chemical formulas have a m/z value most like that of the
experimental spectrum peaks. It displays a preview of the results for the current settings in the
list on the right side of the page.
Table 72. Spectrum List Composition page parameters (Sheet 1 of 3)
Parameter
Description
Label with
Elemental comp.
Select whether the application displays the Composition column. 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.
Formulae
Type a number that specifies how many of the most likely chemical formulas you want the
application to display in the Formulae box.
Theo. mass
The Theo. mass column lists the theoretical m/z of the chemical formulas that the data
system determines.
252
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 72. Spectrum List Composition page parameters (Sheet 2 of 3)
Parameter
Description
RDB equiv.
Select whether the application displays the value of the ring and double-bond equivalents
that the 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+).
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
253
A
Qual Browser
Qual Browser Dialog Boxes
Table 72. Spectrum List Composition page parameters (Sheet 3 of 3)
Parameter
Description
Sim Parameters
Select whether the data system displays the settings in the Limits area of the Qual
Browser – Elemental Composition page.
Sim
parameters
In the Delta column, display 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.
254
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Global Mass Options Dialog Box
IMPORTANT Use the Mass Options dialog box to specify tolerance and precision settings
for the mass data displayed in the chromatogram, spectrum, map, and ion map plots in
the Qual Browser window.
You can also specify the global default values for tolerance and precision on the Mass Options
page of the Xcalibur Configuration dialog box.
For more information, see
Table 73. 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 data system 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
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.
Related Topics
• “Mass Options Page” on page 184
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
255
A
Qual Browser
Qual Browser Dialog Boxes
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 74. 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 data system 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
256
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 74. 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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
257
A
Qual Browser
Qual Browser Dialog Boxes
Table 74. 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 data system 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 data system 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.
258
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 74. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
259
A
Qual Browser
Qual Browser Dialog Boxes
Table 74. 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.
260
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
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 75. 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 data
system computes peak purity for the selected trace only.
Xcalibur Qualitative Analysis User Guide
261
A
Qual Browser
Qual Browser Dialog Boxes
Print Dialog Box
Use the Print dialog box in the Qual Browser window to specify what to print and how to
print it.
Table 76. 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 data system 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.
262
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Ranges Dialog Boxes
Use the Ranges dialog boxes to define the range parameters for the views.
• “Chromatogram Ranges Dialog Box,” on this page
• “Spectrum Ranges Dialog Box” on page 272
• “Map Ranges Dialog Box” on page 277
• “Scan Filter Range Dialog Box” on page 279
• “Scan Header Range Dialog Box” on page 279
• “Spectrum List Ranges Dialog Box” on page 280
• “Status Log Range Dialog Box” on page 283
• “Tune Method Range Dialog Box” on page 283
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,” on this page
• “Ranges Page – Chromatogram Ranges Dialog Box” on page 266
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 77. Automatic Processing page parameters – Chromatogram Ranges dialog box (Sheet 1 of 3)
Parameter
Description
Smoothing
Smoothing
Thermo Scientific
Apply smoothing to all chromatogram plots in the active view.
Xcalibur Qualitative Analysis User Guide
263
A
Qual Browser
Qual Browser Dialog Boxes
Table 77. Automatic Processing page parameters – Chromatogram Ranges dialog box (Sheet 2 of 3)
Parameter
Description
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 data system 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.
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.
264
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 77. Automatic Processing page parameters – Chromatogram Ranges dialog box (Sheet 3 of 3)
Parameter
Description
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.
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 data system 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 data system
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
265
A
Qual Browser
Qual Browser Dialog Boxes
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 78. 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
266
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 data system displays the selected filter. You can also use the scan filter
format to type a scan filter into the Filter combo box.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 78. 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
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
267
A
Qual Browser
Qual Browser Dialog Boxes
Table 78. 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.
268
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 78. 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 data system 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 when a component peak is detected by the mass
spectrometer and the same peak is detected by a UV or analog detector. The valid time
range is –5.0 to +5.0 minutes. To change the value, enter the new delay time in the Delay
box.
You can acquire data from more than one detector during a sample run. Use this parameter
to visually align the chromatograms from different detectors.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
269
A
Qual Browser
Qual Browser Dialog Boxes
Table 79. MS trace combinations parameters
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
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 80. 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.
270
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 81. A/D card trace combinations parameters
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
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 82. PDA trace combinations parameters
Thermo Scientific
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
Xcalibur Qualitative Analysis User Guide
271
A
Qual Browser
Qual Browser Dialog Boxes
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 83. UV trace combinations parameters
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
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:
• “Automatic Processing Page – Spectrum Ranges Dialog Box,” on this page
• “Ranges Page – Spectrum Ranges Dialog Box” on page 274
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 84. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 1 of 3)
Parameter
Description
Smoothing
Enable
272
Turn on the data system 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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 84. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 2 of 3)
Parameter
Description
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.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
273
A
Qual Browser
Qual Browser Dialog Boxes
Table 84. Automatic Processing page parameters – Spectrum Ranges dialog box (Sheet 3 of 3)
Parameter
Description
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.
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.
274
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 85. Ranges page parameters – Spectrum Ranges dialog box (Sheet 1 of 2)
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
Turn on the data system 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.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
275
A
Qual Browser
Qual Browser Dialog Boxes
Table 85. Ranges page parameters – Spectrum Ranges dialog box (Sheet 2 of 2)
Parameter
Description
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 data system 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.
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 data system displays the first time range used for
background subtraction in the Time Range 1 box.
In Qual Browser, the data system 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 data system displays the second time range used for
background subtraction in the Time Range 2 box.
In Qual Browser, the data system enters these settings automatically when you perform a
background subtraction using Actions > Subtract Spectra.
Simulation
276
View whether or not the selected plot contains simulated data.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
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 86. 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 data system 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 100 000.00.
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 data system 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 100 000.00.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
277
A
Qual Browser
Qual Browser Dialog Boxes
Map Ranges Dialog Box (Map)
Use the Map Ranges dialog box to set the mass and time range for a map.
Table 87. 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 data system displays the selected filter. You can also use the scan filter format to type a
scan filter into the Filter combo box.
278
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Scan Filter Range Dialog Box
Use the Scan Filter Range dialog box to set the scan filter time.
Table 88. 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 the acquisition time in minutes of the
raw data file. The ToolTip for this parameter lists the lower and
upper time limits for the raw data file.
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 89. Scan Header Range dialog box parameter
Parameter
Description
Time
View or change the time range in minutes for the active scan
header. The lower time limit depends on the acquisition
instrument: typically 0.01 or 0.00 minutes. The upper time limit
is the acquisition time in the raw data file.
To specify 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 0.00 to 9.10 minutes, type:
0.00–9.10.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
279
A
Qual Browser
Qual Browser Dialog Boxes
Spectrum List Ranges Dialog Box
Use the Spectrum List Ranges dialog box to set the mass range and time for a spectrum list.
Table 90. 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 data system 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 data system displays
your new selection in the Chromatogram Smoothing Type list.
280
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 90. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
281
A
Qual Browser
Qual Browser Dialog Boxes
Table 90. Spectrum List Ranges dialog box parameters (Sheet 3 of 3)
Parameter
Description
Background Subtraction
Background
Subtraction
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.
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 data system
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 data system
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 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 from 0.1 to 50000, and then
select units to apply to the value. The data system 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
282
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Status Log Range Dialog Box
Use the Status Log Range dialog box to set the status log time range.
Table 91. 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 92. 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
283
A
Qual Browser
Qual Browser Dialog Boxes
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 List Page – Search Properties Dialog Box
• Search Parameters Page – Search Properties Dialog Box
Search List Page – 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 93. 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 data system 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 data system.
Buttons
284
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).
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Search Parameters Page – Search Properties Dialog Box
Use the Search Parameters page of the Search Properties dialog box 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 94. 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.
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 (matching) compounds that are 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
Thermo Scientific
Apply a Similarity search algorithm for library matching of
spectra.
Xcalibur Qualitative Analysis User Guide
285
A
Qual Browser
Qual Browser Dialog Boxes
Table 94. Search Parameters page parameters – Search Properties dialog box (Sheet 2 of 3)
Parameter
Description
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.
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 data system 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
286
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 data system sorts
matches by the Forward Match Factor.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
Table 94. Search Parameters page parameters – Search Properties dialog box (Sheet 3 of 3)
Parameter
Description
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 data system uses the parameters in library searches of
spectra that you export from the spectrum view of Qual Browser.
Thermo Scientific
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.
Xcalibur Qualitative Analysis User Guide
287
A
Qual Browser
Qual Browser Dialog Boxes
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 95. 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 data system 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
288
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.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Dialog Boxes
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 data system can simulate a spectrum.
Table 96. 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 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.
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 for the selected trace.
Also Show Separate
Traces for Each
Compound
Thermo Scientific
Select this check box to display a trace for each compound. Use
the Color box to select the color for each trace.
To select a color for the trace, select the trace, and then select the
color.
Xcalibur Qualitative Analysis User Guide
289
A
Qual Browser
Subtract Background Window
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 97. 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 in the toolbar, clear the Large Buttons
check box.
Subtract Background Window
Use the Subtract Background window 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 98. Subtract Background window parameters (Sheet 1 of 3)
Parameter
Description
Input
File
View or change the path name 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.
290
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Subtract Background Window
Table 98. Subtract Background window parameters (Sheet 2 of 3)
Parameter
Description
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 data system 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 path name 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.
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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
291
A
Qual Browser
Subtract Background Window
Table 98. Subtract Background window parameters (Sheet 3 of 3)
Parameter
Description
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 data
system 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
292
Proceed
Start the Subtract Background file operation using the settings in
the dialog box.
Exit
Exit the window and stop the Subtract Background file operation.
Xcalibur Qualitative Analysis User Guide
Thermo Scientific
A Qual Browser
Qual Browser Result File Window
Qual Browser Result File Window
You can open a raw data file (.raw), a result file (.rst), or a sequence file (.sld) in the Qual
Browser window.
 To open a result file (.rst) in the Qual Browser window
Do one of the following:
• From the Qual Browser menu bar, choose File > Open Result File.
–or–
• On the Main toolbar, click the Open Result File icon,
.
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:
• A chromatogram plot in the upper cell with the detected peaks highlighted.
• The spectrum plot 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.
Thermo Scientific
Xcalibur Qualitative Analysis User Guide
293
I
Index
A
A/D Card detector type 270
active and pinned cells 18
Add Graphics dialog box 213
Add Text dialog box 216
adductions 4
amplification factor, specifying 140, 222
Amplify by Other Factor dialog box 222
amplify icons 130
Amplify toolbar 140
analog trace combinations 270
annotation icons 128
audit trail 132
autofilter 79
automatic peak detection 87
Avalon Peak Detection Settings page, Qual Browser 194
Average Filter Selection dialog box 222
axis options
chromatogram view 81
map view 97
spectrum view 234
B
background, subtracting 290
band width, changing 102, 245
baseline marker 89
baseline subtraction 77, 264
C
Cell Information page
chromatogram 46
overview 45, 182
spectrum 47
Cell Size dialog box 223
cell size icons 133
Thermo Scientific
cells
active view 29
copying to clipboard 225
creating 30
deleting 31
expanding 133
information, viewing 45
reducing 134
size, adjusting 32, 133, 223
states 18
view, changing 39
centroiding algorithm 224
chemical formulas, displaying 242, 252
chemical ionization 4
Choose Centroiding Algorithm dialog box 224
Chromatogram Ranges dialog box
Automatic Processing page 263
Ranges page 266
chromatogram view
automatic processing 76
axis options 81, 227
background, subtracting 121
baseline subtraction 77, 264
color options 82, 229
heading 256
icons for 46
label options 83, 230
mass data settings 255
mass tolerance 75, 78
normalization 84, 232
overview 153
peak detection, all chromatogram plots 88
peak detection, selected chromatogram plot 88
peaks 78
plots, inserting and deleting 72
printing 262
ranges, setting 73, 263, 266
reference 153
smoothing 77, 263
style options 86, 233
Qualitative Analysis User Guide
295
Index: D
chromatogram view (continued)
time point, selecting 50
trace combinations 269
viewing 72
color
chromatogram view 82
map view 98
options 225
spectrum view, color options 235
Color dialog box 225
Color page, Display Options dialog box
chromatogram view 229
map and ion map views 246
spectrum view 235
columns, cell grid, grouping 136, 147
composite spectrum 190
Composition page, Display Options dialog box
spectrum list view 252
spectrum view 242
contacting us xii
Copy to Clipboard dialog box 225
cursor actions 20
D
data files, opening 22
data type, scan filter format 62
dataset name 132
dependent scans, scan filter format 62
Display Options dialog box 226
documentation
related x
survey xii
double bonds 186
genesis peak detection settings 199
Global Mass Options dialog box 255
graphics, adding 213
grid icons 133
grid lines 136, 147
Grid menu 133
H
heading, editing 256
Help menu 136
I
ICIS peak detection settings 197
inactive cells 18
Info Bar pages 16, 181
instrument methods
Qual Browser view 157
viewing in Qual Browser 138
Ion Map view
band width 245
color options 246
display options 244, 248
mass settings 255
normalization 247
ranges 277
reference 160
ionization modes
description 3
scan filter format 63
isotopes, selecting 288
L
E
edit buttons 131
Edit menu 131
elemental compositions, displaying 184, 242, 252
error log, viewing 138, 157
Export to Library Browser command 127
F
File menu 131
format, scan filter 62
fragmentation patterns 4
free region, scan filter format 64
296
G
Qualitative Analysis User Guide
labels
chromatogram view 83
overview 237
spectrum view 120
layout
creating and saving 42
opening saved 43
summary information, displaying 44
layout icons 132
library searches
search list 284
search parameters 285
Thermo Scientific
Index: M
M
manual peak detection 89
manuals, user x
map view
axis options 97
band width 245
color options 98, 246
display options 244, 248
heading 256
mass data settings 255
normalization 247
overview 93, 164
printing 262
ranges 278
ranges, setting 94
style options 96
viewing 94
mass analyzer, scan filter format 62
mass chromatograms 6
mass energy, scan filter format 63
mass tolerance 192
mass tolerance, chromatogram view 75, 78
MSn experimental data, analyzing and displaying 188
N
neutral loss 2
Nitrogen Rule 185
noise region 127, 149
Normalization page, Display Options dialog box
chromatogram view 232
map and ion map views 247
spectrum list view 249
spectrum view 240
normalization, chromatogram view 84
Normalize Composite Spectrum check box 190
normalized level 173, 190–191
O
opening
raw data files in Qual Browser 22
result files in Qual Browser 293
sequence files in Qual Browser 24
P
pan icons 129
PDA detector type 271
Thermo Scientific
peak detection
automatic 87
manual 88–89
settings, changing 90
peak properties 28
peak purity 127
Peak Purity dialog box 261
peak purity parameters, setting 261
peaks, chromatographic
adding 88
baseline 89
chromatogram view 78
detection 88
pin icon 18
plot
adding 138
graphics, adding 36
graphics, removing 38
point, selecting 50
regions, amplifying 33
regions, expanding 67
scaling 41
scan filter view 65
text, adding 34, 216
text, removing 38
plot range
one-dimensional 54
two-dimensional 58
plots, chromatogram 72
polarity, scan filter format 62
polynomial order, setting 264
Print dialog box 262
printing 262
Q
Qual Browser window
Display menu 128
overview 9
views displayed for result files 293
R
ranges
chromatogram 73
map 94
scan filters 279
scan header 279
spectrum 115
spectrum list 280
status log 283
tune method 283
Qualitative Analysis User Guide
297
Index: S
rapid scan rate, scan filter format 64
raw data files, opening 22
reagent gas 4
Result File Information page 202
result files
opening in Qual Browser 26
viewing in Qual Browser 293
ring equivalents 186
row, grouping 135, 146
S
sample information view 166
Scan Filter Range dialog box 279
scan filters
format 62
Scan Filter view, Qual Browser 168
selecting 222
using 60
Scan Header Range dialog box 279
scan header view
description 169
scan number, selecting 51
scan mode, scan filter format 62
scan number 173
Search Properties dialog box 284
Select Isotopes dialog box 288
selected ion monitoring 6
Sequence Information page 203
sequences
opening files in Qual Browser 24, 131
Sequence Information page, Info Bar 131
sequence information view, Qual Browser 166
sequence information, Qual Browser 203
simulated isotopic distribution spectrum, creating 204
simulations 289
smoothing, chromatogram 77
Specify Mixture for Simulation dialog box 289
spectra
mass spectra 1
overview 1
Spectrum List Ranges dialog box 280
spectrum list view 171
spectrum normalization, overview 240
298
Qualitative Analysis User Guide
spectrum view
color options 107
display options 250
header information 174
heading 256
icons for 47
labels 120
mass data settings 255
normalization 249
overview 173
printing 262
ranges 274, 280
scan header 173
scan number, selecting 51
smoothing 272
style options 111
spectrum, viewing 164
status log
time range, setting 283
viewing 138, 176
style options
chromatogram view 86
map view 96
spectrum view 111, 241
Style page, Display Options dialog box 233, 241
Subtract Background window 290
survey link xii
synchronous precursor selection, scan filter format 64
T
text, adding to plot 216
theoretical mass, displaying 242, 252
tool
adding 14
button, repositioning 14
removing 15
toolbars
Amplify toolbar 140
customizing 13, 290
displaying or hiding 12
Toolbars dialog box 290
Tools menu 137
trace analysis 7
trace combinations 269
tune method
selecting 283
viewing 137
tune method view 180
Thermo Scientific
Index: U
U
UV detectors 272
V
view
changing 39
display options 226
opening 39
view icons 137
View menu 137
W
Window menu 139
Z
zoom icons 129
Thermo Scientific
Qualitative Analysis User Guide
299
Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement