Thermo Xcalibur

Quantitative Analysis
Version 2.2
User Guide
XCALI-97212 Revision D May 2011
© 2011 Thermo Fisher Scientific Inc. All rights reserved.

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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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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 error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
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Sale shall govern all conflicting information between the two documents.

Release history: Revision A, January 2009; Revision B, September 2010; Revision C, January 2011 (to reflect
Microsoft Windows 7 compatibility); Revision D, May 2011

Software version: Thermo Xcalibur version 2.2

For Research Use Only. Not for use in diagnostic procedures.

 C

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Chapter 1 Overview of Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Acquiring and Quantitatively Processing Data with the Xcalibur Data
System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Integrating and Identifying Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Using External Standards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Using Internal Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 2 Reviewing Quantitation in Quan Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Understanding How Quan Browser Works . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Calibration Replicates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Named Calibration File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Brackets for Sequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Unbracketed Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Open Bracket Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Nonoverlapping Bracket Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Overlapping Bracket Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Starting Quan Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Saving Quan Browser Files With an Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . 16
Using the Quan Browser Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Component List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Results Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Chapter 3 Setting Up Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Editing a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Reviewing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Thermo Scientific Quantitative Analysis User Guide iii

Contents

Chapter 4 Working with Peaks, Chromatograms, and Spectra . . . . . . . . . . . . . . . . . . . . . . .23

Working with Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Viewing Peak Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Setting User Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Changing Peak Detection Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Setting Identification Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Setting Detection Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Integrating Chromatogram Peaks Manually . . . . . . . . . . . . . . . . . . . . . . . . 30
Setting Genesis Integration Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Setting Genesis Advanced Parameter Values. . . . . . . . . . . . . . . . . . . . . . . . 32
Setting Flags Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Working with Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Testing the Suitability of Chromatographic Peaks . . . . . . . . . . . . . . . . . . . . . 35
Checking the Stability of a Chromatographic Method. . . . . . . . . . . . . . . . . . 36
Reviewing a Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Setting Chromatogram Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Working with Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Displaying Spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Reviewing Spectrum Search Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Chapter 5 Working with Calibration Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43

Setting Type Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Setting Curve Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Excluding Calibration Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Changing the Isotope Percentage Value. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Including or Excluding Data Points from the Calibration Curve. . . . . . . . . . . . 52
Restoring an Excluded Data Point. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Chapter 6 Viewing Results and Generating Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55

Using the Results Grid Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Bracket/Group in Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Calibration File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Results Grid Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Reviewing and Reworking Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Hiding or Displaying Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Changing the Sort Order. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Generating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Selecting Samples for Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Printing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Appendix A Quan Browser Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65

Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Title Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Quan Browser Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

iv Quantitative Analysis User Guide Thermo Scientific

 Contents

Quan Browser Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
GoTo Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Options Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Zoom Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Quan Browser Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Quan Browser Results Grid View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Quan Browser Component List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Quan Browser Chromatogram Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Quan Browser Spectrum Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Quan Browser Calibration Curve Plot View . . . . . . . . . . . . . . . . . . . . . . . . . 81
Quan Browser Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Add Sample Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Bracket/Group In Use List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Cal Exclusion List Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Curve Page – Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . 86
Flags Page – Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . 88
Isotope % Page – Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . 89
Levels Page – Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . 91
Type Page – Calibration Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . 92
Display Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Chromatogram Axis Page – Display Options Dialog Box. . . . . . . . . . . . . . 94
Chromatogram Color Page – Display Options Dialog Box . . . . . . . . . . . . 97
Chromatogram Labels Page – Display Options Dialog Box . . . . . . . . . . . . 97
Chromatogram Normalization Page – Display Options Dialog Box. . . . . . 99
Chromatogram Style Page – Display Options Dialog Box . . . . . . . . . . . . 100
Map or Ion Map Axis Page – Display Options Dialog Box . . . . . . . . . . . 101
Map or Ion Map Band Width Page – Display Options Dialog Box . . . . . 102
Map or Ion Map Color Page – Display Options Dialog Box . . . . . . . . . . 103
Map or Ion Map Normalization Page – Display Options Dialog Box . . . 104
Map or Ion Map Style Page – Display Options Dialog Box . . . . . . . . . . . 106
Spectrum Axis Page – Display Options Dialog Box . . . . . . . . . . . . . . . . . 107
Spectrum Color Page – Display Options Dialog Box . . . . . . . . . . . . . . . . 108
Spectrum Labels Page – Display Options Dialog Box. . . . . . . . . . . . . . . . 110
Spectrum Normalization Page – Display Options Dialog Box . . . . . . . . . 112
Spectrum Style Page – Display Options Dialog Box . . . . . . . . . . . . . . . . 113
Spectrum List Composition Page – Display Options Dialog Box . . . . . . . 114
Spectrum List Normalization Page – Display Options Dialog Box . . . . . . 116
Spectrum List Style Page – Display Options Dialog Box . . . . . . . . . . . . . 117
Masses Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Chro Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 121

Thermo Scientific Quantitative Analysis User Guide v

Contents

Flags Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 122

Info Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 125
Info/More Info Page – Peak Information Dialog Box . . . . . . . . . . . . . . . 126
More Flags Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . 127
More Info Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . 128
No Peak Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . 128
Spectrum Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . . 128
Suitability Page – Peak Information Dialog Box . . . . . . . . . . . . . . . . . . . 129
Quantitation Results Sorting Order Dialog Box . . . . . . . . . . . . . . . . . . . . . 130
Reports Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Result List Column Hiding Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Select Level Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Select Report Samples Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
User Identification Settings Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Advanced Page – User Identification Settings Dialog Box . . . . . . . . . . . . 139
Detection Page – User Identification Settings . . . . . . . . . . . . . . . . . . . . . 142
Flags Page – User Identification Settings Dialog Box . . . . . . . . . . . . . . . . 147
Identification Page – User Identification Settings Dialog Box . . . . . . . . . 148
Integration Page – User Identification Settings Dialog Box . . . . . . . . . . . 152
View Sample Types Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .157

vi Quantitative Analysis User Guide Thermo Scientific

 P

Preface
This guide describes how to use the Thermo Xcalibur™ mass spectrometry data system to do
quantitative analysis. It describes how to review and rework your raw file data using the
Xcalibur quantitative reviewing utility, Thermo Xcalibur Quan Browser.

Contents
• Related Documentation
• Safety and Special Notices
• Contacting Us

To provide us with comments about this document, please click the link below. Thank you in
advance for your help.

Before using this guide, read your instrument’s Getting Started Guide and the Xcalibur Getting
Started Guide to become familiar with the basic features of the Xcalibur data system such as
the Home Page and Instrument Setup.

Related Documentation
Thermo Fisher Scientific provides these documents for the Xcalibur data system:
• Xcalibur Getting Started (Quantitative Analysis)
• Acquisition and Processing User Guide
• Quantitative Analysis User Guide
• Qualitative Analysis User Guide
• Creating and Searching Libraries User Guide
• XReport User Guide
• Help from within the software

Thermo Scientific Quantitative Analysis User Guide vii

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 avoid damage to software, loss of data,

invalid test results, or information critical for optimal performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Contacting Us
There are several ways to contact Thermo Scientific for the information you need.

 To contact Technical Support

Phone 800-532-4752
Fax 561-688-8736
E-mail us.techsupport.analyze@thermofisher.com
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 us.customer-support.analyze@thermofisher.com
Web site www.thermo.com/ms

 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.

viii Quantitative Analysis User Guide Thermo Scientific

 Preface

 To suggest changes to documentation or to Help

• Fill out a reader survey online at http://www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at
techpubs-lcms@thermofisher.com.

Thermo Scientific Quantitative Analysis User Guide ix

 1

Overview of Quantitative Analysis

The Xcalibur data system is a complete quantitative and qualitative analysis software package
that you can use to acquire data specifically for analytes of interest, to perform confirmatory
library searches, and to determine the concentration of analytes in samples. The Xcalibur data
system interfaces with the XReport reporting package to print individual sample reports and
sequence summary reports for analyses. For more information on XReport, see the XReport
User Guide.

Quan Browser is a powerful and versatile utility for reviewing and reworking
• Component peak identification and integration criteria
• Standards, QCs, blanks, and unknowns
• Calibration curves for quantitation standards

After making any changes, save the new results with an audit trail describing the reason for the
change.

Quan Browser incorporates a calibration curve display, peak integration, and results view
where you can
• Process quantitation sequences
• Interactively edit processing parameters and audit the changes
• Create new files that keep track of processing results for individual raw files and include a
copy of the method used to generate the results

Result files changed using Quan Browser do not affect the original processing method.

This chapter describes some of the basic principles and terminology of quantitation, and
provides a brief overview of quantitation with the Xcalibur application.

Contents
• Acquiring and Quantitatively Processing Data with the Xcalibur Data
System
• Integrating and Identifying Chromatograms

Thermo Scientific Quantitative Analysis User Guide 1

1 Overview of Quantitative Analysis
Acquiring and Quantitatively Processing Data with the Xcalibur Data System

Acquiring and Quantitatively Processing Data with the Xcalibur Data

System
Quantitative analysis is the process of measuring the amount of a particular component in a
sample. With the Xcalibur application, quantitative analysis usually involves the following
steps:

Note The order of some of these steps is not rigid. For example, you can acquire and
process a set of data files using a sequence that contains both an instrument method and a
processing method, and you can print reports without previewing them first. For more
information, refer to the Acquisition and Processing User Guide.

1. Create an instrument method.

The Xcalibur data system uses an instrument method to store a specific set of parameters
used to operate the autosampler, LC pump or MS pump, gas chromatograph, mass
spectrometer, PDA detector, and so on.
For more information about creating an instrument method, refer to your hardware
documentation.
2. Create an acquisition sequence.
An acquisition sequence identifies the position of the samples in an autosampler tray (if
appropriate), the instrument method used to control the HPLC, GC/MS, or LC/MS
instrument, and the directory and file names for the acquired data files.
For more information about creating an acquisition sequence, refer to the Acquisition and
Processing User Guide.
3. Run the sequence to acquire the raw data files.
Run either one sample or a series of samples from the current sequence.
For more information about running samples, refer to the Acquisition and Processing User
Guide.
4. Create a processing method.
Create processing methods in the Processing Setup view. The Xcalibur application uses a
processing method to identify, detect, and integrate components in a chromatogram,
generate calibration curves, quantify unknowns, and produce reports. The application
contains several built-in report templates. Report templates have an .xrt file extension.
For more information about creating a processing method, refer to the Acquisition and
Processing User Guide.
5. Create a processing sequence by adding the processing method to the original acquisition
sequence.
A processing sequence contains a processing method, consists of a list of sample data files,
and includes information on sample type and calibration or QC level.

2 Quantitative Analysis User Guide Thermo Scientific

 1 Overview of Quantitative Analysis
Acquiring and Quantitatively Processing Data with the Xcalibur Data System

6. Process a representative raw file or the entire sequence with the processing method by
using the Batch Reprocess feature in the sequence Setup view.
Processing a raw file produces a result file. Result files have an .rst file extension. For
instructions on batch processing a sequence, go to the Acquisition and Processing User
Guide.

Tip The report templates provided with the Xcalibur software are generic and might
not produce the results you expect. Preview a report in XReport before printing
reports for an entire sequence. For information about creating and changing reports,
go to the XReport User Guide.

7. After the Xcalibur data system processes the raw data files, you can evaluate the peak
detection settings, the integration settings, and the calibration curve for each component
in Quan Browser. As you evaluate the results of the processing method, modify some of
its parameters in Quan Browser. If the processing method contains a report template,
print reports from Quan Browser.
8. Preview a report for a representative data file from the XReport reporting package.
To produce customized reports, open a representative result file (.rst) in the XReport
reporting package and create a report template.
9. Once you are satisfied with the way a report displays your data, add the report to the
processing method, if you have not already done so, and batch process the sequence to
generate printed reports.

Thermo Scientific Quantitative Analysis User Guide 3

1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

Integrating and Identifying Chromatograms

The Xcalibur data system integrates chromatograms to separate the chromatographic peaks
from the baseline noise, identify the beginning and end of each peak, identify the peak
maxima, and calculate the area or height of each peak (Figure 1). The data system uses one of
the following three algorithms to detect and integrate the peaks in chromatograms: Genesis,
ICIS, or Avalon. To integrate mass chromatograms, use either the Genesis or the ICIS
integration algorithm. To integrate UV/Vis and analog chromatograms, use the Avalon
integration algorithm.
Figure 1. Integrated chromatographic peak, showing peak start and peak end markers

RT 0.68
100

90

80

70
Relative abundance

60

50

40

30
Peak start Peak end
20

10

0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1
Time [min]

For LC data, the Xcalibur application identifies peaks based on their retention times. The
retention time of a peak is the time that elapses between the injection of the sample and the
detection of the peak maxima. For GC data, The application identifies peaks based on either
their retention times or their mass spectra.

During a sequence run, the retention times of chromatographic peaks can vary slightly. As a
result, enter an appropriate retention time window for each peak, in addition to its expected
retention time. A retention time window is a time range bracketing the discrete retention time
setting. The appropriate retention time window for a chromatographic peak depends on
several factors, including the width of the chromatographic peak and the specificity of the
chromatographic method. Due to band broadening as the sample travels through the column,
highly retained compounds produce wider chromatographic peaks. So in general, use a wider
retention time window for late eluting compounds than for early eluting compounds.
Figure 2 shows the effect of retention time on peak width. The chromatogram shown in
Figure 2 contains four peaks. The retention times and widths of these peaks are listed in the
following table. In this example, hydrocortisone, which elutes at 0.68 min, has a peak width
of 0.2 min; whereas, progesterone, which elutes at 3.17 min, has a peak width of 0.6 min.

4 Quantitative Analysis User Guide Thermo Scientific

 1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

Figure 2. Integrated total ion current chromatogram (TIC) for steroids02.raw

Retention time Baseline peak width

Compound
(min) (min)
hydrocortisone 0.68 0.2
deoxycorticosterone 1.40 0.3
methyltestosterone 1.99 0.4
progesterone 3.17 0.6

Because the Xcalibur data system might detect more than one chromatographic peak within
the specified retention time window, identify the target compound as either the highest peak
in a chromatogram or the closest peak to the expected retention time. Use the Genesis and
ICIS integration algorithms (used for mass spectral data) to rule out peaks below a specified
signal-to-noise ratio.

Quantitative analysis of samples containing unknown amounts of the target component is

achieved by first calculating the peak area or height and then computing and applying the
appropriate response to the equation derived from the calibration curve. This process provides
an estimate of the amount of the unknown component. The precision of the measurement
depends on the quality and, to a lesser extent, the quantity of the calibration data.

The detection limit of the quantitation method is the lowest concentration of analyte in a
sample that can be detected but not necessarily calculated as an exact value. The lower and
upper quantitation limits are the lowest and highest concentrations of analytes in a sample
that can be measured with an acceptable level of accuracy and precision, respectively. In an
analytical method, the highest concentration calibration standard defines the upper
quantitation limit. The quantitation range is the range of concentration between the lower
and upper quantitation limits (including these limits) that can be reliably quantified time after
time with acceptable levels of accuracy and precision through the use of a
concentration-response relationship.

Thermo Scientific Quantitative Analysis User Guide 5

1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

There are two basic quantitation techniques:

• External standard (ESTD) quantitation
• Internal standard (ISTD) quantitation

The chosen method determines the calculation method, both for the generation of the
calibration curves and for subsequent quantitation.

This topic contains the following sections:

• Using External Standards
• Using Internal Standards

Using External Standards

An external standard (ESTD) is a separate sample that contains a known amount of the target
compound. To perform an ESTD calibration, prepare a set of standard solutions containing a
known amount of the target compounds. After you inject these solutions, the Xcalibur
application analyzes the resulting chromatograms and constructs a calibration curve for each
target compound by plotting the magnitude of the detector’s response as a function of the
amount of the target compound according to the following equation:
Responsecal = f (Amountcal)

Where:
f = curve type
Amountcal = amount of calibration standard
Responsecal = response for calibration standard

The Xcalibur application determines the amount of the target compounds in each unknown
by comparing the magnitudes of their responses to the calibration curves (see Figure 3).

Use ESTDs if all compounds of interest can be assayed by using a single set of external
standards. This approach offers time- and cost-effective quantitation for applications using
high precision autosamplers and traditional UV/Vis detectors. However, for some types of
analyses, this method cannot achieve the highest level of precision and accuracy. Depending
on the instrumentation, variations in analyte and solution stability, injection reproducibility,
and matrix interference can lead to lower precision levels in the external standard method than
in the internal standard method.

6 Quantitative Analysis User Guide Thermo Scientific

 1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

Figure 3. Calibration curve generated by using an external standard

500000 Response for
Response forsample
Response
unknown for

Compound
Unknown
unknown sampleSample
400000

TargetCompound
compound
300000
for
Response for Target
fortarget

200000
Response
Response

AmountAmount
inAmount
in in
100000 unknown sample
unknown sample
Unknown Sample

0
0 20 40 60 80 100
Amount of Target Compound
AmountAmount
of Target Compound
of target compound

In general, the external standard calibration is an effective quantitation technique; however, if

one or more of the following problems exist, consider using the internal standard calibration
technique instead.
• Lack of injection reproducibility
• Changes in analyte solution volume
• Matrix and coeluter interference (both suppression and enhancement)
• System instability
• Variations in the source conditions

Using Internal Standards

An internal standard (ISTD) is a component that is added to a sample to act as a response
reference for one or more non-ISTD components in the sample. The concentration or
amount of an ISTD in any standard or unknown sample typically remains constant.

Because quantitative mass spectrometric analysis usually involves multiple steps, the total
error in the analysis results from the accumulation of errors at each step. In general, sample
handling errors account for a larger fraction of the total error than detector errors do.
Fortunately, the internal standard method can reduce both sources of error. For example,
internal standards can correct for variations in a component’s peak area that are caused by the
following:
• Lack of injection reproducibility
• Changes in analyte solution volume
• Matrix and coeluter interference (both suppression and enhancement)
• System instability
• Variations in the source conditions

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1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

For maximum precision, add the ISTD component as early as possible to the start of the
sample workup, particularly in those quantitative methods that require sample manipulations
such as extraction, cleanup, and dilution. Since the ISTD and non-ISTD components are
analyzed together and since the ISTD is known and quantifiable, the internal standard
quantitation approach corrects for injection and other sample handling errors. The ISTD
must behave chemically in an identical or similar manner to the target compound through the
extraction, cleanup, and analytical processes.

You can also add the ISTD component as the last step of sample preparation prior to the
sample’s use to compensate for fluctuations in the reproducibility of the sample injection.

In general, ISTDs are used in a quantitation experiment as follows:

1. The Xcalibur data system analyzes series of standard solutions containing known
concentrations of the target compound and the ISTD. Then the data system plots the
ratio of the target compound and the ISTD detector responses as a function of the
corresponding ratio for the two quantities present in the solution.
2. Add a fixed amount of the ISTD to each sample prior to any manipulation. After the
samples are prepared and analyzed, you can obtain the quantity of the target compound
that is present in an unknown sample from the calibration curve (see Figure 4).
Figure 4. Calibration curve generated by using an internal standard

1.4 Response ration for

unknown sample
1.2
Response for target compound /

1.0
Response for ISTD

0.8

0.6

0.4
Amount in
unknown
0.2

0.0
0.0 0.5 1.0 1.5 2.0 2.5
Amount of target compound

8 Quantitative Analysis User Guide Thermo Scientific

 1 Overview of Quantitative Analysis
Integrating and Identifying Chromatograms

The calibration curve is determined by the following equation:

(Response RatioTargetCal/ISTD) = f (AmountTargetCal)

Where:
AmountTargetCal = Amount of target compound in the calibration standards
Response RatioTargetCal/ISTD = ratio of the responses of the target compound to the
internal standard compound in the calibration standard
f = equation of the calibration curve according to the selected fit type

Ideally, an ISTD is closely related to the target component in terms of its physical and
chemical properties. If the ISTD is used only to compensate for injection reproducibility or
changes in the analyte solution volume, it must possess a similar retention (k) to the target
component, but it does not need to be chemically similar to the target component. It must be
pure, not present in the sample, and inert towards the components of the sample. ISTD
components are typically analogs, homologues, or isomers of the target non-ISTD
component. An ideal ISTD is a structural or isotopically-labeled analog of one of the target
components. Stable isotope-labeled ISTDs act almost identically to the analyte throughout
sample manipulation and with regard to ionization tendencies and fragmentation. Internal
standards labeled with two or more deuterium (D) atoms are frequently used for LC/MS.

There can be any number of ISTD components in a sample, but each non-ISTD component
can be calibrated against only one ISTD.

Thermo Scientific Quantitative Analysis User Guide 9

 2

Reviewing Quantitation in Quan Browser

This chapter describes how to use Quan Browser to analyze processed quantitation sequences.
It explains the properties and uses of each component within the Quan Browser window. It
also describes how to use Quan Browser to achieve calibration and quantitation reviewing
tasks. Qual Browser is described in the Xcalibur Qualitative Analysis User Guide. Library
Browser is described in the Xcalibur Creating and Searching Libraries User Guide.

Contents
• Understanding How Quan Browser Works
• Starting Quan Browser
• Saving Quan Browser Files With an Audit Trail
• Using the Quan Browser Window

Understanding How Quan Browser Works

Quan Browser steps you through a sequence and helps you review the results for each
component in each file. Use Quan Browser to quickly review component peak identification
and integration criteria. After making any changes, save the new results with an audit trail that
describes the reason for the change. Result files changed using Quan Browser do not affect the
original processing method. You can only use Processing Setup to edit processing methods
and you can only use Quan Browser to edit result files.

The Xcalibur application has the following quantitation features:

• Calibration Replicates
• Named Calibration File
• Brackets for Sequences

Calibration Replicates
Calibration replicates are multiple injections of the calibration mixture at the same calibration
level or amount. These standard samples all contain the same amount of target compound, so
they correspond to the same calibration level. Choose replicates to include or exclude from the
calibration curve by using the Calibration Companion view.

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2 Reviewing Quantitation in Quan Browser
Understanding How Quan Browser Works

Named Calibration File

After creating a sequence with the Bracket Type set to None, specify a calibration file name in
the Calibration File box. Although in theory a different calibration file name for every sample
is possible, in practice only one name per sequence is common.

Named calibration files are not available with bracketed sequences.

Brackets for Sequences

This section describes different bracket types and when to use them to get a specific result.
• Unbracketed Sequence
• Open Bracket Sequence
• Nonoverlapping Bracket Sequence
• Overlapping Bracket Sequence

Unbracketed Sequence
The Xcalibur application processes an unbracketed sequence using a procedure known as the
continuing calibration method. Each time the application processes an unbracketed sequence,
it creates or updates the calibration files named in the sequence.
Select this process and avoid using Std Clear (Standard Clear) to add replicate data
incrementally to a calibration file without discarding the existing replicate data.
Quan Browser breaks down unbracketed sequences into logical groups that are somewhat
analogous to brackets. It does this by first ordering the samples chronologically with respect to
acquisition date and time. It then examines the sequence and starts a new group whenever it
encounters a standard. The group ends at the nonstandard sample that immediately precedes
the next standard found.
The first group always starts with the first sample, even if it is not a standard. The last group
always ends with the last sample. Further, a Std Clear always starts a new group, even if no
intervening nonstandard sample has been found following one or more Std Updates.

Note The Xcalibur application forms additional logical groups if different named
calibration files have been specified in the Cal File entries of the sequence. Each cal file
entry causes a new group to be formed. Because using multiple-named calibration files is
not typical, their use is not considered any further in this document, but should be
deducible from the discussions on groups.

As Quan Browser processes each group, its samples are quantified against the current
calibration curve. Each standard that Quan Browser encounters is processed and either
replaces (sample type set to Std Clear) or adds to (sample type set to Std Update) the
calibration replicate list, generating a new calibration curve.

12 Quantitative Analysis User Guide Thermo Scientific

 2 Reviewing Quantitation in Quan Browser
Understanding How Quan Browser Works

Quan Browser processing closely emulates that of batch processing (either batch processing
directly after acquisition or, subsequently, as a batch process operation). If Quan Browser
cannot find or open a specified calibration file, the Xcalibur data system displays this message:
Cal File Unavailable - Using Embedded Calibration
in the Calibration File edit box. Quan Browser takes replicate data from the data stored in the
result file. In most cases this data is identical to the data contained within the original
calibration file.
Once Quan Browser has set up the groups, they are independent and are effectively treated as
brackets. In other words, changes in one group do not affect any other group, unlike in batch
processing where subsequent groups might well be affected.
The following list illustrates the procedure (for a single-named calibration file):

Sample 1 Unknown Group 1 start

Sample 2 Unknown Group 1 end

Sample 3 Std Clear Group 2 start

Sample 4 Unknown Group 2 end

Sample 5 Std Update Group 3 start

Sample 6 Std Update
Sample 7 Unknown
Sample 8 Unknown
Sample 9 Blank
Sample 10 QC Group 3 end

Sample 11 Std Update Group 4 start/end

Sample 12 Std Clear Group 5 start

Sample 13 Blank Group 5 end

Open Bracket Sequence

Quan Browser creates a replicate list directly from all standard samples in the sequence
without using any calibration data embedded in result files.

Note When you open Quan Browser with a single result file, it is treated as a sequence
with only one entry and is brought in as an unknown. To show the calibration curve used
to quantitate the sample, the Xcalibur application creates the replicate list from the
embedded information.

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2 Reviewing Quantitation in Quan Browser
Starting Quan Browser

Nonoverlapping Bracket Sequence

Quan Browser creates a separate replicate list for each bracket. The Xcalibur data system
creates each replicate list directly from all standard samples in the bracket without utilizing
any calibration data embedded in result files.

Overlapping Bracket Sequence

Quan Browser creates a separate replicate list for each bracket. The Xcalibur data system
creates each replicate list directly from all standard samples in the bracket without using any
calibration data embedded in result files.

Exceptions occur for shared standard samples between brackets. When a standard that is
shared undergoes a change, that change is reflected in all brackets that contain that sample.
When a shared standard is deleted, the data system deletes the standard in all brackets that
contain that sample and adjusts the replicate lists for all brackets.

Add a sample to any bracket. When it is added as a standard, the Xcalibur system adds it to
the replicate list automatically. To add a sample as a shared sample, add it separately to each
bracket.

The exclusion status of the replicates is independent for each bracket. Even shared samples
might be excluded in one bracket but not in another. This is the only exception to a shared
sample having identical settings.

Starting Quan Browser

 To start Quan Browser

1. Choose one of these options:

• Click the Quan Browser icon from the Home Page.
• Choose GoTo > Quan Browser.
At startup, Quan Browser displays the Open dialog box so you can select an existing file.
If you do not want to select a file, click Cancel in the Open dialog box to close Quan
Browser.
The Xcalibur application supports these file types:
• Sequence files (.sld)
• Result files (.rst)
• Quan Browser files (.xqn)
Quan Browser handles result files as single entry sequences.
2. Select a file in the Open dialog box.

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 2 Reviewing Quantitation in Quan Browser
Starting Quan Browser

When you select a sequence file, the Xcalibur application checks that all the associated
raw and result files are available. When it encounters a problem with the sequence file, the
application provides information about the likely cause in a warning dialog box and
prompts you to exit the application or select a different file.
After the Xcalibur application verifies that the files exist and can be opened, the
View Sample Types dialog box opens (see Figure 5).
Figure 5. View Sample Types dialog box

The two options provided in the View Sample Types dialog box determine how the
Result Grid is configured at startup.
3. Select one of these options:
• To display only Standards and QCs in the Quan Browser Grid view, select the Show
Standard and QC sample types option. Blanks and Unknowns do not display. Click
either the Standards or QCs tab.
• To display Standards, QCs, Blanks, and Unknowns in the Quan Browser Grid view,
select the Show All sample types option. Click one of the following tabs: All,
Standards, QCs, Blanks, or Unknowns.
The View Sample Types dialog box includes a Don’t ask again check box. When you
select this check box, the dialog box is not displayed when you start subsequent sessions in
Quan Browser and the current selection becomes the default.

Note To make this and all other Don’t Ask Again-type dialog boxes active, choose
Options > Enable Warnings.

4. To start the session, click OK. Quan Browser loads the specified sequence or file and
configures the Results Grid using your selected viewing option.

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2 Reviewing Quantitation in Quan Browser
Saving Quan Browser Files With an Audit Trail

Saving Quan Browser Files With an Audit Trail

 To save files with an audit trail

1. After making changes in the view, save a file with the changes by clicking Save As. The
File Summary Information dialog box opens.
Figure 6. File Summary Information dialog box

2. Enter a comment clearly identifying the changes you made and click OK. The Save As
dialog box opens.
Figure 7. Save As dialog box

16 Quantitative Analysis User Guide Thermo Scientific

 2 Reviewing Quantitation in Quan Browser
Using the Quan Browser Window

3. Type a name for the method file in the File Name box.
4. To save the file and close the Save As box, click Save.

Using the Quan Browser Window

The Quan Browser window (see Figure 8) incorporates the following features:
• Component List
• Results Grid
• Chromatogram View

For more information about the Quan Browser window, see “Toolbars” on page 66 and
“Quan Browser Menus” on page 70.
Figure 8. Quan Browser in action

Title bar Results grid Component list

Menu bar

Toolbar

Status bar Chromatogram view Companion view

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2 Reviewing Quantitation in Quan Browser
Using the Quan Browser Window

Component List
The Component list displays all the components within the current bracket sorted by
retention time. To update the Chromatogram view and the Companion view with data for a
specific component, click the component name. For more information about the Component
list, see “Quan Browser Component List View” on page 78.

Results Grid
The Results grid is made up of sequence entries. Each row defines a result file and associated
parameters. For more information about working with the Results grid, see “Using the Results
Grid Window” on page 56.

Chromatogram View
The Chromatogram view displays the chromatogram for the currently selected component
from the currently selected result file.

When a filter is stored within the embedded processing method for the current compound,
the Xcalibur application applies it to the chromatogram. Adjust the chromatogram plot using
the Zoom menu commands or buttons on the toolbar.

The type of integration used appears in the Results grid but can be overridden. The three
types are Method Settings, User Settings, and Manual Integration. Change the Integration
method by using commands from the shortcut menu in the Chromatogram view. For more
information about working with chromatograms, see “Working with Chromatograms” on
page 35.

18 Quantitative Analysis User Guide Thermo Scientific

 3

Setting Up Quantitative Analysis

This chapter describes how to set up quantitative analysis.

Contents
• Editing a Sequence
• Reviewing Samples

Editing a Sequence
 To review and edit an existing sequence

1. Inspect the sequence. Verify that the correct raw files are listed in the Results grid. Ensure
that each raw file in the sequence is properly associated with a calibration level, QC level,
blank, or unknown.
2. To remove raw files from the sequence:
a. Select the row or rows in the sequence to delete.
b. Right-click the sequence to display the shortcut menu.
c. To delete the selected rows in the sequence, choose Delete Selected Samples.
3. To add raw files to the sequence:
a. Select the row in the sequence above where the new row (sample) will be located.
b. Right-click the Results grid to display the shortcut menu.
c. Choose Add Sample. The Open Rawfile dialog box opens.
d. Find the raw file to add to the sequence and click Open. The Add Sample dialog box
opens.
e. Specify sample information in the Add Sample dialog box and click OK.
4. To change the sample type:
a. Click the Sample Type column to display the sample type options list.
b. Select the new sample type. Quan Browser displays the new sample type in the
Sample Type list.

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3 Setting Up Quantitative Analysis
Reviewing Samples

5. To save the sequence with all current detection and calibration settings, choose
File > Save or File > Save As. The resulting Xcalibur Quan file (extension .xqn) contains
all the necessary information required to recreate the current Quan Browser session.

Reviewing Samples
 To review and rework samples

1. Select a component from the Component list. The Xcalibur application automatically
updates the Result list, Chromatogram, and Companion views.
2. Click the Standards tab to display calibration standards results.
3. Inspect the calibration curve in the Companion view. To display this view, do one of the
following:
• Choose View > Set Companion View > Show Calibration Curve.
• Right-click the Companion view and choose Show Calibration Curve from the
shortcut menu.
4. Inspect the calibration curve according to the criteria used in your laboratory.
5. Select a row in the Results grid. Each row corresponds to a data file.
6. Check the peak detection and integration fields in the Results grid for peak detection and
integration problems. Ensure that the selected data file corresponds to the correct level
and sample type.
7. Inspect the plot in the Chromatogram view.
• Confirm that the Xcalibur application found the peak. The application shades found
peaks gray and marks the starting and ending points with square integration markers.
• Confirm that the Xcalibur application integrated the peak properly. Confirm that the
shaded area accurately represents the contribution of the component to the
chromatogram.
8. Modify the peak detection and integration settings:
• Right-click the Chromatogram view and choose User Peak Detection Settings from
the shortcut menu. The User Identification Settings dialog box opens. See “Setting
User Peak Detection Parameters” on page 25 for more information.
• To change the detection method, click the Detection tab to open the Detection page.
Modify the settings. See “Setting Detection Values” on page 29 for more
information.
• If you have problems with noise in the peak, unresolved peaks, or peak tailing, click
the Integration tab. The Integration page opens. Modify the settings. See “Setting
Genesis Integration Values” on page 31 for more information.

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 3 Setting Up Quantitative Analysis
Reviewing Samples

• If baseline noise is interfering with peak identification or integration, click the

Advanced tab. The Advanced page opens. Only use the advanced options if the
standard options do not provide sufficiently selective detection criteria. See “Setting
Genesis Advanced Parameter Values” on page 32 for more information.
• Manually integrate the peak. Manually change the starting and ending points and
baseline of the peak by dragging the square integration markers to the desired
location. See “Changing Peak Detection Parameters” on page 25.
9. Repeat the procedure for the remaining components.
10. Repeat the procedure for all data files to review.

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 4

Working with Peaks, Chromatograms, and Spectra

The Chromatogram view displays the chromatogram for the currently selected component
from the currently selected result file. Most of the commands for manipulating the
Chromatogram view are available from a shortcut menu. For shortcut menu details, see Quan
Browser Chromatogram Plot View.

Contents
• Working with Peaks
• Working with Chromatograms
• Working with Spectra

Working with Peaks

This section describes how to view and change displayed peaks.
• Viewing Peak Information
• Setting User Peak Detection Parameters
• Changing Peak Detection Parameters

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4Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Viewing Peak Information

Quan Browser displays information about the currently displayed component peak, qualifier
ion, or spectrum candidate in the Peak Information dialog box. The title bar contains the
component name.

 To view peak information

Right-click the Chromatogram view and choose Show Peak Info from the shortcut
menu. The Peak Information Dialog Box opens.
The Peak Information Dialog Box is read-only. If you select other components or
samples, the Xcalibur data system updates the dialog box with peak information for the
displayed component chromatogram peak.
Figure 9. Info page – Peak Information dialog box

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Setting User Peak Detection Parameters

When you first open a sequence in Quan Browser component identification, the Xcalibur
application gets peak detection, calibration, and quantitation information from the result file.

Within Quan Browser, apply unique peak detection parameters to the chromatogram from
the User Identification Settings Dialog Box. This box duplicates the parameters available on
the Identification and Detection pages in the Quan view of Processing Setup, so you can
adjust and test the effect of different values. For more information about the parameters and
pages for this dialog box, see “User Identification Settings Dialog Box” on page 138.

Changing Peak Detection Parameters

Use the topics in this section to change peak detection parameters.
• Setting Identification Values
• Setting Detection Values
• Integrating Chromatogram Peaks Manually
• Setting Genesis Integration Values
• Setting Genesis Advanced Parameter Values
• Setting Flags Values

 To change and test component peak detection criteria

1. Review the displayed data for the selected component to determine if the results are
consistent with your expectations:
• Are there peaks that were not found?
• Are neighboring peaks resolved?
• Are tailing peaks detected properly?
2. To modify detection criteria, right-click the Chromatogram view and choose User Peak
Detection Settings from the shortcut menu. The User Identification Settings Dialog Box
opens.

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4Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Figure 10. User Identification Settings dialog box

3. To change the chromatogram information or adjust the retention time window, change
the settings on the Identification page. See “Setting Identification Values” on page 27 for
more information.
4. To change the detection method, change the settings on the Detection page. See “Setting
Detection Values” on page 29 for more information.
5. If you have identified problems with noise in the peak, unresolved peaks, or peak tailing,
change parameters on the Integration page. See “Setting Genesis Integration Values” on
page 31 for more information.
6. If baseline noise is interfering with peak identification or integration, modify the settings
on the Advanced page. Use advanced options only if the standard options do not provide
sufficiently selective detection criteria. See “Setting Genesis Advanced Parameter Values”
on page 32 for more information.
7. To view or change information on the Flags page, see “Setting Flags Values” on page 34
for more information.
8. To save your settings as a new processing method, choose File > Export Method.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Setting Identification Values

The Xcalibur data system uses the Identification page parameters for the following:
• Generating a chromatogram from raw data
• Identifying the component within the chromatogram

 To set identification parameters

1. From the User Identification Settings dialog box, click the Identification tab.
Figure 11. Identification page – User Identification Settings dialog box

2. Select the type of trace and optional trace math operation stored in the processing method
in the adjacent Plot Type lists. Only certain combinations of trace types are possible. For
more information about valid trace types, see “Identification Page – User Identification
Settings Dialog Box” on page 148.
3. To apply a different scan filter, select a new filter from the Scan Filter list, select a new
filter from the Scan Filter list and edit it, or type a new scan filter command string in the
box using the scan filter format.
4. View or change the masses stored in the processing method. This display area changes to
accommodate the type of data required.

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4Working with Peaks, Chromatograms, and Spectra
Working with Peaks

When a single mass range is required, a single edit box displays the current value. If two
mass ranges are required (as in the case of a trace defined as a Mass Range ± Mass Range
or Base Peak ± Mass Range), this box is replaced by two boxes (in the case of Base Peak ±
Mass Range, this box is replaced by the BP and MR boxes). In the case of a TIC (no trace
operator in use), analog, or digital traces, this box is blank.
5. View specific flags stored in the processing method. This is a read-only field.
6. Set Retention Time parameters:
• To change the minimum width that a peak is expected to have if valley detection is
enabled, type a new width in the Expected box.
• To change the time window or to enter a new time window, type the number of
seconds in the Window box.
• To change the current view width, type the desired time in the View Width box.
7. Select a detector type from the Type list of detectors. (You configured this list using the
Instrument Configuration dialog box.)
8. To select an algorithm, select a name in the Peak Detection Algorithm box and click OK.

The Xcalibur application recalculates the current data using the specified algorithm. The
application changes the default parameters for peak detection to parameters specific to
that algorithm.
9. Click OK to save your settings.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Setting Detection Values

The Xcalibur application uses the parameters on the Detection page (see Figure 12) to
confirm the identity of the component within the retention time window defined by the
Identification settings. The options available on this page depend on the Chromatography
mode selected in the original processing method used to generate the raw data.

 To set detection values

1. From the User Identification Settings dialog box, click the Detection tab.
Figure 12. Detection page – User Identification Settings dialog box

2. To use the highest peak in the chromatogram for component identification, select the
Highest Peak option.
3. To use the peak with the nearest retention time in the chromatogram for component
identification, select the Nearest RT option.
4. To change the peak signal-to-noise criterion that needs to be equaled or exceeded for the
Xcalibur application to use the Nearest RT Peak Identification criterion, type a value
from 0 to 999.0 (all peaks) in the Min Pk Ht (S/N) box.
For Component Identification purposes, the application ignores all chromatogram peaks
that have signal-to-noise values that are less than the S/N Threshold value.
5. Click OK to save your changes.

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Working with Peaks

Integrating Chromatogram Peaks Manually

 To modify and test component peak integration criteria

1. To open the Sequence file that contains the calibration standards, from the Quan Browser
window, choose File > Open. The application displays the Open dialog box.
2. In the Files of Type list, select Sequence list files. Browse to find the correct file. Select it
and click Open. The application opens the View Sample Types dialog box.
3. To accept the All Sample Types default option, click OK.
The application displays the Results grid, Component List, Chromatogram Plot, and
Spectrum Plot or Calibration Curve Plot views.
4. To select a component, click a component in the Component List view. The Xcalibur
application displays the chromatogram of the component in the Chromatogram Plot
view.

Not Found chromatogram peaks do not have blue baselines.

Found chromatogram peaks have blue baselines.

5. Examine the Chromatogram Plot view (optional):
• To replot the chromatogram with a different X-axis, drag the cursor horizontally over
the range that you want to expand. The application rescales the axis and replots the
data with the new X-axis range.
• To replot the chromatogram with a different Y-axis, drag the cursor vertically over the
range that you want to expand. The application rescales the axis and replots the data
with the new Y-axis range.
• To cancel the replot and return to the full range of the X-axis and the highest peak
normalized to 100.0 on the Y-axis, click .
6. To change the status of a peak from Found to Not Found (optional), right-click the
Chromatogram Plot view and choose Set Peak to Not Found Status from the shortcut
menu. The Xcalibur application removes the blue baseline to the component peak,
reduces the Area to 0, and changes the Peak Status to Not Found.

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Working with Peaks

7. To change the status of a peak from Not Found to Found [Added] (optional), right-click
in the Chromatogram Plot view and choose Manually Add Peak from the shortcut
menu. The application adds a blue baseline to the component peak, integrates the peak,
displays the Area in the Grid Results view, and changes the Integration Type to Manual
Integration.
8. Edit baseline integration criteria of a Found or Added peak (optional):
a. Click the left or right square editable handle on the blue baseline of the selected peak.
The Xcalibur application changes the cursor to a +:

b. Drag the handle to define a new location of the left or right peak limit. Repeat this
procedure for the opposite side of the peak if required.
The Xcalibur system automatically recalculates the results for the component and displays
them in the Result grid view. If the sample was a standard, the application replots the data
and redraws the calibration curve in the Calibration Curve Plot view.

Setting Genesis Integration Values

The Xcalibur data system applies the settings on the Integration page (see Figure 13) during
peak integration.

 To set Genesis integration parameters

1. From the User Identification Settings dialog box, click the Genesis Integration tab.
Figure 13. Genesis Integration page – User Identification Settings dialog box

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4Working with Peaks, Chromatograms, and Spectra
Working with Peaks

2. To specify the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration, type any odd number between 1 (no smoothing)
through 15 (maximum smoothing) in the Smoothing Points box.
3. To specify the lowest signal-to-noise threshold for integrating peak, type any value from
0.0 to 999.0 in the S/N Threshold box. The Xcalibur application does not integrate
peaks with signal-to-noise less than this value.
4. To use the Xcalibur valley detection approximation method to detect unresolved peaks,
select the Valley Detection Enabled check box. 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.
5. Specify the expected width of the peak in seconds (0.0 to 999.0 seconds).
If you selected Valley Detection, the Xcalibur application ignores any valley points nearer
than the expected width/2 to the top of the peak. If a valley point is found outside the
expected peak width, the application terminates the peak at that point. It always
terminates a peak when the signal reaches the baseline, independent of the value set for
the expected peak width.
6. To specify a limit for the peak width of a component during peak integration of a
chromatogram, select the Constrain Peak Width check box. 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.
7. To adjust the percent of the total peak height (100%) that a signal must be above the
baseline before integration is turned on or off, type a value in the Peak Ht box.
8. To change how the data system integrates the tail of a peak, type a value between 0.5 and
9.0 in the Tailing Factor box. This tailing factor is the maximum ratio of the trailing edge
to the leading side of a constrained peak.
9. To save your changes, click OK.

Setting Genesis Advanced Parameter Values

The Xcalibur data system applies the Genesis Advanced page parameters (see Figure 14)
during Genesis peak detection and integration.

 To set Genesis advanced parameters

1. From the User Identification Settings dialog box, click the Genesis Advanced tab.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Peaks

Figure 14. Genesis Advanced page – User Identification Settings dialog box

2. To calculate noise as RMS, select the RMS option.

3. To have the data system calculate noise as peak-to-peak, select the Peak to Peak option.
4. To specify the region of the chromatogram that the Xcalibur data system uses to
determine noise (retention time), type a retention time (RT) in the RT Range box.
You can also click in the toolbar and drag the cursor horizontally across the region of
the chromatogram that you want to select as the noise region. The data system
automatically fills the RT Range box with the retention time value.
5. To enter a value (in a percentage) that specifies how high the peak trace can rise above the
baseline after passing through a minimum (before or after the peak), type a value from
0.1 to 500.0 in the Rise Percentage box. If the trace exceeds this value, the application
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. To apply
the new peak detection criteria, click OK.
6. To change the valley detection signal-to-noise criteria that the Xcalibur data system uses
for valley detection, type a value from 1.0 to 100.0 in the Valley S/N box. To apply the
new peak detection criteria, click OK.
7. To change the Peaks S/N Cuttoff value, type a value from 50.0 to 10000.0 in the Peak
S/N Cutoff box. To apply the new peak detection parameter, click OK.
For example, if the signal-to-noise at the apex is 500 and the Peak S/N Cutoff value is
200, the application defines the right and left edges of the peak when the S/N reaches a
value less than 200.

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4Working with Peaks, Chromatograms, and Spectra
Working with Peaks

8. To change how the baseline is drawn in the noise data, type a value from 0.0 to 100.0 in
the Baseline Noise Tolerance box. To apply the new peak integration parameter, click
OK.
The higher the baseline noise tolerance value, the higher the baseline is drawn through
the noise data.
9. To change the minimum number of scans that the Xcalibur application uses to calculate a
baseline, type a new value from 2 to 100.0 in the Min Number of Scans in Baseline box.
To apply the new baseline parameter, click OK.
A larger number includes more data in determining an averaged baseline.
10. To change the number of background scans used to determine the background, type a
value from 1 to 100 in the Number of Background Scans box. To apply the new baseline
parameter, click OK.
11. Click OK to save your changes.

Setting Flags Values

 To use the Flags page

1. From the User Identification Settings dialog box, click the Flags tab.
Figure 15. Flags page – User Identification Settings dialog box

2. To test the validity of detected peaks, check values on the Flags page.
3. Type a value in the current Area Threshold (AT) box. The Xcalibur application sets the
AT flag in the results file if the quantified peak has an area that is lower than the entered
value.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Chromatograms

4. Type a value in the current Height Threshold (HT) box. The application sets the HT flag
in the results file if the quantified peak has a height that is lower than the entered value.
5. To save the settings in a Quan Browser file (*.xqn), choose File > Save or File > Save As.
6. To export the user settings as a full processing method, choose File > Export Method.
7. Click OK to save your changes.

Working with Chromatograms

The Xcalibur data system integrates chromatograms to separate the chromatographic peaks
from the baseline noise, identify the beginning and end of each peak, identify the peak
maxima, and calculate the area or height of each peak.

See these topics for more information about working with chromatograms.
• Testing the Suitability of Chromatographic Peaks
• Checking the Stability of a Chromatographic Method
• Reviewing a Chromatogram
• Setting Chromatogram Display Options

Testing the Suitability of Chromatographic Peaks

To check the suitability of chromatographic peaks, use the System Suitability page of the
Quan view in Processing Setup (see Figure 16).

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4Working with Peaks, Chromatograms, and Spectra
Working with Chromatograms

Figure 16. System Suitability page in Processing Setup, Quan view

Use the parameters on this page to determine if the LC column is degrading and to identify
suspicious peaks eluting at the same time as the target compound. Suspicious peaks due to
highly retained compounds from a previous injection tend to have a broader than expected
peak profile. Tailing peaks frequently indicate a degrading LC column.

Checking the Stability of a Chromatographic Method

Check the stability of the chromatographic method during a sequence run by injecting check
standards at specified intervals. Specify the amounts of the target compounds in the QC check
standards on the Levels page (see Figure 17).

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Chromatograms

Figure 17. Levels page, Quan View, showing the QC table for the selected component, estrogen

The Xcalibur application estimates the amount of the target compound in the QC standard
from a least squares fit calibration curve. It then compares the measured amount of the target
compound in the QC check standard to the amount specified in the QC table.

Use the % Test box to enter an acceptable difference (as a percentage) between the expected
amount and the calculated (measured) amount of the target compound for each QC level. If
the calculated amount differs by more than the specified percentage, the peak status is listed as
QC Failed in the Results grid view of Quan Browser.

Reviewing a Chromatogram
 To review a chromatogram in Quan Browser

1. In Quan Browser, open a file and choose View > Chromatogram.

2. Right-click the Chromatogram view and choose Show Peak Info from the shortcut
menu. The Peak Information Dialog Box opens. Review the chromatogram peak data in
these areas:
• The properties of the detected peak on the Info page
• The integration information and flags on the Flags page
• The System Suitability test results on the Suitability page
• The spectrum for the peak apex scan on the Spectrum page
3. Adjust the chromatogram in the Chromatogram view:
• Change detection or integration parameters. See “Changing Peak Detection
Parameters” on page 25.
• Manually integrate peaks. See “Integrating Chromatogram Peaks Manually” on
page 30.

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4Working with Peaks, Chromatograms, and Spectra
Working with Spectra

• Change chromatogram peak labeling. To change the labels, right-click the

Chromatogram view and choose Display Options from the shortcut menu. In the
Display Options dialog box, click the Labels tab. On the Labels page, select the labels
to display.
4. To view spectra for the chromatogram peak, display the Spectrum Companion view by
choosing one of these options:
• From the Quan Browser menu, choose View > Set Companion View > Show
Spectrum Plot.
• Right-click the Companion view and choose Show Spectrum Plot from the shortcut
menu.
See Reviewing Spectrum Search Results for detailed information.
5. View spectra across the chromatogram. Pin the Spectrum Plot Companion view. Click
points of interest in the chromatogram to view the corresponding spectrum.
6. To do a detailed qualitative analysis of the chromatogram, export the results file to Qual
Browser. Right-click the Results grid and choose Send to Qual Browser from the
shortcut menu. For more information about using Qual Browser, go to the Qualitative
Analysis User Guide.

Setting Chromatogram Display Options

The Display Options dialog box contains a small display area showing the active cell. Use this
display to preview the effects of different settings before applying them. For information
about changing display options, go to the Qualitative Analysis User Guide.

Working with Spectra

The Spectrum Companion view displays a spectrum from the current chromatogram in the
Chromatogram view. View spectra from the apex, left peak edge, or right peak edge using
commands from the shortcut menu. When the view is active (pinned), view scans from any
part of the chromatogram by clicking the chromatogram.

Displaying Spectra
Use the Spectrum Companion view to examine the identity of peaks and other features (such
as the background) in the chromatogram. For further analysis, including library matching of
spectra, export data to Qual Browser using the Send to Qual Browser option in the Result
list shortcut menu.

Initially, the Xcalibur application displays the spectrum corresponding to the scan at the
current chromatogram’s apex retention time. If no peak is detected, the application displays
the expected retention time as defined by the processing method.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Spectra

 To display the Spectrum Companion view

1. Choose View > Set Companion View > Show Spectrum Plot, or right-click the view
and choose Show Spectrum Plot from the shortcut menu.
2. To change the Spectrum Companion view, make the cell active by pinning the cell and
selecting a scan in the Chromatogram view.
3. To change the Spectrum value, right-click the Spectrum Companion view and choose one
of these options from the shortcut menu:
• To display the spectrum at the apex retention time of the current chromatogram,
choose Spectrum at Peak Apex.
• To display the spectrum at the left edge retention time of the current integration
baseline, choose Spectrum at Peak Left Edge.
• To display the spectrum at the right edge retention time of the current integration
baseline, choose Spectrum at Peak Right Edge.
• To change the Companion view to display the calibration curve, choose Show
Calibration Curve.
• To display the full spectrum in a normalized window, choose Reset Scaling.

4. To display spectra from other regions of the chromatogram, click the pin in the spectrum
companion view. Any click in the Chromatogram view updates the Spectrum
Companion view with a spectrum corresponding to the scan at the clicked retention time.

To rescale the plot, in an active (pinned) Spectrum view, use the cursor to select an area to
magnify or use the Zoom menu commands and buttons on the toolbar.

Reviewing Spectrum Search Results

The following are typical spectrum search settings in the Processing Setup window:

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4Working with Peaks, Chromatograms, and Spectra
Working with Spectra

The Xcalibur application only performs ion spectrum searches on GC data. To enter peak
detection and spectrum search settings, from the Processing Setup window, use the Detection
page in the Quan view. The detection criteria for the component are selected using the
settings in the Peak Integration box and in the Advanced Detection Options dialog box
(optional). Spectrum search criteria are selected from the Peak Detection box on the
Detection page. Spectrum search is only available if you select the Spectrum option.

 To review the results of a spectrum search

1. From the Quan Browser window, choose File > Open. The Open dialog box opens.
From the Files of type list, select either .sld, .rst, or .xqn. Browse to find the file you want
to review.
2. Select it and click Open. The View Sample Types dialog box opens.
3. Select the Show All sample types option, and click OK.
4. To select a component to review, click a component in the Component list view that has
had a spectrum search as specified in the Processing Setup method. The Xcalibur data
system displays the chromatogram in the Chromatogram Plot view.
5. To view the plot, right-click the Chromatogram Plot view.
Depending upon the spectrum search results, the data system displays 0, 1, 2, or 3
candidates in the Chromatogram Plot shortcut menu. Candidates are ranked in the order
of spectrum fit as 1, 2, or 3.
Choose a spectrum search option:
• Show Peak Info: (Not Found): The data system did not find any peaks or could not
find a spectrum match.
• Show Peak Info: The data system found a spectrum match and this was the best
spectrum match—Candidate 1.
• Show Peak Info - Candidate 2: The data system found a spectrum match and this
was the second best spectrum match.
• Show Peak Info - Candidate 3: The data system found a spectrum match and this
was the third best spectrum match.

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 4 Working with Peaks, Chromatograms, and Spectra
Working with Spectra

This shortcut menu displays a spectrum search result that found two candidates to match
the criteria.

6. To review main component Candidate 1 results, choose the Show Peak Info command
(the first of the two choices) from the Chromatogram Plot shortcut menu.
The Xcalibur system opens the Peak Information dialog box with the following title:
Peak Information – Component– Spectrum Candidate
and with the following pages:
Info, More Info, Flags, More Flags, Suitability, and Spectrum
Review the read-only results.
7. To review the other spectrum search results, choose the Show Peak Info - Candidate N
command from the Chromatogram Plot shortcut menu.
The Xcalibur system opens the Peak Information dialog box with the following title:
Peak Information – Component – Spectrum Candidate
This dialog box displays the following pages:
Info, Chro, and Spectrum
The Chro page displays a total ion current plot of the Spectrum Candidate. The view is
centered around the mass of interest and has the width used by the component peak
display.
Review the read-only results. Repeat this step for other candidates of interest.
8. To close the Peak Information dialog box, click Close.

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 5

Working with Calibration Settings

To display the Calibration Companion view, choose View > Set Companion View > Show
Calibration Curve or use the shortcut menu from within the Companion view. If the
companion view is currently displaying a spectrum plot, right-click it and choose Show
Calibration Curve. For more information about the Calibration Companion view, see
“Calibration Settings Dialog Box” on page 86.

Contents
• Setting Type Parameters
• Setting Curve Parameters
• Excluding Calibration Levels
• Changing the Isotope Percentage Value
• Including or Excluding Data Points from the Calibration Curve
• Restoring an Excluded Data Point

When you first open a sequence in Quan Browser component identification, the Xcalibur
data system performs peak detection, calibration, and quantitation according to the settings of
the associated processing method.

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5 Working with Calibration Settings

Within Quan Browser, apply unique calibration parameters and level definitions to the
chromatogram using the Calibration Settings dialog box. This box duplicates most of the
parameters available on the Calibration and Levels pages in the Quan view of Processing
Setup, so you can adjust and test the effect of different calibration and quantitation
parameters.

 To modify the sequence calibration

1. From Quan Browser, select a target component. The Xcalibur application automatically
updates the Results grid, and the Chromatogram and Companion views.
2. To display calibration standards results, click the Standards tab.
3. Inspect the calibration curve according to the criteria used in your laboratory. The
Calibration Companion view displays the calibration equation, the goodness of fit
parameter, R2, and the weighting, W. If the calibration curve is not currently displayed,
do one of the following:
• Choose View > Set Companion View > Show Calibration Curve.
• Right-click the Chromatogram view and choose Set Companion View > Show
Calibration Curve from the shortcut menu.
4. To adjust the calibration settings, right-click the Calibration Companion view and choose
Calibration Settings from the shortcut menu. The Calibration Settings dialog box
opens.
Figure 18. Calibration Settings dialog box

• To adjust the ISTD associated with the component, select a new ISTD on the Type
page. For more information, see “Setting Type Parameters” on page 46.
• To adjust the calibration equation, weighting, or units, make new selections and
entries on the Curve page. For more information, see “Setting Curve Parameters” on
page 47.

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 5 Working with Calibration Settings

• To view the calibration or QC levels, click the Levels tab. For more information, see
the Acquisitions and Processing User Guide.
• To make corrections for isotope contributions to ISTD or Target components, type
new values on the Isotope% page. For more information, see “Changing the
Isotope Percentage Value” on page 50.
• To change calibration and quantitation flag thresholds, type new values on the Flags
page. For more information, see Setting Calibration and Quantitation Flags in the
Acquisitions and Processing User Guide.
• To apply any changes to the sequence, click Apply.
5. To exclude a point or sample from the calibration curve, right-click it and choose Exclude
from the shortcut menu. To include a previously excluded point, right-click it and select
Include from the shortcut menu. For both actions, make sure your cursor is on the point.
For more information, see “Including or Excluding Data Points from the Calibration
Curve” on page 52.
6. To exclude a level, right-click the Calibration Companion view and choose Exclusion
List from the shortcut menu to open the Cal Exclusion List dialog box for the selected
component.
• To exclude a level, click the Exclude column adjacent to the level to be excluded. For
more information, see “Excluding Calibration Levels” on page 49.
• To restore an excluded level, click the Exclude column adjacent to the level to be
restored (on the word Yes).
7. To export the calibration settings with peak integration and detection parameters as a new
method, choose File > Export Method.

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5 Working with Calibration Settings
Setting Type Parameters

Setting Type Parameters

 To define the type for a component

1. From the Quan view of the Processing Setup window, click the Calibration tab. The
Calibration page opens.
2. To select a component, click a component in the Component list located at the far right
of the Processing Setup window.
3. To define the type of the selected component, select the Target Compound option or the
ISTD option.

Note When creating an internal standard method, you must define at least one
component to be an ISTD before you can define any other components as target
compounds.
Figure 19. Calibration page

• If you select the Target Compound option, the Target Compounds area becomes
active. Go to step 4.
• If you select the ISTD option, the ISTD box becomes active. Go to step 5.
4. To select an ISTD for the target compound option, use the ISTD box to select an internal
standard for the calibration. To correct for Isotope Contributions, click Isotope %.
5. To define the ISTD for the ISTD option, type values for the amount of the ISTD and the
number of units.
6. Repeat this procedure for all components.

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 5 Working with Calibration Settings
Setting Curve Parameters

Setting Curve Parameters

Use the Curve page (see Figure 20) to change the way the Xcalibur data system calculates and
plots the calibration curve from the data points.

 To set calibration curve parameters

1. From Quan Browser, choose View > Set Companion View > Show Calibration Curve.
Then right-click the calibration curve and select Calibration Settings from the shortcut
menu. Click the Curve tab.
Figure 20. Curve page – Calibration Settings dialog box

2. Select a calibration curve type:

Use the Calibration Curve list to select Locally Weighted for the calibration curve type.
If you select Linear or Quadratic, the Weighting box becomes active. Go to Step 6. If you
select any of the other curve types, the Weighting box is not active. Go to Step 7.
3. To select calibration point weighting, select from these options: Equal, 1/X, 1/X^2, 1/Y,
1/Y^2, or 1/s^2. This selection makes sure the Xcalibur application applies the correct
regression weighting method when it calculates the least-squares regression calibration
curve.
4. Select how to treat the origin in the calibration curve calculation:
• To not include the origin in the calibration curve calculation, select the Ignore
option.

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5 Working with Calibration Settings
Setting Curve Parameters

• To require that the calibration curve passes through the origin, select the Force
option.
• To include the origin as one data point, select the Include option.
5. To select the units to be displayed on graphs and reports, type the required units label in
the Units box.
6. Select the response:
• To quantitate based on the integrated area of component peaks, select the Area
option. Go to step 8.
• To quantitate based on the calculated height of component peaks, select the Height
option. Go to step 8.
7. To select internal standard settings, specify the units of the internal standard injected into
each sample in the Units box.
8. To save the new settings and close the dialog box, click OK.

These parameters are identical to those in the Target Compounds area on the Calibration
page of Quan view in Processing Setup. These are described in more detail in “Calibration
Settings Dialog Box” on page 86.

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 5 Working with Calibration Settings
Excluding Calibration Levels

Excluding Calibration Levels

Use the Cal Exclusion List dialog box (see Figure 23 on page 53) to exclude levels from the
calibration. (For a description of the procedures used to generate this list, see “Understanding
How Quan Browser Works” on page 11.) Excluding calibration levels is particularly useful
when you cannot use the Include and Exclude commands because of overlapping points on
the calibration curve. If you are using a named calibration file, levels might not be represented
in the Results grid but will always be listed in the Cal Exclusion List dialog box.

 To change the exclusion status of a level

1. Right-click the Calibration Companion view and choose Exclusion List from the
shortcut menu.
Figure 21. Cal Exclusion List dialog box

The dialog box lists all the replicates used in the current bracket or group and their
exclusion status. Levels are listed under the following headings:

Level Shows the name for the level.

Expected Displays the expected amount for the level.
% Diff Shows the percentage difference between measured and expected
amounts.
Exclude Denotes excluded levels by the word Yes.

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5 Working with Calibration Settings
Changing the Isotope Percentage Value

2. To exclude a level, click the Exclude column adjacent to the level to be excluded. The
application does the following:
• Recalculates the calibration curve without any samples using the level.
• Updates the corresponding Peak Status and Exclude fields in the Results grid to show
that the samples are excluded.
• Redraws excluded data points as unfilled squares.
3. To restore an excluded level, click the Exclude column adjacent to the level to be restored
(on the word Yes). The application does the following:
• Incorporates all samples using the level into the calibration and recalculates the curve.
• Updates corresponding Peak Status and Exclude fields in the Results grid to show
that the points are now included.
• Redraws the included data point as a filled square.
4. To save the new settings and close the dialog box, click OK.

Changing the Isotope Percentage Value

Use the Isotope% page (see Figure 22) to correct data in these situations:
• An impurity in the internal standard compound that elutes at the same time as the target
compound
• An impurity in the target compound that elutes at the same time as the internal standard

These parameters are identical to those in the Correction For Isotope Contribution dialog
box, accessed from the Calibration page of Quan view in Processing Setup.

 To set Isotope% parameters

1. From Quan Browser, show a calibration curve in the Companion view.

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 5 Working with Calibration Settings
Changing the Isotope Percentage Value

2. Right-click the Companion view and choose Calibration Settings from the shortcut
menu. Click the Isotope% tab.
Figure 22. Isotope% page – Calibration Settings dialog box

3. Choose from these options:

• If you have an impurity in your internal standard that elutes at the same time as the
target molecule, use the ISTD to Target Compound box to type the ratio ISTD
impurity/ISTD pure.
To determine this ratio experimentally, analyze the ISTD reagent using the method
to be used for quantitation of the target compound. Use the respective peak areas or
heights to determine the ratio of impurity peak at retention time of TM to pure
compound peak at retention time of ISTD: ISTD impurity/ISTD pure.
• If you have an impurity in your target molecule reagent that elutes at the same time as
the ISTD molecule, use the Target Compound to ISTD box to type the ratio TM
impurity/TM pure.
To determine this ratio experimentally, analyze the TM reagent using the method to
be used for quantitation of the target compound. Use the respective peak areas or
heights to determine the ratio of impurity peak at the retention time of ISTD to pure
compound peak at retention time of TM: TM impurity/TM pure.
The Xcalibur application corrects for the ISTD impurity, TM impurity, or both using
the data you provide in Steps 1 and 2, and reports the corrected amounts of ISTD
and TM.

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5 Working with Calibration Settings
Including or Excluding Data Points from the Calibration Curve

4. To save the settings and close the dialog box, click OK.

Including or Excluding Data Points from the Calibration Curve

 To review the results of a spectrum search

1. To open the sequence file that contains the calibration standards, from the Quan Browser
window, choose File > Open. The Open dialog box opens. In the Files of type list,
select .sld. Browse to find the correct file. Select it and click Open. The View Sample
Types dialog box opens. Select the Show All sample types option, and click OK.
The Results grid, Component list, Chromatogram Plot, and either Spectrum Plot or
Calibration Curve Plot view open.
2. To select the component for the calibration curve you want to view, click a component in
the Component list view. The calibration curve in the Calibration Curve Plot view opens.
3. Examine the Calibration Curve Plot data:
• To replot the data with a different X-axis, drag the cursor horizontally over the range
that you want to expand. The Xcalibur application rescales the axis and replots the
data with the new X-axis range.
• To replot the data with a different Y-axis, drag the cursor vertically over the range that
you want to expand. The Xcalibur application rescales the axis and replots the data
with the new Y-axis range.
• To cancel the replot and return to the full range of the X-axis and Y-axis, click .
4. To exclude or include a point, right-click the Calibration Curve Plot view and choose
Exclusion List from the shortcut menu. The Cal Exclusion List dialog box opens. The
application displays the level name, expected amount, % difference, and whether the
point is Excluded [Yes] or Excluded [Blank] for each calibration data point on the list.
Excluded [Blank] indicates that the data point is to be included.

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 5 Working with Calibration Settings
Including or Excluding Data Points from the Calibration Curve

Figure 23. Cal Exclusion List dialog box

5. Select to include or exclude data points in the calibration curve:

• To include an excluded point, click Yes in the Exclude column for the data point.
The Xcalibur application changes the Excluded [Yes] to Excluded [Blank].
• To exclude an included point, click the Exclude column for the data point. The
Xcalibur application changes Excluded [Blank] to Excluded [Yes].
6. To replot the calibration curve and recalculate results, click Apply.
The Xcalibur application plots included data points as filled squares and excluded data
points as outlined squares; replots the calibration curve using only included points; and
recalculates the values for Calculated Amount, % Diff, and % RSD in the Results grid.
7. Repeat steps 5 and 6 until you obtain the desired results:
Click Apply. The application plots included data points as filled squares and excluded
data points as outlined squares; replots the calibration curve using only included points;
and recalculates the values for Calculated Amount, % Diff, and % RSD in the Results
grid.
8. To close the Cal Exclusion List, click OK.

Note When you close Quan Browser, your selections and recalculations are erased.
Save your selections and recalculations by choosing File > Save As to create a Quan
Browser file (*.xqn).

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Restoring an Excluded Data Point

Restoring an Excluded Data Point

To restore a data point that you have previously excluded, right-click the data point and
choose Include from the shortcut menu. The Xcalibur data system does the following:
• Incorporates the data point into the calibration and recalculates the curve.
• Updates the corresponding Peak Status and Exclude field in the Results grid and
Exclusion List to show that the point is now included.
• Redraws the included data point as a filled square.

Include or exclude samples that are shared between brackets. Their status is unique to the
bracket. For example, excluding a shared sample in bracket 1 has no effect on the inclusion
status in bracket 2.

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Viewing Results and Generating Reports

Read the following for details about viewing and changing quantitative analysis results and
generating reports.

Contents
• Using the Results Grid Window
• Reviewing and Reworking Results
• Generating Reports

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Using the Results Grid Window

Using the Results Grid Window

The Results grid window is made up of sequence entries. Each row defines a result file and
associated parameters. Above the Results grid, The Xcalibur data system displays the Bracket
in use box and the Calibration File box. For more information about the Results grid, see
“Quan Browser Results Grid View” on page 76.

The Results grid is made up of these key areas:

• Bracket/Group in Use
• Calibration File
• Results Grid Columns
Figure 24. The Results grid

Bracket/Group in Use
For bracketed sequences, this list shows the available brackets in sequential order. The
Xcalibur application selects the first bracket in the list when the file is first loaded into Quan
Browser and displays the samples within this bracket in the Results grid.

When you load an unbracketed sequence, the samples are broken into logical groups (see
“Brackets for Sequences” on page 12). The list shows the available groups.

Selecting a new bracket or group from the list refills the Results grid with the samples from
the selected bracket or group. The application updates all the other Views and dialog boxes
automatically.

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Reviewing and Reworking Results

Calibration File
This read-only box shows the calibration method applied to the current bracket or group.
When the calibration information for the current bracket is obtained from the embedded
processing method and not from a separate calibration file, the box displays Embedded
Calibration.

For unbracketed sequences, the box displays the name of the calibration file associated with
the current group in the sequence. To change the calibration file, choose File > Replace
Calibration. This option is not available for bracketed sequences.

Results Grid Columns

The Xcalibur application lists samples under some or all of the headings described in “Quan
Browser Results Grid View” on page 76.

Reviewing and Reworking Results

 To review and rework results

1. To open the Quan Browser window, click , or choose GoTo > Quan Browser from
any Xcalibur window.
The Open dialog box opens so that you can select a file to review and rework. You can
select a sequence list file (.sld extension), a result file (.rst extension), or a Quan Browser
file (.xqn extension).
2. Select the file and click OK.
The View Sample Types dialog box opens.
3. Select either the Show Standard and QC sample types or Show All sample types
option. Click OK.
The Quan Browser window opens with the Results grid view, Component list view,
Spectrum Plot view, and Calibration or Spectrum Plot view.
4. To select a component, click a component in the Component list view.
5. To display calibration standards results, click the Standards tab.
6. Inspect the calibration curve in the Calibration Curve Plot view. Evaluate the calibration
curve according to the criteria used in your laboratory.
• You can right-click the Calibration Curve Plot view to display commands in the
shortcut menu for modifying the information in this view.
• You can right-click a data point in the Calibration Curve Plot view to display
commands in the shortcut menu for modifying the data in this view.

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Reviewing and Reworking Results

7. To select the first data file, click the first row in the Results grid view.
8. Check the entries in the Result grid view for peak detection and integration problems.
Ensure that the selected data file corresponds to the correct level and sample type.
You can right-click the Results grid view to display commands in the shortcut menu for
modifying the information in the Results grid view.
9. Change the information in any of the following columns by clicking the appropriate grid
cell:
• In the Sample Type column, click a cell and select Standard, QC, Blank, or
Unknown from the list.
• In the Integration Type column, click a cell and select Method Settings, User
Settings, or Manual Integration from the list.
• In the Levels column, click a cell and select another defined level from the list.
• In the Exclude column, select or clear the Exclude check box in a cell to exclude or
include the sample in the bracket calibration. Selecting excludes the data and is
indicated in the grid by Yes.
When a sample is shared between two brackets, you cannot change its sample type. The
Xcalibur application notifies you when a sample is part of two overlapping brackets if you
attempt to change its Integration Type, Level, or Exclude state.
10. Inspect the component peak in the Chromatogram Plot view:
• Make sure that the Xcalibur application found the peak. The application shades all
found peaks gray and marks the starting and ending points with square integration
markers.
• Make sure that the Xcalibur application integrated the peak properly. The shaded
area should accurately represent the contribution of the component to the
chromatogram. For more information, see “Working with Peaks” on page 23.
If necessary, perform steps 11 and 12.
11. To modify the peak detection and integration settings (optional), right-click the
Chromatogram Plot view to display commands in the shortcut menu for modifying the
information in this view.
Choose User Peak Detection Settings to display the User Identification Settings dialog
box. For more information, see “Setting User Peak Detection Parameters” on page 25.
• To modify the peak detection settings, click the Detection tab.
• If you have problems with noise in the peak or peak tailing, click the Integration tab
to modify the settings.
• If baseline noise is interfering with peak identification or integration, click the
Advanced tab to modify the settings.

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Reviewing and Reworking Results

12. To manually change the starting and ending points and baseline of the peak, drag the
square integration markers to the desired location.
13. To select the next data file, click the next row in the Results grid view.
Go to step 8.
14. To display quality control (QC) results, click the QCs tab.
15. To review and rework the QC results, perform steps 7 through 13 for the QCs. Evaluate
the QCs according to the criteria used in your laboratory.
16. To display Blank results, click the Blanks tab.
17. To review and rework the Blank results, perform steps 7 through 13 for the blanks.
Evaluate the blanks according to the criteria used in your laboratory.
18. To display unknown results, click the Unknowns tab.
19. To review and rework the Unknown results, perform steps 7 through 13 for the
Unknowns. Evaluate the Unknowns according to the criteria used in your laboratory.
20. To review and rework the next component, perform steps 8 through 16 for the remaining
components.

Hiding or Displaying Columns

The Quan Browser Results grid contains many columns. Choose to display some or all of
these columns using the Result List Column Hiding dialog box.
Figure 25. Result List Column Hiding dialog box

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Reviewing and Reworking Results

 To open the Result List Column Hiding dialog box

1. Right-click the Results grid and choose Columns from the shortcut menu.
2. Select the check box for a column heading to display it. Clear the check box to hide the
column.
3. To save your changes, click OK.

Changing the Sort Order

 To change the sort order for entries in the Results grid

1. Right-click the grid and choose Set Sorting Order from the shortcut menu. The
Quantitation Results Sorting Order dialog box opens.
Figure 26. Quantitation Results Sorting Order dialog box

2. To choose a heading for the primary sort of the Results grid, select any of the following
column headings or file properties:

• <none> • Area/Height • Level Name

• %Difference • Area/Height Ratio • Peak Status
• %RSD • Exclude • Sample ID
• Acquisition Date • File Name • Sample Type
• Integration Type

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Generating Reports

By default, the Xcalibur application sets the first order sort to the acquisition date of the
file. Select and sort with any of these sort options even if the corresponding column is not
currently displayed. For example, you can sort by Sample Type even if you have selected
the Sample Name check box in the Result List Column Hiding dialog box.
3. Set any remaining column headings or file properties as the second and third sort criteria,
even if the column is currently hidden.
4. To replace the default sorting criteria with your new selections, click Save As Default.
5. To sort the Results grid display, click OK.

Generating Reports
 To generate reports for the current sequence

1. Click on the toolbar or choose View > Reports dialog.

The Reports dialog box (see Figure 27) duplicates the Reports view in Processing Setup.
When opened, it displays the reports specified in the processing method associated with
the active sequence. The displayed parameters might change as you select different
brackets.
Figure 27. Reports dialog box

2. To include sample reports in any print run, select the Include Sample Reports check
box.

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Generating Reports

3. To include summary reports in any print run, select the Include Summary Reports
check box.
4. To open the Select Report Samples dialog box and choose samples in the sequence for
report generation and printing, click Select Samples. For more information, see
“Selecting Samples for Reports” on page 62.
5. To initiate report generation and printing as defined in the dialog box, click Print
Reports. For more information, see “Printing Reports” on page 63.

Selecting Samples for Reports

After clicking Select Samples in the Reports dialog box, use the Select Report Samples dialog
box (Figure 28) to choose the samples to be processed during report generation.
Figure 28. Select Report Samples dialog box

 To include a sample in report processing

1. Select the sample name in the Sample Choices list.

2. Click Add to add the sample in the Sample Choices list to the Selected Samples list. You
can add all of the samples by clicking Add All.
Select multiple files using the SHIFT and CTRL keys:
• To select a range of samples, hold the SHIFT key down.
• To select multiple samples, hold the CTRL key down.

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Generating Reports

 To exclude a sample from report processing

1. Select the sample name in the Selected Samples list.

2. To remove the sample from the Selected Samples list, click Remove. You can remove all of
the samples from the Selected Samples list by clicking Remove All.

Printing Reports
 To print reports

1. Choose GoTo > Quan Browser or click . The Open dialog box opens.
2. To select a sequence, select the name of the sequence file with an .sld extension containing
the samples you want to print reports from.
3. Click Open. The View Sample Types dialog box opens.
4. Select the default Show All sample types option and click OK. The Xcalibur application
displays the Results grid, Component list, Chromatogram Plot, Spectrum Plot (optional),
and Calibration Curve Plot (optional) views.
5. Choose View > Reports Dialog. The Reports dialog box opens.
6. To make a row in the Sample Reports table active, select the Enabled box in the first row.
7. Select the Enabled box again. A check box appears in the box.
8. Select the check box. When you click a different cell, the word Yes appears in the Enabled
box to indicate that the entire row of options is selected.
9. To select the report type that you want to print, click one of the following boxes: Stds,
QCs, Unks, or Other. A check box appears.
10. Select the check box. When you click a different cell, the Xcalibur application displays the
word Yes in the report type cell to indicate that reports are to be printed for all selected
samples of this sample type.
11. Repeat step 9 for all sample types for which you want printed reports.
12. Display the Open Report Template dialog box:
Double-click a cell in the Report Template Name column. In the Open Report Template
dialog box, select the document that you have previously prepared. Click Open. The
Xcalibur application displays the full path and the name of the Report Template
document with an .xrt extension in the Report Template Name box.
13. Repeat steps 6 through 12 for the next row for each Report Template document that you
want to use to print reports.
14. To select all of the sample reports you have selected for printing, select the Include
Sample Report check box at the bottom of the Reports dialog box.

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Generating Reports

15. Click Select Samples. The Select Report Samples dialog box opens. The samples
available from the .sld file you opened in step 2 appear in the Sample Choices box.
16. Select the samples for which you want to print reports.
• For a group of contiguous (continuous) samples, click the first of the sequence, scroll
until you see the last sample in the sequence, and hold down the SHIFT key while
you click. The Xcalibur application highlights the selected sequence.
• For a group of non-contiguous (non-continuous) samples, hold down the CTRL key
while you click each sample to select or clear it. The application highlights the
selected samples.
17. To copy the selected samples to the Selected Samples box, click Add.
18. To close the Select Report Samples dialog box, click OK.
19. From the Reports dialog box, click Print Reports. Prior to printing reports, The Xcalibur
application does the following:
• Displays the Printer Activity icon at the bottom of the Quan Browser window.
• Combines the data in the sample file you selected with the Report Template
document you selected.
• Displays the Save As dialog box.
Choose a file name for your report and click Save. The Xcalibur application adds the
prefix, ~Resolved, to your report file name.
• Adds the report printing task to the processing queue, and then displays the Printing
message box.
The Xcalibur application returns you to the Quan Browser window after the reports
print.

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 A

Quan Browser Reference

Use the Quan Browser window to review sequence results for each component in each file.
You can quickly review component peak identification and integration criteria. If you make
any changes, you can save the new results with an audit trail describing the reason for the
change.

Use Quan Browser to interactively edit processing parameters and audit changes for
individual result files. It also creates new result files that contain the processing results for
individual raw files. These result files include a copy of the method used to generate the
results.

Result files changed using Quan Browser do not affect the original processing method. To edit
processing methods, refer to the Acquisition and Processing User Guide.

Contents
• Toolbars
• Quan Browser Menus
• Quan Browser Views
• Quan Browser Dialog Boxes

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A Quan Browser Reference
Toolbars

Toolbars
Quan Browser provides a series of toolbars to help you move around the product functions.
Click below to get more information about these toolbars:
• Title Bar
• Menu Bar
• Quan Browser Toolbar

Title Bar
The title bar, located in a horizontal band at the extreme top of the window, contains the
following:
• Application name
• Current process
• Current file name
• Any optional parameters that are relevant

For example, if the active result file is ABC.sld, the Xcalibur application might display:
Quan Browser - Browser - ABC.sld [Bracket 1, View All].

Menu Bar
The Quan Browser window, main menu bar, provides access to these menus:
• File Menu
• View Menu
• Zoom Menu
• Options Menu
• GoTo Menu
• Help Menu

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Toolbars

Quan Browser Toolbar

Choose View > Customize Toolbar to add any of these buttons to the main toolbar.
Table 1. Quan Browser toolbar buttons (Sheet 1 of 3)
Button Description
File
Open Open previously saved data files. The Xcalibur data system supports these
file types: sequence (*.sld), result (*.rst), and Quan Browser (*.xqn) files.
Save Create a new Quan Browser file with a *.xqn extension. This file contains
all the necessary information required to recreate the current browser
session.
Save As Create a new Quan Browser file with*.xqn. This file contains all the
necessary information required to recreate the current browser session.
Save All Update all result files with the current information. Each result file comes
from a results row in the Results grid. Since each row can use method, user,
or manual integration, and the result file can contain only one method, the
Xcalibur data system uses the currently selected method for that row when
creating the result file. The system flags the embedded processing method
as modified. This means that each result file can potentially contain
different embedded processing methods. If read back into Quan Browser,
the system uses the first sample’s embedded processing method for the
entire bracket’s method settings. When read in, it sets each sample that has
a modified processing method in the User integration mode. The operator
must reintegrate and quantitate using a common method.
Reports Dialog Select and turn Report Templates on or off along with other options for
sample reports and summary reports.
Print All Enabled Reports Print all active and currently selected sample reports as well as all active
summary reports.
Print Enabled Sample Reports Print active and currently selected sample reports.

Print Enabled Summary Print all active summary reports.

Reports

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Toolbars

Table 1. Quan Browser toolbar buttons (Sheet 2 of 3)

Button Description
View
Show Calibration Curve View the Calibration Curve Plot view in the lower right corner of the
Quan Browser window.
Show Spectrum Plot View the Spectrum Plot view in the lower right corner of the Quan
Browser window.
Reports Dialog Select and enable previously created report templates and other options for
sample reports and summary reports.
Show Large Toolbar View either the large or small Quan Browser toolbar. The Xcalibur data
system displays the large toolbar when you select the checkbox to the left of
the command. The system displays the small toolbar when you clear the
check mark to the left of the Show Large Toolbar command.
Zoom
Zoom In Y To show more detail, zoom in on the Y-axis by a factor of two (2) from the
current baseline.
Zoom Out Y To show more data, zoom out on the Y-axis by a factor of two (2).

Auto Range View the chromatogram, which is normalized from the minimum to the
maximum signal. (This zoom feature is recommended 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% to 0-100%.
Zoom In X To show more detail, zoom in on the X-axis by a factor of two (2).

Zoom Out X To show more detail, zoom out on the X-axis by a factor of two (2) from
the center.
Display All View all data on the X-axis or all text in a report.

Reset Scaling To Full Scale To display the maximum amount of data, reset the scaling of both the
X- and Y-axis.

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Toolbars

Table 1. Quan Browser toolbar buttons (Sheet 3 of 3)

Button Description
Noise
Manual Noise Region
Specify a noise region manually. Click and drag the cursor
horizontally across the region of the chromatogram to be the noise region.
The Xcalibur application marks the region with a red baseline.

The application calculates noise based on the data points you select. It uses
all selected data points as noise points and calculates noise based on those
points. You can select the noise region from an individual trace or different
noise regions from multiple traces.

Open a raw file and select a chromatogram to make this button active.
Delete Manual Noise Region
Remove a designated manual noise region. Click and drag the cursor
over the region that was previously selected as the noise region. Release the
mouse button to delete the noise region.
Options
View Stds And QCs View all components or just standards and quality control samples in the
Results grid.
GoTo
Instrument Setup Open the Instrument Setup window.

Processing Setup Open the Processing Setup window.

Qual Browser Open the Qual Browser window.

Library Browser Open the Library Browser window.

Xcalibur Home Page Open the Home Page window if it is closed or display the Home Page
window if it is already open. This command closes the Instrument Setup
window so that all instrument setup methods are closed when samples that
use these methods are run from the Home Page window.
Help
Quan Browser Help View Help for Quan Browser.

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Quan Browser Menus

Quan Browser Menus

The Quan Browser window, main menu bar, contains the following menus:
• File Menu
• GoTo Menu
• Help Menu
• Options Menu
• View Menu
• Zoom Menu

File Menu
Table 2. File menu commands (Sheet 1 of 2)
Command Description
Open Open new data files. The supported file types are sequence (*.sld), result (*.rst), and
Quan Browser (*.xqn) files.

Save Create a new Xcalibur Quan Browser file with an *.xqn extension. This file
contains all the necessary information required to recreate the current browser
session.

Save As Create a new Xcalibur Quan Browser file with a *.xqn extension. This file contains
all the necessary information required to recreate the current browser session.
Save All Update all result files with the current information. Each result file comes from a
results row in the Results grid. Since each row can use method, user, or manual
integration and the result file can contain only one method, the currently selected
method for that row is used when creating the result file. The embedded processing
method is flagged as modified. This means that each result file can potentially
contain different embedded processing methods. If read back into Quan Browser,
the first sample’s embedded processing method is used for the method settings of
the entire bracket. When read in, each sample that has a modified processing
method is set in the User integration mode, and it is up to the operator to
reintegrate and quantitate using a common method if desired.
Export Method Export the processing method of the currently selected row. If no processing
method is available, the Xcalibur application uses the original processing method.

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Quan Browser Menus

Table 2. File menu commands (Sheet 2 of 2)

Command Description
Export Data To Excel
Short Report Create a short Microsoft Excel report. The short report displays the data contained
in the current bracket and contains the same information that is available in each
Results grid row.
Long Report Create a long Microsoft Excel report. The Xcalibur application reports on the data
contained in the current bracket and contains the same information that is available
in each Results grid row, as well as other information that is not displayed in the
grid.
Summary Information View summary information for the current *.xqn file.
Change Dataset Name Select a dataset from a predefined list of names.

The text of this menu item might be different if the administrator chooses to use
another name for a dataset. For example, this menu item might be Change Job
Name.
Audit Trail View all auditable events and changes made to data files in the current application.
Print Setup Select a printer, paper, and page orientation.
Print
Reports Dialog Select and turn Report Templates on and off along with other options for sample
reports and summary reports.
All Enabled Reports Print all active and currently selected sample reports as well as all active summary
reports.
Enable Sample Reports Print active and currently selected sample reports.
Enable Summary Reports Print all active summary reports.

Recently Used Files View the paths and names of the most recently used files, located above the Exit
command. The Xcalibur application displays both open and closed files. Click a
displayed file to load it. If the selected file is closed, the application reopens it.
Exit Close the Quan Browser window. This option does not close any other Xcalibur
windows. The Home Page window is not closed.

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Quan Browser Menus

GoTo Menu
Table 3. Go To menu commands
Command Description
Instrument Setup Open the Instrument Setup window.

Processing Setup Open the Processing Setup window.

Qual Browser Open the Qual Browser window.

Library Browser Open the Library Browser window.

Xcalibur Home Page Open the Home Page window.

Help Menu
Table 4. Help menu commands
Command Description
Quan Browser Help Open Xcalibur Help and view Help for the Quan Browser window.
Xcalibur Help Open Xcalibur Help.
Glossary Open the glossary.
How To Use Help Open Help that describes how to use the Help viewer.
About Quan Browser Open the About Quan Browser dialog box. This dialog box displays the installed
version number of the Quan Browser program and the Thermo Fisher Scientific
copyright notice.

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Quan Browser Menus

Options Menu
Table 5. Options menu commands
Command Description
Delete ComponentName Delete the currently selected component from analysis. This command results in a
recalibration.
Masses View or change the default settings for mass tolerance and mass precision.
View Stds And QCs/ View All View either all components or just standards and quality control samples in the
Results grid view.
Enable Warnings View, as needed, all warnings boxes, even though their display has been previously
suppressed.

View Menu
Table 6. View menu commands
Command Description
Set Companion View
Show Calibration Curve View the Calibration Curve Plot view in the lower right corner of the Quan
Browser window.

Show Spectrum Plot View the Spectrum Plot view in the lower right corner of the Quan Browser
window.

Reports Dialog Specify the report template name to be used for sample reports or summary reports.

Toolbar View or hide the toolbar. The toolbar appears if it was previously hidden or hides if
it is currently displayed.
Status Bar View or hide the status bar. The status bar appears if it was previously hidden or
hides if it is currently displayed.
Show Large Toolbar View either the large or small Quan Browser toolbar. The large toolbar is displayed
when a check mark appears to the left of the command. The small toolbar is
displayed when the check mark to the left of the Show Large Toolbar command is
cleared.
Customize Toolbar Drag any toolbar icon from this dialog box to any location on the Quan Browser
toolbar and from the toolbar to this dialog box.

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Zoom Menu
Table 7. Zoom menu commands
Command Description
Zoom In Y To show more detail, zoom in on the Y-axis by a factor of two (2)
from the current baseline.
Zoom Out Y To show more data, zoom out on the Y-axis by a factor of two (2).

Auto Range View the chromatogram, which is normalized from the minimum
to the maximum signal. (This zoom feature is recommended 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% to 0-100%.
Zoom In X To show more detail, zoom in on the X-axis by a factor of two (2).

Zoom Out X To show more detail, zoom out on the X-axis by a factor of two (2)
from the center.
Display All View all data on the X-axis or all text in a report.

Reset Scaling To display the maximum amount of data, reset the scaling of both
the X- and Y-axis.

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Quan Browser Views

Quan Browser Views

Table 8. Quan Browser views
Quan Browser Results Grid View View the sample rows that are retrieved from the sequence or Result files. You
can right-click this view to display a shortcut menu. Use this menu to review
and edit the Results grid view.
Quan Browser Component List View a list of all of the components contained in the current bracket. This list
View is in the order of user data entry in the processing method. Found/Not Found
symbols are placed to the left of the component names depending on whether
or not the Xcalibur data system found the component based on the current
detection criteria for the component.
Quan Browser Chromatogram Plot View the currently selected component chromatogram from the currently
View selected result file. This view, located in the lower left corner of the Quan
Browser window, displays a plot of relative abundance versus time in minutes
for the selected component. You can right-click this view to display a shortcut
menu to review and change peak detection and integration settings.
Companion View Located to the right of the Chromatogram Plot view (its companion) in the
lower right corner of the Quan Browser window. In the companion view you
can choose either the Spectrum view or the Calibration Curve Plot view.
Quan Browser Spectrum Plot View View a plot of relative abundance (Y-axis) versus mass-to-charge ratio for the
selected component. You can right-click this view to display a shortcut menu to
display the spectrum at the left edge, apex, and right edge of the chromatogram
peak. Also, you can reset the scaling of the view.
Quan Browser Calibration Curve View a plot of area or area ratio (Y-axis) versus concentration or amount
Plot View (X-axis) for the selected component. You can right-click this view to display a
shortcut menu to review and change calibration settings, reset the scaling of the
view, and copy the graph. If you right-click a calibration point, the Calibration
Point shortcut menu appears so that you can exclude/include the point, review
calibration settings, reset the scaling of the view, or copy the graph.

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Quan Browser Results Grid View

The Results grid view displays sequence or result sample data entries. Each row defines a result
file and its associated parameters. Selecting any cell within the Results grid causes the
additional views to refresh, using data from the newly selected sequence row. The Xcalibur
data system validates any changes made to the sequence row and updates displays
automatically.
Figure 29. Results grid view

In the Options menu, if you choose to view to View Stds and QCs, the Results grid view
displays three tabs: All, Stds, and QCs. The All page displays all Stds and QCs, the Stds page
displays only standards, and the QCs page displays only QCs.

In the Options menu, if the viewing preference is set to View All, the Results grid view
displays five tabs: All, Stds, QCs, Blanks, Unknowns. The All page in this case displays all
Stds, QCs, Blanks and Unknowns. The Stds page displays only standards, the QCs page
displays only QCs, the Blanks page displays only blanks, and the Unknowns page displays
only unknowns.

Depending on the current settings of the Result List Column Hiding dialog box, the Results
grid view can display different parameters for each sample row.
Table 9. Results grid parameters (Sheet 1 of 2)
Parameter Description
File Name View the raw file that contains the acquisition data for this run.
Sample Type View the sample type that has been assigned to the sample. Every sample must be designated
one of these four basic types: Standard, QC, Blank, or Unknown.

You cannot change sample type of a sample that is shared between two brackets. If you try
to make this type of change, the Xcalibur application displays a warning message:
You cannot change the sample type of a sample shared between brackets. Reverting back
to original sample type.

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Table 9. Results grid parameters (Sheet 2 of 2)

Parameter Description
Integration Type View the method the data system used to integrate the peak. The options are Method, User,
and Manual. Select Method to apply the integration parameters defined during the
processing setup phase. Select User to override the integration parameters within Quan
Browser. Select Manual when the integration baseline was selected by dragging the baseline
handles.
Area Or Height View the integrated area (count-seconds) or height (counts) under the detected peak.
Internal Standard View the integrated area (count-seconds) or height (counts) under the detected Internal
(ISTD) Area/Height Standard peak.
Area Ratio or Height View the area or height ratio between the selected peak and the Internal Standard peak.
Ratio
Specified Amount View the amount of the component at the Cal or QC level.
Calculated Amount View the component amount, as determined by the response ratio and calibration curve.
% Difference View the percentage difference between the calculated amount and the specified amount.
% Relative Standard View the standard deviation of the difference between the calculated amount and the
Deviation specified amount, as expressed as a percentage of the specified value.
Peak Status View the peak status:

Low: if the %Difference is < 0

High: if the %Difference is > 0

Fail: if the %Difference is > the QC fail percentage test value

Level View the calibration or QC level of the sample. To change this value, click the grid cell and
select another level from the list.
Units View the units used for quantity or concentration.
Retention Time View the retention time in minutes at the peak maximum.
Sample ID View the unique sample identification string.
Exclude Indicate whether to include or exclude the sample point from the calibration curve. Include
or exclude a point by clicking the grid cell; select the check box to include the data or clear it
to exclude the data.

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Table 10. Results grid shortcut commands

Parameter Description
Column View the list of possible columns that can be viewed in the Results grid view. Placing a check
next to an entry displays that column in the Results grid view of the Quan Browser window.
Removing the check removes the column from the Results grid view.
Delete Selected Remove the currently selected samples from the Results grid view. If you delete standard
Samples samples, the Xcalibur application recalibrates the data. If you delete either standard samples
(stds) or quality control samples (QCs), the application recalibrates the % Relative Standard
Deviation.
Add Sample Select a new file from a browse dialog box. The Xcalibur application adds it to the Results
grid view and sorts it according to the sort order. If you add standard samples, the
application recalibrates the data. If you add either standard samples (stds) or quality control
samples (QCs), the Xcalibur system recalibrates the % Relative Standard Deviation.
Copy Row Duplicate the currently selected row and add it to the next row of the Results grid view. If
the row added is a standard sample (std), then a recalibration takes place. If it is either a
standard sample (std) or a quality control sample (QC), then the Xcalibur application
recalculates the % Relative Standard Deviation.
Set Sorting Order Set the sort order for the samples in the Results grid view.
Send To Qual Browser Open the results file for the sample that you selected in Quan Browser.

Quan Browser Component List View

This view, located on the right side of the Quan Browser window, consists of a list of
components. The list displays the components in the currently loaded sequence. To select a
component of interest, select the component name from the list. All Quan Browser views are
automatically updated to reflect the settings and data for the selected component. The
Component list view provides the only method of selecting a component of interest.
Figure 30. Component list view

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Quan Browser Chromatogram Plot View

Table 11. Chromatogram Plot view shortcut commands (Sheet 1 of 2)
Command Description
Method Settings Reset the integration method to those specified in the original method stored within the
results file.
User Settings Apply a set of user-defined peak detection parameters to the integration of this peak. See
“Setting User Peak Detection Parameters” on page 25 for more information.
Manual Integration If active, this command indicates that the integration baseline has been adjusted by dragging
the control boxes on the plot. This command is inactive until you adjust the baseline by
using the graphical dragging operation at least once.
Show Peak Info View peak information in a read-only format. The information displayed reflects the
settings for the currently displayed chromatographic peak. Select other compounds or other
result files to get detailed information on the found peak. To close the dialog box, click
Close.

The compound identification name is displayed in the title bar. For example:
Peak Information – drugx
User Peak Detection Apply unique peak detection parameters to the chromatogram. The tabbed pages on this
Settings dialog box differ for GC and LC processing methods. These differences are described in the
appropriate sections. The type of processing used to create the results file comes from the
processing method (also stored within the results file) and are not available for changes
within Quan Browser.
Display Options Place labels, such as retention time, scan number, base peak, signal-to-noise, flags, area, and
height, on your chromatograms.

This menu command is not active if no chromatogram data is displayed in the

Chromatogram Plot view.
Manually Add Peak Manually place a baseline on the Chromatogram Plot and set the current integration
method for the current component to Manual Integration. The Xcalibur data system
changes the entry in the Integration Type box of the Results grid view.

If no peak has been detected for the currently selected compound, there is no integration
baseline on the chromatogram plot for you to manually adjust.
Set Peak To Not Found Tag the current peak as Not Found, do another peak search (possibly with new integration
Status parameters), or do a manual integration to restore the peak.

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Table 11. Chromatogram Plot view shortcut commands (Sheet 2 of 2)

Command Description
Update Expected Update the retention time specified in the processing method with the retention time that
Retention Time the Xcalibur data system detected.

Update Component In Current Row command: This command updates the retention
time of the current component in the current row of the active sequence and recalculates the
data for the row in the Results grid view.

Update All Components In Current Row command: This command updates the
retention time of all the components in the current row of the active sequence and
recalculates the data for the row in the Results grid view.
Reset Scaling This command resets the plot scale to include the full peak in a normalized window.

Quan Browser Spectrum Plot View

When you select the Spectrum Plot view located in the lower right corner of the Quan
Browser window as the companion plot, the Xcalibur application displays a spectrum from
the current chromatogram. From this view, you can change the retention time used to select
the spectrum in two ways. Right-click the Spectrum Plot view to display the shortcut menu.

Table 12. Spectrum Plot view shortcut commands (Sheet 1 of 2)

Command Description
Spectrum At Peak Apex View the spectrum at the apex retention time of the displayed chromatogram peak.
Spectrum At Peak Left Edge View the spectrum of the left edge of the displayed chromatogram peak. The left
edge is defined at the retention time corresponding to the left baseline box
(handle).

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Table 12. Spectrum Plot view shortcut commands (Sheet 2 of 2)

Command Description
Spectrum At Peak Right Edge View the spectrum of the right edge of the displayed chromatogram peak. The right
edge is defined at the retention time corresponding to the right baseline box
(handle).
Display Options Select the style, color, labels, axis, and normalization options for your spectrum
from the Display Options dialog box.

This menu command is not active if no spectrum data is displayed in the Spectrum
Plot view.
Show Calibration Curve View the Calibration Curve Plot view in the lower right corner of the Quan
Browser window.
Reset Scaling Reset the plot scale to include the full peak in a normalized window.

Quan Browser Calibration Curve Plot View

Right-click in the Calibration Curve Plot view (except on a calibration point) to display the
shortcut menu.
Table 13. Calibration Curve Plot view shortcut commands
Command Description
Calibration Settings Select values for the following parameters: type, curve, levels, isotope%, and flags. These
options appear when you display a valid calibration curve.
Save Calibration File Name and save the calibration file to the directory of your choice.
Exclusion List Select points in the Calibration Curve Plot to include or exclude.
Show Spectrum Plot View the Spectrum Plot view in the lower right corner of the Quan Browser window. To
display the Spectrum Plot view, choose one of these options:
• Choose View > Set Companion View > Show Spectrum Plot.
• Click in the toolbar.
• Right-click the Calibration Curve Plot view and select the Show Spectrum Plot
command.
Reset Scaling Reset the plot scale to include the full peak in a normalized window.
Copy Graph Copy the Calibration Curve Plot view to the clipboard so that you can transfer it to another
open application, such as Microsoft Word™, using the Paste command. This operation is
useful when you are writing a report and want to include the calibration curve.

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Table 14. Calibration Plot view shortcut commands

Command Description
Include/Exclude Include or exclude data points on the Calibration Plot.

If the current data point was previously excluded, the first menu item is Include instead of
Exclude. Select this command to include the data point and recalculate the calibration
curve. The data system updates the excluded entry in the Results grid to show that this
point is now included and redraws the included data point on the calibration curve using a
filled square.

If the data point is currently included in the calibration, selecting the Exclude command
forces the calibration curve to be recalculated without the selected data point. The excluded
entry in the Results grid view is updated to show that this point is excluded and the
excluded data point is redrawn on the calibration curve using an unfilled square.

You can include or exclude samples that are shared between brackets. Sample status is
unique to the bracket—that is, excluding a shared sample in bracket 1 has no effect on its
inclusion status in bracket 2.
Calibration Settings Select values for the following parameters: type, curve, levels, isotope%, and flags. These
options appear when you display a valid calibration curve.
Exclusion List Select points in the Calibration Curve Plot to include or exclude.
Show Spectrum Plot View the Spectrum Plot view in the lower right corner of the Quan Browser window.
Reset Scaling Reset the plot scale to include the full peak in a normalized window.
Copy Graph Copy the Calibration Curve Plot view to the clipboard so that you can transfer it to another
open application, such as Microsoft Word, using the Paste command. This operation is
useful when you are writing a report and want to include the calibration curve.

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Quan Browser Dialog Boxes

Quan Browser has the following dialog boxes:
• Add Sample Dialog Box
• Bracket/Group In Use List
• Cal Exclusion List Dialog Box
• Calibration Settings Dialog Box
• Display Options Dialog Box
• Masses Dialog Box
• Peak Information Dialog Box
• Quantitation Results Sorting Order Dialog Box
• Reports Dialog Box
• Result List Column Hiding Dialog Box
• Select Level Dialog Box
• Select Report Samples Dialog Box
• User Identification Settings Dialog Box
• View Sample Types Dialog Box

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Add Sample Dialog Box

Use the Add Sample dialog box to change information about the sample that you are adding
to the Results grid view using the Open dialog box.
Table 15. Add Sample dialog box parameters
Parameter Description
Sample Type Select a sample type for a new sample.
Level Select a level for a new sample.
Sample ID Enter the sample ID for a new sample.
ISTD Corr Amt Enter the ISTD amount for a new sample.
Dilution Factor Enter the Dilution Factor for a new sample.

Bracket/Group In Use List

Use this list to select the current bracket or group being browsed. Select a new bracket or
group from the list to refill the Results grid view with the samples from the selected bracket.
The Xcalibur data system updates all additional plots and dialog boxes automatically.
Table 16. Brack/Group In Use list parameters
Parameter Description
Bracket in use If a bracketed sequence is open, the Bracket in use list is active and displays the available
brackets numbered sequentially from one to the number of brackets in the sequence, for
example: Bracket 1, Bracket 2, Bracket 3, and so on. If the sequence contains multiple
brackets, the Xcalibur application selects the first bracket in the list and displays the samples
related to that bracket in the Results grid view. If the sequence contains only one bracket,
then the list displays only one entry: Bracket 1.
Group in use If an unbracketed sequence is open, the Group in use list is active and displays groups
broken up logically. For example: Group 1, Group 2, Group 3, and so on. Groups are
separated by standards and are created using the following rules:

The Xcalibur application scans the sequence file in chronological order until the first
standard (either Std Clear or Std Update) is encountered. The first standard begins a new
group. The application continues looking through the sequence, adding all samples to this
group until the next standard after the first nonstandard is found. There are two deviations
from this rule. The first exception is that the first group does not have to start with a
standard. The first sample, by definition, begins the first group. The second exception is
that any Std Clear begins another group even if it immediately follows a Std Update.

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Cal Exclusion List Dialog Box

The Cal Exclusion List dialog box displays a list of all the replicates used in creating the
current calibration curve. In some cases there might appear be more entries in this list than are
displayed in the calibration curve. Typically, this is because some points lie on top of each
other and cannot be seen on the plot of the calibration points. If this is the case, it is
impossible to change the exclusion status of all the overlapping points by right-clicking the
graphed point. The Xcalibur data system sees the first point in its list that meets the position
requirement and changes its status. The application never sees the other data points.

All overlapping points can be included or excluded in the Results grid if they are listed there.
However, when using external calibration files, these data points might not have
corresponding result rows in Quan Browser. These replicates data points are accessible using
the Cal Exclusion List dialog box.

The title bar of the Cal Exclusion List dialog box contains the name of the selected
component:
Cal Exclusion List – ComponentName

The exclusion list displays all the replicates used in the current bracket or group and their
exclusion status. If there is a Yes in the exclude column, then the Xcalibur data system excludes
this replicate data point in the calibration curve plot. If the column is blank, then the Xcalibur
system includes the replicate in the calibration curve plot. To change the status of any
replicate, click the exclude column in the row containing the replicate data point. This
changes the value. Click Apply to make the changes, but keep the Exclusion List dialog
visible. Click OK to accept the changes and close the dialog box. Click Cancel to abandon the
changes and close the dialog box.
Table 17. Cal Exclusion List dialog box parameters
Parameter Description
Level View the read-only calibration level names for the sample data points displayed in the
Calibration Curve Plot view.
Expected View the read-only expected quantity values for the data points displayed in the Calibration
Curve Plot view.
% Diff View the read-only percent difference values for the data points displayed in the Calibration
Curve Plot view. These values are the percentage difference between the calculated amount
and the expected amount.
Exclude Click each row (replicate) in the Exclude column to turn Yes on and off. Yes indicates that
the data point is excluded from the data points displayed in the Calibration Curve Plot view.

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Calibration Settings Dialog Box

The Xcalibur data system displays particular pages in the Calibration Settings dialog box,
based on whether the component is an Internal Standard or a Target.
• Available pages if the component is an internal standard

Type Page – Calibration

Settings Dialog Box

• Available pages if the component is a target

Curve Page – Calibration Flags Page – Calibration Isotope % Page – Calibration

Settings Dialog Box Settings Dialog Box Settings Dialog Box
Levels Page – Calibration Type Page – Calibration
Settings Dialog Box Settings Dialog Box

Curve Page – Calibration Settings Dialog Box

Use the Curve page to modify component type settings that you specified on the Calibration
page in the Quan view of the Processing Setup window.

To test the results of the new setting, click Apply or OK.

Table 18. Curve page parameters – Calibration Settings dialog box (Sheet 1 of 2)
Parameter Description
Calibration Curve View the selected calibration curve type.
Specify how to use the origin in your calibration curve. You can choose to ignore the origin
Origin as a data point, force the curve to pass through it, or include it as a single point on the
calibration curve.
Ignore Exclude the origin as a valid point in your calibration curve. If you select this option, the
calibration curve might or might not pass through the origin.
Force Specify that the calibration curve passes through the origin of the data point plot.
Include Include the origin as a single data point in the calculation of the calibration curve. If you
select this option, the calibration curve might or might not pass through the origin.
Use the area or the height of the target compound peak to acquire the data used for the
Response
calibration.
Area Use the area of the target compound peak to acquire the data used for the calibration.
Height Use the height of the target compound peak to acquire the data used for the calibration.

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Table 18. Curve page parameters – Calibration Settings dialog box (Sheet 2 of 2)
Parameter Description
Weighting
Equal Give all calibration data points equal weight during the least-squares regression calculation
of the calibration curve.
1/X Specify a weight value of 1/X for all calibration data points during the least-squares
regression calculation of the calibration curve. The Xcalibur application assigns a weight
value of the inverse of their quantity.
1/X^2 Specify a weight value of 1/X^2 for all calibration data points during the least-squares
regression calculation of the calibration curve. The Xcalibur application assigns a weight
value of the inverse of the square of their quantity.
1/Y Specify a weight value of 1/Y for all calibration data points during the least-squares
regression calculation of the calibration curve. The Xcalibur application assigns a weight
value of the inverse of their response (or response ratio).
1/Y^2 Specify a weighting of 1/Y^2 for all calibration data points during the least-squares
regression calculation of the calibration curve. The Xcalibur application assigns a weight
value of the inverse of the square of their response (or response ratio).
1/s^2 Specify a weighting of 1/s^2 for all calibration data points during the least-squares
regression calculation of the calibration curve. Calibrants at a given level are weighted by the
inverse of the standard deviation of their responses (or response ratios). For this weighting
factor to be used, there must be two or more replicates at each level. If only one calibrant is
available for any level, 1/s^2 weighting cannot be used.
View the units set on the Calibration page of the Quan view of Processing Setup. The units
Units
are also used in reports and in Quan Browser.

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Flags Page – Calibration Settings Dialog Box

The Flags page of the Calibration Settings dialog box displays the current calibration and
quantitation flags in use for the selected compound. The Xcalibur data system uses these
values in determining if the calibration or quantitation is within user specified criteria. They
do not alter the way calculations are made. An entered value of zero forces the flag to be false.

During entry of the values in the Quantitation Flags box, the Xcalibur system checks to make
sure that the relationships between the four fields are maintained. If an entry in one field
forces a change to occur in another field, the Automatic Adjustment message box is displayed
with the following message:
The last change made has forced an automatic change in one or more of the remaining
edit boxes. This is due to the fact that each value and the acceptable ranges for that value
are linked.
Table 19. Flags page parameters – Calibration Settings dialog box
Parameter Description
Calibration Flag
R-Squared View or change the current value of R-squared. The Xcalibur application sets the R-Squared
(RS) flag in the results file if the computed coefficient of determination is lower than the
entered R-Squared value.
Quantitation Flags
Limit Of Detection View or change the current value for the limit of detection. The Xcalibur application sets
the Limit of Detection (LOD) flag in the results file if the peak concentration is less than
the entered Limit of Detection.
Limit Of Quantitation View or change the current value for the limit of quantitation. The Xcalibur application sets
the Limit of Quantitation (LOQ) flag in the results file if the peak concentration is less than
the entered Limit of Quantitation.
Linearity Limit View or change the current value for the linearity limit. The Xcalibur application sets the
Limit of Linearity (LL) Flag in the results file if the peak concentration is greater than the
entered Linearity Limit. Linearity Limit + 10 percent is the calibration curve's X-axis upper
value (default) when displayed in the Quan Browser window. The user can then go on to
change this X-axis range.
Carry Over Limit View or change the current value for the carryover limit. The Xcalibur application sets the
Carry Over Limit (COL) flag in the results file if the peak concentration is greater than the
entered Carry Over Limit.

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Isotope % Page – Calibration Settings Dialog Box

Use the Isotope % page of the Calibration Settings dialog box to correct for an impurity in the
internal standard compound that elutes at the same time as the target compound or to correct
for an impurity in the target compound that elutes at the same time as the internal standard.
Table 20. Isotope % page parameters – Calibration Settings dialog box (Sheet 1 of 2)
Parameter Description
Contribution of
ISTD To Target View the ratio:
Compound
ISTD [impurity]/ISTD [pure]

Where:
ISTD [impurity] is an impurity compound in the internal standard reagent that elutes
at the same time as the target compound.
ISTD [pure] is the pure internal standard compound.

To determine this ratio experimentally, analyze the ISTD reagent using the method to be
used for quantitation of the target compound. Use the respective peak areas or heights to
determine the ratio of impurity to pure compound.

The valid range is 0.00 to 100.00 percent. To change the impurity ratio, type a new value in
the Contribution of ISTD to Target Compound box.

The Xcalibur application uses this ratio as the value x in the following impurity correction
expressions:
ISTD [corr] = [ISTD [obs] - y TM [obs]]/[1-yx]
TM [corr] = [TM [obs] - x ISTD [obs]]/[1-yx]

Where:
ISTD [corr] is the corrected amount of internal standard.
ISTD [obs] is the apparent amount of ISTD, as measured by the application at the
retention time for ISTD. This peak consists of ISTD [corr] + TM [impurity].
TM [corr] is the corrected amount of the target molecule.
TM [obs] is the apparent amount of TM, as measured by the application at the
retention time for TM. This amount consists of TM [corr] + ISTD [impurity].

See Contribution of Target Compound to Internal Standard box for a complete description
of the variable: y.

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Table 20. Isotope % page parameters – Calibration Settings dialog box (Sheet 2 of 2)
Parameter Description
Target Compound To View the ratio:
ISTD
TM [impurity]/TM [pure]

Where:
TM [impurity] is an impurity compound in the target molecule reagent that elutes at
the same time as the internal standard.
TM [pure] is the pure target compound.

To determine this ratio experimentally, analyze the TM reagent using the method to be used
for its quantitation. Use the respective peak areas or heights to determine the ratio of
impurity to pure compound.

The valid range is 0.00 to 100.00 percent. To change the impurity ratio, type a new value in
the Contribution of Target Compound to Internal Standard box.

The Xcalibur application uses this ratio as the value y in the following impurity correction
expressions:
ISTD [corr] = [ISTD [obs] - y TM [obs]]/[1-yx]
TM [corr] = [TM [obs] - x ISTD [obs]]/[1-yx]

Where:
ISTD [corr] is the corrected amount of internal standard.
ISTD [obs] is the apparent amount of ISTD, as measured by the Xcalibur application
at the retention time for ISTD [pure]. This peak consists of ISTD [corr] + TM
[impurity].
TM [corr] is the corrected amount of the target molecule.
TM [obs] is the apparent amount of TM, as measured by the Xcalibur application at
the retention time for TM [pure]. This amount consists of TM [corr] + ISTD
[impurity].

See Contribution of Internal Standard to Target Compound box for a complete description
of the variable: x.

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Levels Page – Calibration Settings Dialog Box

Use the Levels page of the Calibration Settings dialog box to review the current component
type settings that you specified during method development.
Table 21. Levels page parameters – Calibration Settings dialog box
Parameter Description
Cal Level View the calibration levels for the selected component.
Amount View the amount of target compound used for each calibration level.
QC Level/ View QC (quality control) level names, quality control level amounts, and % test values.
Amount/%Test Table QC samples containing known amounts of a component can be utilized to help ensure the
settings accuracy of an analysis. The Xcalibur application measures the quantity of the QC
component in the same manner as unknown components and compares the measured
quantity with a user-defined expected quantity and a user-defined percent test.
QC Level View the quality control levels for the selected component. The application can
accommodate up to 15 QC levels.
Amount View the quantity used for each QC level, as defined by the user.
% Test View a value for the acceptable difference (as a percent) between the known amount and the
calculated (measured) amount of each QC level.
Units View the units set on the Calibration page of the Quan view in Processing Setup. The
application also uses the units in reports and in Quan Browser.

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Type Page – Calibration Settings Dialog Box

The appearance of the Type page of the Calibration Settings dialog box changes depending on
whether the selected component is a Standard or a Target.
Use the Type page for an Internal Standard component to change the Amount and Units
settings that you specified on the Calibration page in the Quan view of the Processing Setup
window.
Use the Type page for a Target component to change the Internal Standard (ISTD) that you
specified on the Calibration page in the Quan view of the Processing Setup window. The
Xcalibur application selects the Target Compound option and the ISTD option, which are
read-only.
Table 22. Internal Standard component parameters
Parameter Description
The Xcalibur application recognizes two component types for component calibration
purposes: Target Compound components and Internal Standards (ISTD) components. You
can initially define, select, and characterize components of interest using the Calibration
Component Type
page in the Quan view of the Processing Setup window. You can then revise these
parameters using the Type page of the Calibration Settings dialog box available in the Quan
Browser window.
Target Compound Specify that the selected component is a target compound. This button is only active if you
have defined at least one component as an internal standard and selected another
component as a Target Compound component type: Target Compound.
ISTD Specify that the selected component is an internal standard.
Internal Standard (ISTD)
Amount View the amount of the selected component that is added to each sample to provide an
internal standard. Type amounts with up to three decimals of precision. This box becomes
active when you select the ISTD component type.
Units View the units used for the internal standard amount or concentration, for example, ng or
pg/mL. This box becomes active when you select the ISTD component type.

Table 23. Target component parameters (Sheet 1 of 2)

Parameter Description
The Xcalibur application recognizes two component types for component calibration
purposes: Target Compound components and Internal Standards (ISTD) components.
Components of interest are initially defined, selected, and characterized using the
Component Type
Calibration page in the Quan view of the Processing Setup window. These parameters can
then be revised using the Type page of the Calibration Settings dialog box available in the
Quan Browser window.
Target Compound Specify that the selected component is a target compound. This button is only active if you
have defined at least one component as an internal standard and selected another
component as Component Type: Target Compound.

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Table 23. Target component parameters (Sheet 2 of 2)

Parameter Description
ISTD Specify that the selected component is an internal standard.The ISTD option is unavailable
if you have selected the External Standard option in the Calibration Options dialog box.
This box displays the selected internal standard component to be used for calibration of the
ISTD
target compound.

Display Options Dialog Box

Use the pages of the Display Options dialog box to select Style, Color, Labels, Axis, and
Normalization settings. The options presented by these pages depend on whether the view in
the active cell is a chromatogram, spectrum, map, ion map, or spectrum list:
• Page options if a chromatogram is the active view

Style Page Color Page Labels Page

Axis Page Normalization Page

• Page options if a spectrum is the active view

Style Page Color Page Labels Page

Axis Page Normalization Page

• Page options if a map (or ion map) is the active view

Style Page Color Page Axis Page

Normalization Page Band Width Page

• Page options if a spectrum list is the active view

Style Page Normalization Page Composition Page

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Chromatogram Axis Page – Display Options Dialog Box

Use the Axis page of the Display Options dialog box to modify the appearance of your
chromatogram. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 24. Chromatogram Axis page parameters – Display Options dialog box (Sheet 1 of 3)
Parameter Description
X
Name View or change the current axis names for the X-, Y-, and Z-axes, as appropriate for the
active chromatogram, spectrum, or map. To change an axis name, type the new name in the
Name box. The Xcalibur application displays the results of the current settings in the
adjacent graphic.

The default axis names are as follows:

• X: Time
• Y: Relative Abundance
Show name View or change when the Xcalibur application displays the axis name next to the
corresponding axis. The Xcalibur system can display the axis label displayed in the axis
Name box at the following times:
• Never: The application does not display the axis label when the graphic is displayed or
printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.

The current option is displayed in the list.

To change the time when the application displays the axis label, select from the Show name
list of options. Click Never, On Print, or Always.

Since standard reports are not displayed on the screen, the On Print and Always Show
name list options for standard reports are identical.
Offset Set the location for the displayed plot a specified distance from the X and/or Y axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.
Split time range Split the time scale of the active chromatogram into two or more divisions. To split the time
scale, select the Split time range check box. The Xcalibur application activates the divisions
box so that you can select the number of divisions.

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Table 24. Chromatogram Axis page parameters – Display Options dialog box (Sheet 2 of 3)
Parameter Description
Divisions View or change the current number of divisions for a chromatogram with a split time range.
This box is only active if you select the Split time range check box. The number of divisions
can be two, three, or four. To change the number of divisions, type the new number in the
Divisions (time) box. The Xcalibur data system displays the multiple chromatograms in the
adjacent graphic.
Y
Separate labels Apply a distinct label to the Y-axis of each plot in the active chromatogram view. To label
the chromatogram plots separately, select the Separate labels check box. The Xcalibur
application activates the Plot box so you can specify the plot to get a specific label. Select
multiple plots on the Ranges page of the Chromatogram Ranges dialog box.
Plot Specify a plot to apply a particular label to.
Source Specify that the Xcalibur application apply either a custom (user-defined) label or a label
from the detector to the Y-axis of a map plot.

When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If no.lyt file exists, it retrieves the parameters from the default values
you specified on the Labeling and Scaling Page.
Units Apply absolute or relative scaling to the Y-axis of a chromatogram plot.
Name View or change the current axis names for the X-, Y-, and Z-axes, as appropriate for the
active chromatogram, spectrum, or map. To change an axis name, type the new name in the
Name box. The Xcalibur application displays the results of the current settings in the
adjacent graphic.

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Table 24. Chromatogram Axis page parameters – Display Options dialog box (Sheet 3 of 3)
Parameter Description
Show name View or change when the Xcalibur data system displays the axis name next to the
corresponding axis. The Xcalibur system can display the axis label displayed in the axis
Name box at the following times:
• Never: The application does not displays the axis label when the graphic is displayed or
printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.

The current option is displayed in the list.

To change the time when the application displays the axis label, select from the Show name
list of options. Click Never, On Print, or Always.

Since standard reports are not displayed on the screen, the On Print and Always Show
name list options for standard reports are identical.
Offset Set the location for the displayed plot a specified distance from the X and/or Y axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.

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Chromatogram Color Page – Display Options Dialog Box

Use the Color page of the Display Options dialog box to modify the appearance of a
Chromatogram view. The Xcalibur data system displays the results of the current settings in
the graphic on the right side of the page.
Table 25. Chromatogram Color page parameters – Display Options dialog box
Parameter Description
Plots Change the colors of any of the plots within a chromatogram view.

In Processing Setup, the chromatogram preview corresponds to Plot 1. Plot buttons 2

through 8 are not used.
Plots 1to 8 Change the color of a plot. The current plot color is displayed to the right of its Plot
number button.

To select the color of a plot, click the Plot number button, for example, Plot 3. The
Xcalibur application opens the Color dialog box with a color palette so that you can select a
preset color or customize a color.
Backdrop Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. Click Backdrop to display a background.

The Xcalibur application displays the current plot color to the right of the Backdrop button.
To select the color of the backdrop, click Backdrop. The application opens the Color dialog
box with a color palette so that you can select a preset color or customize a color. The
application displays the results of the current settings in the adjacent graphic.

Chromatogram Labels Page – Display Options Dialog Box

Use the Labels page of the Display Options dialog box to modify the appearance of your
chromatogram. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 26. Chromatogram Labels page parameters – Display Options dialog box (Sheet 1 of 3)
Parameter Description
Label with
Retention time Add a retention time label above chromatogram peaks.

The order of chromatogram labels for an undetected peak, from top to bottom, is scan
number, retention time, and base peak. The Xcalibur 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.

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Table 26. Chromatogram Labels page parameters – Display Options dialog box (Sheet 2 of 3)
Parameter Description
Scan number Add the active scan number in the label above chromatogram peaks.

The scan number of a detected peak is indicated by the letters S# to the left of the value.
Base Peak Add m/z for the base peak of the active scan above chromatogram peaks.

The base peak of a detected peak is indicated by the letters BP to the left of the value.
Signal-To-Noise Add the signal-to-noise ratio above chromatogram peaks.

When you select this check box and use the Genesis peak detection algorithm, the Xcalibur
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.
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 application 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.

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Table 26. Chromatogram Labels page parameters – Display Options dialog box (Sheet 3 of 3)
Parameter Description
Size View or change the amount that the Xcalibur application moves a label from its normal
position to avoid conflict with another label. This box is 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 above which the data system labels peak. The
valid range is 0.0 to 100.0%. For example, if the base peak is 100% and the label threshold
setting is 50.0%, the Xcalibur application labels all peaks at or above 50%.

Chromatogram Normalization Page – Display Options Dialog Box

Use the Normalization page of the Display Options dialog box to modify the appearance of
your chromatogram. The Xcalibur data system displays the results of the current settings in
the graphic on the right side of the page.
Table 27. Chromatogram Normalization page parameters – Display Options dialog box
Parameter Description
Normalize method
Auto range Select the auto range normalization method for chromatograms. The
Xcalibur application reviews the chromatogram data, detects the minimum
and maximum signal data points, and assigns these values to the extremes
on the Y-axis. The entire dynamic range of the chromatogram is then
displayed in the active view, normalized over the full range of the Y-axis.
Intensity range Specify the minimum and maximum ranges of the chromatogram plot to
display in the Y-axis. The valid range of values is -200.000 to 200.000%.
The default range is 0.000-100.000%.
Normalize each plot to
Largest peak in subsection Set the Y-axis maximum for each subsection (division) equal to the largest
peak in the subsection (division). Set the number of subsections on the
Axis page.
Largest peak in selected time range Set the Y-axis maximum equal to the largest peak in the time range. (The
time range is the sum of all subsections [divisions]). Each subsection
(division) has the same Y-axis maximum. Set the number of subsections on
the Axis page.
Largest peak in all times Set the Y-axis maximum equal to the largest peak in all times. Each
subsection (division) has the same Y-axis maximum. Set the number of
divisions on the Axis page.

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Chromatogram Style Page – Display Options Dialog Box

Use the Style page of the Display Options dialog box to modify the appearance of a
Chromatogram view. The Xcalibur data system displays the results of the current settings in
the graphic on the right side of the page.
Table 28. Chromatogram Style page parameters – Display Options dialog box
Parameter Description
Plotting
Point To Point Select a graphic style that displays the active chromatogram or spectrum using a
point-to-point peak profile.
Stick Select a graphic style that displays the active chromatogram or spectrum using vertical lines.
Arrangement
Stack (2D) Stack plots vertically, with no overlap, for plots in the active cell.
Overlay (3D) Overlay plots vertically with optional horizontal skew (time offset) for chromatogram or
spectrum plots in the active cell.
3D
Elevation Set the elevation angle (amount of overlay) to a value from 0 to 60 degrees for an overlay
arrangement of plots in the active cell. To set the elevation angle, either drag the Elevation
slider or click the Elevation slider left or right arrow until you reach the desired angle.

The Xcalibur application displays the current angle setting below the scroll box.
Skew Set the skew angle (time offset) to a value from 0 to 45 degrees for an overlay arrangement
of plots in the active cell. To set the skew, either drag the Skew slider or click the Skew slider
left or right arrow until you reach the desired angle.

The Xcalibur application displays the current angle setting below the scroll box.
Draw Backdrop Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.

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Map or Ion Map Axis Page – Display Options Dialog Box

Use the Axis page of the Display Options dialog box to modify the appearance of your Map or
Ion Map view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 29. Map or Ion Map Axis page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
X
Name View or change the current axis names for the X-, Y-, and Z-axes, as appropriate for the
active chromatogram, spectrum, or map. To change an axis name, type the new name in the
Name box. The Xcalibur application displays the results of the current settings in the
adjacent graphic.

The default axis names are as follows:

• X: Time
• Y: Relative Abundance
• Z: m/z
Show View or change when the Xcalibur application should display the axis name next to the
corresponding axis. The system can display the axis label displayed in the axis Name box at
the following times:
• Never: The application does not display the axis label when the graphic is displayed or
printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.

The current option is displayed in the list.

To change the time when the Xcalibur application displays the axis label, select from the
Show name list of options and click Never, On Print, or Always.

Since standard reports are not displayed on the screen, the On Print and Always Show
Name list options for standard reports are identical.
Offset Set the location for the displayed plot at a specified distance from the X and/or Y axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.

The amount of the offset is specified in the Size box.

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Table 29. Map or Ion Map Axis page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
Y
Source Specify that the Xcalibur application apply either a custom (user-defined) label or a label
from the detector to the Y-axis of a map plot.

When you specify a custom label in Qual Browser, the application retrieves the parameters
from a layout (.lyt) file. If no.lyt file exists, it retrieves the parameters from the default values
you specified in the Labeling and Scaling Page of the Xcalibur Configuration dialog box.
Units Apply absolute or relative scaling to the Y-axis of a chromatogram plot.
Other
Grid Lines Determine whether or not to display lines from major tic marks on the axis scale.
Split time range Split the time scale of the active chromatogram into two or more divisions. To split the time
scale, select the Split time range check box. The Xcalibur application activates the divisions
box so that you can select the number of divisions. If you want to display only one time
range, clear the Split time range check box.
Divisions View or change the current number of divisions for a spectra with a split mass range. This
box is only active if you select the Split time range check box. The number of divisions can
be two, three, or four. To change the number of divisions, type the new number in the
Divisions (m/z) box. The Xcalibur application displays the multiple spectra in the adjacent
graphic.

Map or Ion Map Band Width Page – Display Options Dialog Box
Use the Band Width page of the Display Options dialog box to modify the appearance of a
Map or Ion Map view. You can specify the size of the bands displaying relative abundance to
make the display clearer. The band width value specifies the band width in amu units.
Table 30. Map or Ion Map Band Width page parameters – Display Options dialog box
Parameter Description
m/z Band Width (amu) View or change the current value for the map view band width.

Set a value for the width of bands displayed in the Map view. The range of acceptable values
is from 0.001 to 50.0, with a default value of 1.0.

To see specific resolution detail, set the value as large as is necessary.

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Map or Ion Map Color Page – Display Options Dialog Box

Use the Color page of the Display Options dialog box to modify the appearance of a Map or
Ion Map view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 31. Map or Ion Map Color page parameters – Display Options dialog box
Parameter Description
Line Change the color of framing lines for the active map. The current color is displayed to the
right of the Line button.

To change the color of the framing lines, click Line. The Xcalibur application opens the
Color dialog box with a color palette so that you can select a preset color or customize a
color. It displays the results of the current settings in the adjacent graphic.
Fill solid Change the color of the solid fill for the active map. The current color is displayed to the
right of the Fill solid button.

To change the color of the solid fill, click Fill solid. The Xcalibur application opens the
Color dialog box with a color palette so that you can select a preset color or customize a
color. It displays the results of the current settings in the adjacent graphic.
Backdrop Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. Click Backdrop to display a background. The
Xcalibur application displays the current plot color to the right of the Backdrop button.

To select the color of the backdrop, click Backdrop. The application opens the Color dialog
box with a color palette so that you can select a preset color or customize a color. It 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 allowable
values are 1.1 to 20. Selecting the Log scale check box activates the Factor box.
Shade
Shade % Change the color of the map at 0%, 20%, 40%, 60%, 80%, and 100% relative abundance.
To change the color, click a Shade % button. The Xcalibur application opens the Color
dialog box with a color palette so that you can select a preset color or customize a color.

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Map or Ion Map Normalization Page – Display Options Dialog Box

Use the Normalization page of the Display Options dialog box to modify the appearance of a
Map or Ion Map view. The Xcalibur data system displays the results of the current settings in
the graphic on the right side of the page.
Table 32. Map or Ion Map Normalization page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
Mass grouping
Specify the mass grouping compression method. Mass grouping describes how the Xcalibur application 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 Xcalibur application normalize the map
to the largest peak in the raw file.
Fix scale Select this check box to have the Xcalibur application normalize the map
to a fixed intensity value. Type an intensity value between 0.01 and 1e+20
in the Fix scale box.
Normalize method
Auto range Select the Auto range normalization method for chromatograms. The
Xcalibur application reviews the chromatogram data, detects the minimum
and maximum signal data points, and assigns these values to the extremes
on the Y-axis. The entire dynamic range of the chromatogram is then
displayed in the active view, normalized over the full range of the Y-axis.
Intensity Range Display the relative abundance range of mass peaks that the Xcalibur
application 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%, type
50.000 - 100.000. The Xcalibur application then excludes spectrum peaks
with relative abundances that range from 0.000 to 49.999 from the
displayed Map or Ion Map view.
Normalize each mass to
Largest peak in subsection Set the Y-axis maximum for each subsection (division) equal to the largest
peak in the subsection (division). Set the number of subsections on the
Axis page.

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Table 32. Map or Ion Map Normalization page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
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.
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.

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Map or Ion Map Style Page – Display Options Dialog Box

Use the Style page of the Display Options dialog box to modify the appearance of a Map or
Ion Map view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 33. Map or Ion Map Style page parameters – Display Options dialog box
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 Xcalibur application 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 Xcalibur application displays the current angle setting below the scroll box.
Fill View or change the current fill option for the active map. The Xcalibur application fill
options are Plain Lines, Colored Lines, None, Solid color, Intensity shaded, and Shaded
with frame.
Draw backdrop Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.

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Spectrum Axis Page – Display Options Dialog Box

Use the Axis page of the Display Options dialog box to modify the appearance of your
spectrum. The Xcalibur data system displays results of the current settings in the graphic on
the right side of the page.
Table 34. Spectrum Axis page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
X, Y, Z
Name View or change the current axis names for the X-, Y-, and Z-axes, as appropriate for the
active chromatogram, spectrum, or map. To change an axis name, type the new name in the
Name box. The system displays results of the current settings in the adjacent graphic.

The default axis names are as follows:

• X: m/z
• Y: Relative Abundance
• Z: Scan
Show (name) View or change when the Xcalibur data system displays the axis name next to the
corresponding axis. The system can display the axis label displayed in the axis Name box at
the following times:
• Never: The application does not display the axis label when the graphic is displayed or
printed.
• On Print: The application displays the axis label whenever the graphic is printed as a
report.
• Always: The application displays the axis label whenever the graphic is displayed or
printed.

The current option is displayed in the list.

To change the time when the application displays the axis label, from the Show list of
options, select Never, On Print, or Always.

Since standard reports are not displayed on the screen, the On Print and Always Name list
options for standard reports are identical.
Offset (X and/or Y) Set the location for the displayed plot at a specified distance from the X and/or Y axes. The
X-axis offset moves the Y-axis slightly above the X-axis so that you can see baseline details.
The Y-axis offset moves the X-axis slightly to the right of the Y-axis so that you can see plot
details at low X-axis values.

The amount of the offset is specified in the Size box.

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Table 34. Spectrum Axis page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
Split time range Split the m/z scale of the active spectrum into two or more divisions. To split the mass scale,
select the Split time range check box. The Xcalibur data system activates the Divisions box
so that you can enter the number of divisions.
Divisions View or change the current number of divisions for a spectra with a split mass range. This
box is only active if you select the Split time range check box. The number of divisions can
be two, three, or four. To change the number of divisions, type the new number in the
Divisions (m/z) box. The Xcalibur application displays the multiple spectra in the adjacent
graphic.
Y-axis
Source Specify that the 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 Xcalibur application retrieves the
parameters from a layout (.lyt) file. If no .lyt file exists, it retrieves the parameters from the
default values you specified in the Labeling and Scaling Page of the Xcalibur Configuration
dialog box.
Units Apply absolute or relative scaling to the Y-axis of a chromatogram plot.

Spectrum Color Page – Display Options Dialog Box

Use the Color page of the Display Options dialog box to modify the appearance of a
Spectrum view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 35. Spectrum Color page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
Centroid
Regular (peaks) Change the color of regular, unflagged, peaks. The current color for regular peaks is
displayed to the right of the Regular (peaks) button. To select the color of regular peaks,
click Regular. The Xcalibur application opens the Color dialog box with a color palette so
that you can select a preset color or customize a color. The application displays the results of
the current settings in the adjacent graphic.
Saturated (peaks) Change the color of saturated peaks (amplitude is greater than range). The current color is
displayed to the right of the Saturated (peaks) button. To change the color of saturated
peaks, click Saturated. The Xcalibur application opens the Color dialog box with a color
palette so that you can select a preset color or customize a color. It displays the results of the
current settings in the adjacent graphic.

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Table 35. Spectrum Color page parameters – Display Options dialog box (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
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.
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 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.
Other
Profile Change the color of the profile style. The Xcalibur application 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
Xcalibur application displays the results of the current settings in the adjacent graphic.
Backdrop Change the color of the backdrop (background) of a map view, overlaid (3D) spectrum
view, or overlaid (3D) chromatogram view. The Xcalibur application displays the current
plot color to the right of the Backdrop button. To select the color of the backdrop, click
Backdrop. The application opens the Color dialog box with a color palette so that you can
select a preset color or customize a color. It displays the results of the current settings in the
adjacent graphic.
Shade
Shade % Change the color of the map at 0%, 20%, 40%, 60%, 80%, and 100% relative abundance.
To change the color, click a Shade % button. The Xcalibur application opens the Color
dialog box with a color palette so that you can select a preset color or customize a color.

These changes are only visible if you have selected the Shade option on the Spectrum Style
Page – Display Options Dialog Box.

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Spectrum Labels Page – Display Options Dialog Box

Use the Spectrum Labels page of the Display Options dialog box to modify the appearance of
your spectrum. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 36. Spectrum Labels page parameters – Display Options dialog box (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 Xcalibur application 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 Display a wavelength label at the top of spectrum peaks. The Decimals box becomes active.
(non-MS data only)
The Xcalibur application displays the Wavelength check box only if you are not using MS
data.
Flags Display letters above the colored spectrum peaks. The letters indicate why the peaks are
colored.

The possible flags are as follows:

• S Saturated peaks are peaks with a signal too large to measure (over range from A to
D converter).
• R Reference peaks are peaks from a reference compound used for an internal
recalibration of a scan (for example, in MAT95 series).
• L Lock peaks are local references used to calculate accurate mass of nearby peaks (for
example, in Quantum™ AM).
• E Exception peaks are also peaks from a reference compound, but not used for
recalibration. These are typically small isotopes or fragments of the main references.
Decimals View or change the number of digits the Xcalibur application displays to the right of the
decimal when it positions m/z labels over the peaks in a spectrum. This box is only active if
you select the Mass check box. The valid range is 0 to 5.
Resolution Display 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 resolution information, you
can select to have the Xcalibur application centroid the data after acquisition by selecting
the centroid check box. This action turns on the Resolution check box.

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Table 36. Spectrum Labels page parameters – Display Options dialog box (Sheet 2 of 3)
Parameter Description
Charge Display the charge state 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 the charge state information is stored in the raw file.
Baseline Display the baseline 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 the baseline information is stored in the raw file.
Noise Display noise 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 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 application
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-axis, Y-axis, or both
X- and 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 View or change the amount that the Xcalibur 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.

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Table 36. Spectrum Labels page parameters – Display Options dialog box (Sheet 3 of 3)
Parameter Description
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.

Only the peak labels are rotated. The flags are not rotated.
Boxed Select whether or not the Xcalibur application places a box around each peak label. To box
your label, select the Boxed check box. If you do not want to have a box around the label,
clear the check box. Use the adjacent graphic to view the result of the current label settings.

Only the peak labels are boxed. The flags are not boxed.
Threshold
Label peaks that are at or above a minimum percent of the base peak. This option sets the minimum percent. The
valid range is 0.0 to 100.0%. For example, if the base peak is 100% and the label threshold setting is 50.0%, the
Xcalibur application labels all peaks at or above 50%. To change the label threshold, type a different percent value in
the Label Threshold box. Use the adjacent graphic to view the result of the current label settings.

Spectrum Normalization Page – Display Options Dialog Box

Use the Spectrum Normalization page of the Display Options dialog box to modify the
appearance of your spectrum by specifying the following normalization parameters. The
Xcalibur data system displays the results of the current settings in the graphic on the right side
of the page.
Table 37. Spectrum Normalization page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
Normalize method
Auto range Select the auto range normalization method for chromatograms. The Xcalibur
application reviews the chromatogram data, detects the minimum and maximum
signal data points, and assigns these values to the extremes on the Y-axis. The entire
dynamic range of the chromatogram is then displayed in the active view,
normalized over the full range of the Y-axis.
Intensity Range View or change the relative abundance range of mass spectrum peaks that the
Xcalibur application 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%, enter 50.000 – 100.000. The application then excludes
spectrum peaks with relative abundances that range from 0.000 to 49.999 from the
displayed spectrum.

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Table 37. Spectrum Normalization page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
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.

Spectrum Style Page – Display Options Dialog Box

Use the Spectrum Style page of the Display Options dialog box to modify the appearance of a
Spectrum view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 38. Spectrum Style page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
Plotting
Automatic Have the 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.

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Table 38. Spectrum Style page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
3D
Elevation Set the elevation angle (the amount of overlay) to a value between 0 and 60 degrees for an
overlay arrangement of plots in the active cell. To set the elevation angle, either drag the
Elevation slider or click the Elevation slider left or right arrow until you reach the desired
angle.

The Xcalibur application displays the current angle setting below the scroll box.
Skew Set the skew angle (time offset) to a value between 0 and 45 degrees for an overlay
arrangement of plots in the active cell. To set the skew, either drag the Skew slider or click
the Skew slider left or right arrow until you reach the desired angle.

The Xcalibur application displays the current angle setting below the scroll box.
Draw Backdrop Select a graphic style that includes a drawn perspective backdrop for an overlay arrangement
of plots in the active cell.

Spectrum List Composition Page – Display Options Dialog Box

Use the Spectrum List Composition page of the Display Options dialog box to calculate
elemental compositions and to add columns containing the results to your Spectrum List. The
Xcalibur data system determines which chemical formulas have a m/z value most like that of
the experimental spectrum peaks. The application displays the results of the current settings
in the graphic on the right side of the page.
Table 39. Spectrum List Composition page parameters – Display Options dialog box (Sheet 1 of 2)
Parameter Description
Label with
Elemental comp. Select whether the Xcalibur application displays the chemical formula labels at the top of
spectrum peaks. The application determines which chemical formulas have a m/z value most
like that of the spectrum peaks. To turn on elemental composition labeling, select the
Elemental comp. check box.

If the application displays the elemental composition values in light gray, close Qual
Browser and choose Xcalibur Roadmap > Tools > Configuration to display the
Configuration page. Select 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
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 data system determines. The
Xcalibur system displays the theoretical m/z to the right of the formula separated by =.

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Table 39. Spectrum List Composition page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
RDB equiv. View the value of the ring and double-bond equivalents that the Xcalibur application
calculates for the chemical formulas. The application displays the ring and double-bond
equivalent value under the chemical formula.

Ring and double-bond equivalents measure the number of unsaturated bonds in a

compound—and limit the calculated formulas to only those that make sense chemically.
You can specify limits in a range from -100.0 to +100.0.

The value is calculated by the following formula:

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.

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Spectrum List Normalization Page – Display Options Dialog Box

Use the Spectrum List Normalization page of the Display Options dialog box to modify the
appearance of your Spectrum List. The Xcalibur data system displays the results of the current
settings in the graphic on the right side of the page.
Table 40. Spectrum List Normalization page parameters – Display Options dialog box
Parameter Description
Intensity range View or change the relative abundance range of mass spectrum peaks that the
Xcalibur application 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%, type 50.000–100.000. The application then excludes
spectrum peaks with relative abundances that range from 0.000 to 49.999 from the
displayed Spectrum List.
Normalize list to
Largest peak in subsection Set the value listed in the Relative column equal to a percentage of the largest peak
in the subsection (division).
Largest peak in (mass) range Set the value listed in the Relative column equal to a percentage of the
mass-to-charge ratio of the largest peak in the mass range. (The mass range is the
sum of all subsections [divisions].)
Largest peak in scan Set the value listed in the Relative column equal to a percentage of the largest peak
in the full mass range.

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Spectrum List Style Page – Display Options Dialog Box

Use the Spectrum List Style page of the Display Options dialog box to modify the appearance
of a Spectrum view. The Xcalibur data system displays the results of the current settings in the
graphic on the right side of the page.
Table 41. Spectrum List Style page parameters – Display Options dialog box (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 you clear the All peaks check box. The valid range is 1 to 1000.

If you order the list by mass (m/z), the Xcalibur application displays the specified number of
peaks having the greatest intensity in ascending mass (m/z) order. For example, if you type
the value 10 in the Top box, the application displays a Spectrum List with the 10 greatest
intensity peaks sorted in ascending order by m/z.

If you order the list by intensity, the Xcalibur application 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 application 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 Fragmented peaks are peaks separated into multiple peaks by the centroiding
activity.

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Table 41. Spectrum List Style page parameters – Display Options dialog box (Sheet 2 of 2)
Parameter Description
Resolution Specify whether or not the data system displays resolution information in the Spectrum List.

Resolution is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.

Resolution can also be active if you have centroided a profile scan. The Xcalibur application
shows the results returned by the centroider.
Charge Specify whether or not the data system displays charge information in the Spectrum List.

Charge is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.
Baseline Specify whether or not the data system displays baseline information in the Spectrum List.

Baseline is a Label Stream parameter and is active if your raw file has Label Stream data.
These values are written by the instrument.
Noise Specify whether or not the data system displays noise information in the Spectrum List.

Noise is a Label Stream parameter and is active if your raw file has Label Stream data. These
values are written by the instrument.
Centroid Apply the same algorithm used in the firmware to convert from profile data to centroid.
When you select centroid, both the Resolution check box and the Choose Algorithm button
become active.

Centroid and Choose Algorithm are active when you have a profile scan.
Choose algorithm Select a centroiding algorithm.

The Choose algorithm button is activated when you have a profile scan and select the
Centroid check box.
Order by
Mass Order the Spectrum List in ascending m/z value order.

Sort by mass to make sure 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 make sure the highest intensity peak (with relative intensity 100.00) is
always the first entry in the list.
Precision
Decimals 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.

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Masses Dialog Box

Use this dialog box to specify tolerance and precision settings for the mass data displayed in
the chromatogram, spectrum, map, and ion map plots.

Specify the default values for tolerance and precision on the Mass Options Page of the
Configuration dialog box.
Table 42. Masses dialog box parameters
Parameter Description
Mass tolerance
Mass tolerance Specify the value for mass tolerance. Type a value in the range of 0.1 to 50000 and select
units to apply to the value. The Xcalibur data system uses the tolerance value to create the
limits of a range of masses.
Units Specify the units of measurement in which the Xcalibur application processes your data.
Select mmu (millimass units) or ppm (parts per million).
Mass precision
Decimals Specify the number of decimal places (mass precision) that the Xcalibur application 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.

Peak Information Dialog Box

The Peak Information dialog box provides read-only information about the currently
displayed chromatogram peak or one of the peaks used by the spectrum search or ion ratio
confirmation routines. You can use this dialog box to quickly get detailed information on the
found peak by selecting other components or other results files.

The current component name is displayed in the title bar, for example:
Peak Information – drugx

If the current peak is for a Qualifier Ion, the title bar also contains the text Qual Ion Mass
xxx.x where the xxx.x represents the mass of the qualifier ion.

If the peak is for a spectrum candidate, the title bar also contains the text Spectrum Candidate.

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The pages displayed in the Peak Information dialog box depend on the type of peak that is
currently displayed, as follows:

No Peak
If no peak has been found for the component, the Xcalibur data system displays only the No
Peak page with the following message:
No Peak Found. Cannot show Peak Info.

No Peak Page – Peak

Information Dialog Box

Standard Peak
This series of pages is only available if the inlet is a liquid chromatograph:

Note When a liquid chromatograph is used for the inlet, the Ion Ratio Confirmation
option is not available.

Info Page – Peak Flags Page – Peak More Flags Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box
Suitability Page – Peak Spectrum Page – Peak
Information Dialog Box Information Dialog Box

Qualifier Ion Peak

This series of pages is only available if the inlet is a gas chromatograph:

Note Along with the five pages used for a standard peak, the More Info page and Chro
page are available.

Info Page – Peak More Info Page – Peak Flags Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box
More Flags Page – Peak Suitability Page – Peak Chro Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box
Spectrum Page – Peak
Information Dialog Box

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Spectrum Candidate Peak (First Candidate)

Info Page – Peak More Info Page – Peak Flags Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box
More Flags Page – Peak Suitability Page – Peak Spectrum Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box

Spectrum Candidate Peak (Second and Third Candidates)

More Info Page – Peak Chro Page – Peak Spectrum Page – Peak
Information Dialog Box Information Dialog Box Information Dialog Box

Chro Page – Peak Information Dialog Box

The Chro page of the Peak Information dialog box is a read-only page that displays the single
mass chromatogram of the current qualifier ion. The view centers on the retention time of the
peak apex and has View Width specified in the Component Identification view of the
Processing Setup window. The mass of the qualifier ion is displayed in the title bar Qual Ion
Mass xxx.x. You cannot change this display.

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Flags Page – Peak Information Dialog Box

Use the Flags page of the Peak Information dialog box to review the following peak properties
for the current component.
Table 43. Flags page parameters – Peak Information dialog box (Sheet 1 of 3)
Parameter Description
Integration info
Detected By View the method that the Xcalibur data system used to detect the peak:
Spectrum: The application uses the user-defined mass/intensity pairs and applies a
spectral-matching algorithm to find the peak that contains the closest match to the
comparison spectrum. Up to 50 entries are allowed to define the comparison spectrum.

Highest Peak: The application searches for the highest peak within the search window.

Nearest RT: The application searches for the peak nearest to the expected retention time.
Left Edge Type View how the data system detected the left baseline edge of the current peak. The Xcalibur
application displays one of the following peak baseline detection methods:

Edge Type Reported by Xcalibur: Peak Criteria Met

Baseline (B): The edge of the peak is at baseline level.

Valley (V): The edge of the peak is in a peak valley.

Manual (M): The edge of the peak has been adjusted manually.

Stripe (S): The edge of the peak reached the Constrain Peak Height Percent specified in the
method.

Tail (T): The edge of the peak reached the Constrain Peak Height Trailing Factor limit
before the Height Percent.

Tilt (-): An error occurred before the data system could determine the edge of the peak.

Unknown (?): An unknown error occurred.

View the edge type on many reports using a one-letter abbreviation for the left edge type
and a one-letter abbreviation for the right edge type, as follows:
Peak ID Left Edge Right Edge
BB Baseline Baseline
BT Baseline Tail
-B Tilt Baseline
SS Stripe Stripe
Valid View whether or not the data system successfully detected the peak indicated by selecting
the Valid check box.

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Table 43. Flags page parameters – Peak Information dialog box (Sheet 2 of 3)
Parameter Description
Right Edge Type View how the Xcalibur application detected the right baseline edge of the current peak. The
application displays one of the following peak baseline detection methods:
Edge Type Reported by Xcalibur

Baseline (B): The edge of the peak is at baseline level.

Valley (V): The edge of the peak is in a peak valley.

Manual (M): The edge of the peak has been adjusted manually.

Stripe (S): The edge of the peak reached the Constrain Peak Height Percent specified in the
method.

Tail (T): The edge of the peak reached the Constrain Peak Height Trailing Factor limit
before the Height Percent.

Tilt (-): An error occurred before the edge of the peak could be determined.

Unknown (?): An unknown error occurred.

View the edge type on many reports using a one-letter abbreviation for the left edge type
and a one-letter abbreviation for the right edge type, as follows:
Peak ID Left Edge Right Edge
BB Baseline Baseline
BT Baseline Tail
-B Tilt Baseline
SS Stripe Stripe
Flags
Saturated View whether or not any of the scans in the peak were saturated. The Xcalibur application
indicates one or more saturated scans were detected by displaying in the Saturated check
box.
Calculated Amount View the amount of sample, as calculated by the data system using the response ratio and
the calibration curve.
Valley Detect View whether or not valley detection was turned on in the processing method. The Xcalibur
application indicates that valley detection was activated if the Valley Detect check box is
selected.

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Table 43. Flags page parameters – Peak Information dialog box (Sheet 3 of 3)
Parameter Description
QC Failed View whether or not a sample failed a QC check.

If the calculated amount is greater than the specified percentage difference from the
expected amount, then a sample fails the QC test. For example, if the tolerance level is 10%
and the expected amount is 100%, calculated amounts less than 90% or greater than 110%
fail.

The Xcalibur application selects the check box to indicate that the sample type was QC and
that it failed the QC test.
RT Ref OK View whether or not the Xcalibur data system found the retention time reference
component and whether it was used correctly by the processing method.

If there was a retention time reference, then the check box indicates whether or not the
retention time reference peak was found. The Xcalibur application indicates it found the
peak by selecting the check box. The application indicates it looked for the peak but did not
find it by leaving the box blank.

If there is no retention time reference, then the check box is selected because there is no
correction to be made.
Response OK View whether or not a response factor was calculated.

The Xcalibur application selects the check box to indicate that it found the peak and the
peak’s internal standard and correctly calculated the response ratio.
Response Low View whether the calculated amount for the peak was less than the lowest specified standard
amount of the component in the calibration curve. In this case the calculated amount has
been determined by extrapolation from the lowest level. The Xcalibur application selects the
check box to indicate that the amount was calculated by extrapolation. If you force or
include the origin, the application defines the lowest level to be 0.0.
Response High View whether or not the calculated amount for the peak was greater than the highest
specified standard amount of the component in the calibration curve. In this case, the
calculated amount has been determined by extrapolation from the highest level. The
Xcalibur application selects the check box to indicate that the amount was calculated by
extrapolation.

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Info Page – Peak Information Dialog Box

Use the Info page of the Peak Information dialog box to review the following peak properties
for the current component.
Table 44. Info page parameters – Peak Information dialog box
Parameter Description
Left View the left extreme of the integration baseline for the current component in minutes
(read-only).
Apex View the apex point in minutes of the integration baseline for the current component
(read-only).
Right View the right extreme of the integration baseline for the current component in minutes
(read-only).
Height View the height of the current component peak apex in units of counts (read-only).
Area View the area of the current component peak in units of count-seconds (read-only).
Baseline View the baseline height directly below the apex of the current component peak in units of
counts (read-only).
Base Peak View the mass-to-charge ratio of the ion with the largest response in the current component
peak (read-only).
Signal To Noise View the measured signal-to-noise ratio at the apex of the current component peak.
Expected RT View the expected retention time of the current component (read-only).
ISTD Response View the integrated area in units of count-minutes or the height of the apex in units of
counts for the current component peak (read-only).
Response Ratio View the ratio of the peak sample peak area or height to the internal standard area or height
(read-only).
Calculated Amount View the amount of sample calculated by the Xcalibur data system using the response ratio
and the calibration curve (read-only).

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Info/More Info Page – Peak Information Dialog Box

The Info/More Info page of the Peak Information dialog box is displayed if you have
conducted a spectrum search.
• If the main component peak was detected using the spectrum search, then this page has
the More Info tab and displays only the Spectrum box. In this case, the pages displayed
are Info, More Info, Flags, More Flags, Suitability, and Spectrum.
• If peaks other than the main component were detected using the spectrum search, then
this page has the Info tab and displays both the Spectrum box and the Peak Info box. In
this case, the pages displayed are Info, Chro, and Spectrum.

Use this page to review the following peak properties for the current search component.
Table 45. Info/More Info page parameters – Peak Information dialog box
Parameter Description
Spectrum Results View the calculated Forward, Reverse, and Match results for the found peak (read-only).

This box appears on the More Info page for Candidate #1 of a spectrum search and on the
Info page for Candidate #2 and Candidate #3 of a spectrum search.
Forward View the forward threshold result for the current component (read-only).
Reverse View the reverse threshold result for the current component (read-only).
Match View the match threshold result for the current component (read-only).
Peak Info View the calculated peak characteristics for Candidate #2 or Candidate #3 of a spectrum
search (read-only). The Left, Apex, and Right peak boundaries in minutes, and the Area and
Height of the peak are given in units of counts.

This box on the More Info page does not appear for Candidate #1 of a spectrum search.
This information is provided on the More page that appears for Candidate #1.
Left View the left extreme of the integration baseline for the current component in minutes
(read-only).
Apex View the apex point in minutes of the integration baseline for the current component
(read-only).
Right View the right extreme of the integration baseline for the current component in minutes
(read-only).
Area View the area of the current component peak in units of count-seconds (read-only).
Height View the height of the current component peak apex in units of counts (read-only).

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More Flags Page – Peak Information Dialog Box

Use the More Flags page of the Peak Information dialog box to review the following peak
properties for the current component.
Table 46. More Flags page parameters – Peak Information dialog box
Parameter Description
Detection Thresholds
Area Set a specified area tolerance value to compare with the peak area and determine if the peak
area is outside or within the tolerance.
Height Set a specified height tolerance value to compare with the peak height and determine if the
peak height is outside or within the tolerance.
Cal and Quan Thresholds
R-Squared Set a specified coefficient tolerance value to compare with the coefficient of determination
and determine if the coefficient of determination is outside or within the specified tolerance.
Detection Limit Set a specified detection threshold tolerance value to compare with the concentration of the
quantified peak and determine if the detection threshold is outside or within the specified
tolerance.
Linearity Limit Set a specified linearity threshold tolerance value to compare with the linearity threshold for
the concentration of the quantified peak to determine if the linearity threshold is outside or
within the specified tolerance.
Quantitation Limit Set a specified quantitation threshold tolerance value to compare with the quantitation
threshold for the concentration of the quantified peak and determine if the quantitation
threshold is outside or within the specified tolerance.
Carry over Limit Set a specified carry-over threshold tolerance value to compare with the carry-over threshold
for the concentration of the quantified peak and determine if the carry-over threshold is
outside or within the specified tolerance.

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More Info Page – Peak Information Dialog Box

Use the More Info page of the Peak Information dialog box to review the results of the
following peak tests for the current component.
Table 47. More Info page parameters – Peak Information dialog box
Parameter Description
Ion Coelution Test
Passed View whether the qualifier ion displayed in the title bar “Qual Ion Mass xxx.x” passed or did
not pass the Ion Coelution test.

If the check box is not selected, no Ion Ratio test was performed and the Ion Ratio Test box
is not displayed. If the check box is selected, the Ion Ratio test was performed and the Ion
Ratio Test box on the Mass Info page is displayed at the bottom of the Mass Info page.
Ion Ratio Test
Passed View whether the qualifier ion displayed in the title bar “Qual Ion Mass xxx.x” passed or did
not pass the Ion Ratio test.

The Xcalibur data system does not display this box if the current qualifier ion did not pass
the Ion Coelution test.
Target Ratio % View the calculated Target Ratio Percentage that Xcalibur calculated during the Ion Ratio
test (read-only).

The application does not display this box if the current qualifier ion did not pass the Ion
Coelution test.
Absolute Window % View the calculated Absolute Window Percentage that Xcalibur calculated during the Ion
Ratio test (read-only).

The application does not display this box if the current qualifier ion did not pass the Ion
Coelution test.

No Peak Page – Peak Information Dialog Box

If the Xcalibur data system does not find a peak for the component, only the No Peak page is
displayed with the following message:
No Peak Found. Cannot show Peak Info.

Spectrum Page – Peak Information Dialog Box

This read-only page displays the spectrum of the current peak at the apex retention time. You
cannot make adjustments to this display.

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Suitability Page – Peak Information Dialog Box

The Suitability page of the of the Peak Information dialog box displays the results of specific
tests that might have been performed (as specified by the processing method) on the
component peak to determine its suitability to be considered a valid peak. Each test is listed
with the result of that test displayed to the right. There are three possible responses for each
test: Passed, Failed, and Not Tested.
Table 48. Suitability page parameters – Peak Information dialog box
Parameter Description
Suitability Flags
Symmetrical View the results of the Symmetrical test as Passed, Failed, or Not Tested. This test indicates
whether the peak is symmetrical about the apex.
Resolution View the results of the Resolution test as Passed, Failed, or Not Tested. This test indicates
whether multiple peaks are resolved. If neither peak baseline endpoint is valley detected,
then the resolution passes.
Peak Width View the results of the Peak Width test as Passed, Failed, or Not Tested. This test indicates
whether the peak width is within specified limits.
Tailing View the results of the Tailing test as Passed, Failed, or Not Tested. This test indicates
whether the peak has tailing.
Column Overload View the results of the Column Overload test as Passed, Failed, or Not Tested. This test
indicates whether or not it is likely that the column was overloaded during acquisition. This
test is based on an analysis of the baseline and peak shape.
Baseline Clipping View the results of the Baseline Clipping test as Passed, Failed, or Not Tested. This test
indicates whether the baseline is clipped outside the peak. This can occur if the
chromatogram was started or terminated prematurely.
Signal-to-noise Ratio View the results of the Signal-to-noise test as Passed, Failed, or Not Tested. This test
indicates whether the minimum signal-to-noise ratio criteria are met.
Concave View the results of the Concave test as Passed, Failed, or Not Tested. This test indicates
whether the peak exhibits a concave depression (local minimum) due to noise.
Saturation View the results of the Saturation test as Passed, Failed, or Not Tested. This test indicates
whether the detector was saturated during acquisition.

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Quantitation Results Sorting Order Dialog Box

Use the Quantitation Results Sorting Order dialog box to set the sort order for the samples in
the Results grid view of the Quan Browser window. The sort order defines the priority for
each parameter used in the sort.
Table 49. Quantitation Results Sorting Order dialog box parameters – Peak Information dialog box
Parameter Description
Sorting
First Order Base the first sort order of the Results grid view on any of the following column headings or
file properties: <none>, %Difference, %RSD, Area/Height, Area/Height Ratio, Exclude,
File Name, Integration Type, Level Name, Peak Status, Sample ID, Sample Type, or
Acquisition Date. By default, the first order sort is set to the acquisition date of the file. You
can select and sort with any of these sort options, even if the corresponding column is not
currently displayed. For example, you can sort by sample type, even if you have selected the
Sample Name check box in the Result List Column Hiding dialog box.
Second Order Base the second sort order of the Results grid view on any of the following column headings
or file properties: <none>, %Difference, %RSD, Area/Height, Area/Height Ratio, Exclude,
File Name, Integration Type, Level Name, Peak Status, Sample ID, Sample Type, or
Acquisition Date. You can select and sort with any of these sort options, even if the
corresponding column is not currently displayed. For example, you can sort by sample type,
even if you have selected the Sample Name check box in the Result List Column Hiding
dialog box.
Sort in descending Sort the second criterion in descending (reverse) order. If you do not select this check box,
order the sort is in ascending order.
Third Order Base the third sort order of the Results grid view on any of the following column headings
or file properties: <none>, %Difference, %RSD, Area/Height, Area/Height Ratio, Exclude,
File Name, Integration Type, Level Name, Peak Status, Sample ID, Sample Type, or
Acquisition Date. You can select and sort with any of these sort options, even if the
corresponding column is not currently displayed. For example, you can sort by sample type,
even if you have selected the Sample Name check box in the Result List Column Hiding
dialog box.
Sort in descending Sort the third criterion in descending (reverse) order. If you do not select this check box, the
order sort is in ascending order.
Button
Save As Default Save your current selection of second and third sort orders as your default set. The Xcalibur
application uses these sort orders to display the Results grid view until you use the
Quantitation Results Setting Order dialog box to change your column sorting preferences.

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Reports Dialog Box

Use the Reports dialog box to generate reports on each sample row within the current bracket.

The Reports dialog box opens with a selection of Report templates and data files preloaded.
These are obtained from the processing method that was previously defined and loaded along
with the results file. This means that the values loaded might change as various brackets are
selected.

Note Prior to using the Reports dialog box you must create a reports template. For
additional information on how to create a report template, see the XReport User Guide.

Table 50. Reports dialog box parameters (Sheet 1 of 4)

Parameter Description
Sample Reports
Enabled Specify whether or not the reports marked with Yes in their row are processed using the
template that appears in the Report Template Name box. For example, if Yes appears in
the QCs and Unknowns boxes and the Enable box in the row displays Yes, then the
Xcalibur application prints these sample reports. If the Enabled box in the row is clear,
then the application does not print any sample reports.

When you click an Enabled box, a check box control appears. If you select this check
box and you click another cell, the application displays the word Yes to indicate that the
report is enabled. If you do not select the check box, the cell remains blank when you
click another cell.
Stds Specify whether or not the Standards (Stds) sample reports marked with Yes are
processed using the report template that appears in the Report Template Name box of
the same row.

To print a Standard sample report, the Xcalibur application must display Yes in the
Enabled box in the same row. For example, if the Std box displays Yes and the Enable
box in the same row displays Yes, then the application prints the Std sample report.
However, if the Enabled box in the row is clear, then the application does not print the
Std sample report.

When you click a Stds box, a check box control appears. If you select this check box and
you click another cell, the Xcalibur application displays the word Yes to indicate that the
report is enabled for Standard samples. If it is not selected, the cell remains blank when
you click another cell.

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Table 50. Reports dialog box parameters (Sheet 2 of 4)

Parameter Description
QCs View whether or not the Quality Controls (QCs) sample reports marked with Yes are
processed using the report template that appears in the Report Template Name box of
the same row.

To print a Quality Controls sample report, the Xcalibur application must display Yes in
the Enabled box in the same row. For example, if the Std box displays Yes and the
Enable box in the same row displays Yes, then the application prints the QCs sample
report. However, if the Enabled box in the row is clear, then the application does not
print the QCs sample report.

When you select a QCs box, a check box control appears. If you select this check box
and you click another cell, the Xcalibur application displays the word Yes to indicate
that the report is enabled for QC samples. If you do not select the check box, the cell
remains blank when you click another cell.
Unks View whether or not the Unknowns (Unks) sample reports marked with Yes are
processed using the report template that appears in the Report Template Name box of
the same row.

To print an Unknowns sample report, the Xcalibur application must display Yes in the
Enabled box in the same row. For example, if the Unks box displays Yes and the Enable
box in the same row displays Yes, then the application prints the Unks sample report.
However, if the Enabled box in the row is clear, then the application does not print the
Unks sample report.

When you select an Unks box, a check box control appears. If you select this check box
and you click another cell, the Xcalibur application displays the word Yes to indicate
that the report is enabled for Unk samples. If you do not select the check box, the cell
remains blank when you click another cell.
Other View whether or not the Other sample reports marked with Yes are processed using the
report template that appears in the Report Template Name box of the same row.

To print an Other sample report, the Xcalibur application must display Yes in the
Enabled box in the same row. For example, if the Other box displays Yes and the Enable
box in the same row displays Yes, then the application prints the Other sample report.
However, if the Enabled box in the row is clear, then the application does not print the
Other sample report.

When you select an Other box, a check box control appears. If you select this check box
and you click another cell, the application displays the word Yes to indicate that the
report is enabled for Other samples. If you do not select the check box, the cell remains
blank when you click another cell.

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Table 50. Reports dialog box parameters (Sheet 3 of 4)

Parameter Description
Save As View the selected file export option for the sample report. These are the valid export file
types:
• None: print only, no exported file
• Text: ASCII text file (*.txt)
• Doc: Microsoft Word file (*.doc)
• HTML: HTML file (*.html)
• PDF: Adobe™ Acrobat™ file (*.pdf )
• RTF: rich text file (*.rtf )
• XLS: Microsoft Excel file (*.xls)

The Xcalibur application saves the exported file with the sample file name and the
appropriate extension in the Data folder where result files are stored.
Report Template Name View the name of the report template to be used in processing the data and generating
the reports indicated by Yes in each row. The sample report is printed using a previously
created template.

Double-click the grid cell to open a browse dialog box so that you can select a template
file. Select the cell and press the <F2> key to edit the box entry. For additional
information on how to create a report template, refer to the XReport User Guide.
Summary Reports
Summary Reports Select summary reports from displayed boxes. The report to be printed is defined in the
Report Template Name box. You can enable the processing of a summary report by
entering Yes in the Enabled box or turn off the processing by clearing the box.
Enabled Specify whether or not the summary reports are processed using the templates that
appear in the Report Template Name boxes. For example, if the Enable box in the row
displays Yes, then the Xcalibur application prints the summary report defined by the
report template in the row. If the Enabled box in the row is clear, then the application
does not print this summary report.

When you select an Enabled box, a check box control appears. If you select this check
box and you click another cell, the application displays the word Yes to indicate that the
report is enabled. If you do not select the check box, the cell remains blank when you
click another cell.

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Table 50. Reports dialog box parameters (Sheet 4 of 4)

Parameter Description
Save As View or change the selected file export option for the sample report. These are the valid
export file types:
• None: print only, no exported file
• Text: ASCII text file (*.txt)
• Doc: Microsoft Word file (*.doc)
• HTML: HTML file (*.html)
• PDF: Adobe Acrobat file (*.pdf )
• RTF: rich text file (*.rtf )
• XLS: Microsoft Excel file (*.xls)

The Xcalibur application saves the exported file with the sample file name and the
appropriate extension in the Data folder where result files are stored.
Report Template Name View the name of the summary report template to be used in processing the summary
report. The summary report is printed using a previously created template.

Double-click the grid cell to open a browse dialog box so that you can select a template
file. Select the cell and press the F2 key to edit the box entry. For additional information
on how to create a report template, refer to the XReport User Guide.
Other Controls
Include Sample Report Select whether or not to print sample reports when you process the current data. This
option controls the printing of all of the sample reports defined in the Sample Reports
box.
Include Summary Report Select whether or not to print summary reports when you process the current data. This
option controls the printing of all of the summary reports defined in the Summary
Reports box.
Select Samples Select the samples for which you want to print reports.
Print Reports Print the reports for the samples you have selected.

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Result List Column Hiding Dialog Box

The Result List Column Hiding dialog box contains the list of possible columns that can be
viewed in the Results grid. Selecting an entry forces that column to be displayed, and clearing
the check box removes the column from the grid.
Table 51. Result List Column dialog box parameters
Parameter Description
Selected Columns These settings indicate whether or not to display a column in the
Results grid. The following columns are available:
• File Name
• Sample Type
• Sample Name
• Integration Type
• Area/Height
• ISTD Area/Height
• Area/Height Ratio
• Specified Amount
• Calculated Amount
• Percent Difference
• Percent RSD
• Peak Status
• Levels
• Units
• Retention Time
• Sample ID
• Exclude

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Select Level Dialog Box

Note Whenever you change a QC, Blank, or Unknown sample type to a Standard sample
type in the Quan Browser window Results grid view, the Select Level dialog box opens so
that you can select one of the available levels for the Standard sample.

Table 52. Select Level dialog box parameters

Parameter Description
Levels Select one of the available levels for the Standard sample whenever you change a QC, Blank,
or Unknown sample type to a Standard sample type in the Quan Browser window Results
grid view.

When you select a level from the Levels list, the read-only information in the lower list
displays the other component names that are assigned to the selected level and the amount
assigned to the selected level for each component.
Levels Table
Name View the components that are assigned the same level as the one currently selected in the
Levels list.
Amount View the Component Amount assigned to the level currently selected in the Levels list for
the component name selected in the Name column.

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Select Report Samples Dialog Box

The Select Report Samples dialog box displays the samples in the current bracket or group in
the Sample Choices box.

From the Sample Choices dialog box, you can pick which samples are to be processed when
sample reports are selected. Use the SHIFT and CTRL keys to select multiple samples. The
Xcalibur data system remembers the selected samples for each bracket until the application is
terminated or a new file is opened.
Table 53. Select Report Samples dialog box parameters
Parameter Description
Sample Choices
Raw File View or change the raw files in the current bracket or current group of samples. These are
the sample files that you select from for processing and for printing a report.
Sample Type View the sample type of the raw file displayed to the left on the same row.
Selected Samples
Raw File View or change the raw files that have been selected from the Sample Choices box. These
are the sample files to be processed so that you can print a report.
Sample Type View the sample type of the raw file displayed to the left on the same row.
Buttons
Add Add files selected in the Sample Choices box to the Selected Samples box.
Remove Return files selected in the Selected Choices box back to the Sample Choices box.
Add All Add all of the files in the Sample Choices box to the Selected Samples box.
Remove All Return all files in the Selected Choices box back to the Sample Choices box.

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User Identification Settings Dialog Box

Use the User Identification Settings dialog box to select and test mass, scan filter, relative peak
height threshold, peak identification, and peak integration settings. If these standard options
do not provide the desired results, Quan Browser also provides advanced options using the
Advanced page. The pages that are displayed depend on whether you are currently using the
Genesis, the ICIS, or the Avalon peak detection algorithm.

The User Identification Settings dialog box includes the following pages:

Genesis

Advanced Page – User Detection Page – User Genesis Integration Page

Identification Settings Identification Settings Parameters
Dialog Box
Flags Page – User
Identification Settings
Dialog Box

ICIS

Advanced Page – User Detection Page – User ICIS Integration Page

Identification Settings Identification Settings Parameters
Dialog Box
ICIS Advanced Page Flags Page – User
Parameters Identification Settings
Dialog Box

Avalon

Detection Page – User Flags Page – User

Identification Settings Identification Settings
Dialog Box
Avalon Integration Page
Parameters

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Advanced Page – User Identification Settings Dialog Box

Use the Advanced page of the User Identification Settings dialog box to change the current
advanced component detection criteria. Use these additional criteria if the standard detection
criteria do not provide the desired results. You can then test the results of the new criteria by
clicking Apply or OK. You can apply the new criteria to all files in the Result list by clicking
Apply To All.

Advanced parameters used for the detection and integration of peaks are less often used but
can provide adequate peak detection with the default parameters.

Depending on which peak detection algorithm you use, one of two Advanced pages is
available:
Table 54. Genesis Advanced page parameters – User Identification Settings dialog box (Sheet 1 of 2)
Parameter Description
Report Noise As
RMS Select this option to calculate noise as RMS.
Peak To Peak Select this option to calculate noise as peak-to-peak.
Manual Noise Region Specify the region of the chromatogram that the Xcalibur data system uses to determine
noise.

You can click and drag the cursor horizontally across the region of the chromatogram
that you want to select as the noise region or type the retention time (RT) in the RT Range
box. The Xcalibur application marks the region with a red baseline.
RT Range Specify the retention time (RT) range. The RT range should be within the chromatogram
range.

You can click and drag the cursor horizontally across the region of the chromatogram
that you want to select as the noise region or type a value in the RT Range box. The
Xcalibur application marks the region with a red baseline.
Rise Percentage View or adjust 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
application 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, type a value in the Rise
Percentage box. Click OK to apply the new peak detection criteria.
Valley S/N View or adjust the signal-to-noise criteria that the Xcalibur application uses for valley
detection. The valid range is 1.0 to 100.0. To change the valley detection signal-to-noise
criteria, type a value in the Valley S/N box. Click OK to apply the new peak detection
criteria.

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Table 54. Genesis Advanced page parameters – User Identification Settings dialog box (Sheet 2 of 2)
Parameter Description
Peaks S/N Cutoff View or adjust the signal-to-noise below which the Xcalibur application defines the peak
edge. For example, if the signal-to-noise at the apex is 500 and the Peak S/N Cutoff value is
200, the application defines the right and left edges of the peak when the S/N reaches a
value less than 200. The valid range is 50.0 to 10000.0.
Baseline Noise View or adjust a value that controls how the baseline is drawn in the noise data. The higher
Tolerance the baseline noise tolerance value, the higher the baseline is drawn through the noise data.
The valid range is 0.0 to 100.0.
Min Number Of View or adjust the minimum number of scans that the Xcalibur data system uses to
Scans In Baseline calculate a baseline. A larger number includes more data in determining an averaged
baseline. The valid range is 2 to 100.0.
Number Of View or adjust the number of background scans used to determine the background. The
Background Scans valid range is 1 to 100

ICIS Advanced Page Parameters

Table 55. ICIS Advanced page parameters – User Identification Settings dialog box (Sheet 1 of 2)
Parameter Description
Manual Noise Specify the region of the chromatogram that the Xcalibur data system uses to determine noise.
Region
You can click and drag the cursor horizontally across the region of the chromatogram that
you want to select as the noise region or type the retention time (RT) in the RT Range box. The
Xcalibur application marks the region with a red baseline.
RT Range Specify the retention time (RT) range. The RT range should be within the chromatogram range.

You can click and drag the cursor horizontally across the region of the chromatogram that
you want to select as the noise region or type a value in the RT Range box. The Xcalibur
application marks the region with a red baseline.
Noise Method
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 Specify that the Xcalibur application calculates noise as RMS. By default, the Xcalibur
application uses peak-to-peak for the noise calculation. RMS is automatically selected if you
determine the noise region manually.
Min Peak Width Type 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 Type the minimum separation in scans between the apexes of two potential peaks. This is a
Resolution criteria to determine 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.
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Table 55. ICIS Advanced page parameters – User Identification Settings dialog box (Sheet 2 of 2)
Parameter Description
Area Tail Type the number of scans past the peak endpoint to use in averaging the intensity. The valid
Extension range is 0 to 100 scans. The default value is 5 scans. This value is used by the ICIS peak
detection algorithm.
Area Scan Type the number of allowable scans on each side of the peak apex. The valid range is 0 to 100
Window 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.

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Detection Page – User Identification Settings

Use the Detection page from the User Identification Settings dialog box to change the current
peak detection criteria for component detection. The controls on the Detection page vary
depending on whether you use a GC or LC and also on whether the detection method is
Spectrum, Highest Peak, or Nearest RT.
Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 1 of 6)
Parameter Description
Spectrum This option is only available in the Xcalibur GC chromatography mode (set in the
Chromatography Options Dialog Box). You can use a reference spectrum defined in the
processing method for component identification. The Xcalibur application attempts to match
the reference spectrum with a series of unknown spectra and calculates a score value for each
comparison.
If you select the Spectrum option, the following parameters appear:
• Spectrum Peak Detection: Displayed only in the Xcalibur GC Chromatography mode when
you select the Spectrum option. You must also have selected the MS detector type on the
Identification page.
• Spectrum Peak Identification table: Enter mass/charge [m/z] and intensity data for up to 50
spectrum peaks. The Xcalibur application uses this data to identify the active component in
the Find algorithm. It displays this table only when you select the Spectrum option in its
GC Chromatography mode.
• m/z: View the mass/charge [m/z] value for one peak in the reference spectrum. The intensity
for this m/z value is given in the adjacent Intensity table box. Use the other rows of the table
to enter as many as 50 m/z values. The Xcalibur application uses this data to identify the
active component in the Find algorithm. It displays this table only when you select the
Spectrum option in its GC Chromatography mode.
• Intensity: Enter intensity data for one peak in the reference spectrum. The m/z value for this
intensity is given in the adjacent m/z Table box. Use the other rows of the table to enter as
many as 50 intensity values. The Xcalibur application uses this data to identify the active
component in the Find algorithm. It displays this table only when you select the Spectrum
option in its GC Chromatography mode.
Thresholds
Forward Set a threshold value for Forward comparisons between the reference spectrum and candidates in
the chromatogram. A Forward search is a direct matching algorithm comparing unknowns
against the reference spectrum in the peak identification table. The match is scored on a scale
of 0 to 999. A perfect match results in a score of 999. As a general guide, 900 or greater is an
excellent match; 800 to 900 a good match; 700 to 800 a fair match. Less than 600 is a poor
match. Unknown spectra with many peaks tend to score lower than similar spectra with fewer
peaks.

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Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 2 of 6)
Parameter Description
Reverse Set a threshold value for Reverse comparisons between the reference spectrum and candidates in
the chromatogram. A Reverse search ignores any peaks in the unknown that are not in the
reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A
perfect match results in a score of 999. As a general guide, 900 or greater is an excellent match;
800 to 900 a good match; 700 to 800 a fair match. Less than 600 is a poor match. A spectrum
with many peaks tends to score more highly in a Reverse match than a Forward match.
Match Set a threshold value for Match comparisons between the reference spectrum and candidates in
the chromatogram. Match is scored on a scale of 0 to 999. The Match algorithm is a complex
probability factor based on the differences between the Forward factors of all the candidates. If
one candidate has a Forward matching factor of 900 and the next best is only 300, the
probability of the component being correctly identified is high and so the Match factor is scored
highly for the first candidate. If the Forward factors for all the candidates are similar, whether
high or low, the Match factor is low.
Highest Peak Use the highest peak in the chromatogram for component identification.
Nearest RT Use the peak with the nearest retention time in the chromatogram for component identification.

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Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 3 of 6)
Parameter Description
If you are in GC mode and you select the Highest Peak or Nearest RT options, the following
parameters appear:

Ion Ratio Confirmation: Displayed only in the Xcalibur GC Chromatography mode when you
select either the Highest Peak or Nearest RT option. You must also have selected the MS
detector type on the Identification page.

Specify up to five qualifier ions in this box to confirm the detection of a target analyte. You can
also set the coelution window and select a method for calculating the target ion ratio window
and tolerance.

Enable: Indicates whether or not Ion Ratio Confirmation is enabled.

Ion Ratio Using: Area or Height: View the currently selected peak quantitation method: area
or height. The Xcalibur application uses the same method to calculate qualifier ion peak
response and then target ratio. You can change this parameter by selecting the Area or Height
options in the Response box on the Calibration page.

Qualifier Ion Table: Use this table to enter mass/charge [m/z] and target ratio tolerances
(Window ± %) data for up to five qualifier ions.
• If you are using Area response, the Xcalibur application integrates each qualifier ion peak
and ratios it with the quantitation peak area. The application then compares this ratio with
your specified target ratio. If the calculated ratio is outside of the target ratio by more than
your specified tolerance (Window ± %), the quantitation peak is rejected.
• If you are using Height response, the Xcalibur application ratios the qualifier ion peak
height with that of quantitation peak. The application then compares this ratio with your
specified target ratio. If the calculated ratio is outside of the target ratio by more than your
specified tolerance (Window ± %), the quantitation peak is rejected.

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Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 4 of 6)
Parameter Description
m/z: This box in the Qualifier Ion table displays the mass/charge [m/z] value for a qualifier ion.
The target ratio tolerance for this m/z value is displayed in the adjacent Window ± % table box.
Use other rows of the table to enter data for five qualifier ions. The Xcalibur application uses this
data to confirm the identity of a quantitation peak by comparing the relative responses of
qualifier ion and quantitation peaks with predetermined values.

Target Ratio: This box in the Qualifier Ion table displays the Target Ratio (%) value for a
qualifier ion. The m/z value and target ratio tolerance for the qualifier ion are given in the
adjacent m/z and Window ± % table boxes. Use other rows of the table to enter data for five
qualifier ions. The Xcalibur application uses this data to confirm the identity of a quantitation
peak by comparing the relative responses of qualifier ion and quantitation peaks with
predetermined values.

Window: Use this box in the Qualifier Ion table to specify the Target Ratio tolerance for a
qualifier ion. Use other rows of the table to enter data for five qualifier ions. The Xcalibur
application uses this data to confirm the identity of a quantitation peak by comparing the
relative responses of qualifier ion and quantitation peaks with the specified values.

Qualifier Ion Coelution: Set the Qualifier Ion Coelution window.

• Prior to ion ratio confirmation, the Xcalibur application generates a mass chromatogram for
each specified qualifier ion. Each of these chromatograms must feature a peak, matching
that of the quantitation masses. If the retention time of the qualifier ion peak apex lies
outside of the Qualifier Ion Coelution window (centered on the quantitation peak), the
application rejects the quantitation peak.
• Quantitation peaks with matching qualifier ion peaks (within the Coelution window) are
tested by Xcalibur for ion ratio confirmation.

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Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 5 of 6)
Parameter Description
Window
• Relative: Specify that the target ratio tolerance values in the Window ± % column of the
qualifier ion table are relative values.
For example, if the target ratio is 50% and the Window ± % parameter is 20%, the expected
target ion ratio range is 40% to 60% (with the Absolute option this would be 30% to 70%).
If the ion ratio is outside this range, the ion ratio confirmation test has failed and the
Xcalibur application sets the IRC Flag to false. If the qualifier ion peak/quantitation peak
ratio is within range, the ion ratio confirmation test passes and the application sets the IRC
Flag to true. The response of all specified qualifier ions must be within the respective ratio
ranges for IRC to succeed.
In assessing a target ion ratio range, the application truncates the range at 0% to avoid
negative values.
• Absolute: Specify that the target ratio tolerance values in the Window ± % column of the
qualifier ion table are absolute values.
For example, if the target ratio is 50% and the Window ± % parameter is 20%, the expected
target ion ratio range is 30% to 70% (with the Relative option this would be 40% to 60%).
If the qualifier ion peak/quantitation peak ratio is outside this range, the ion ratio
confirmation test has failed and the Xcalibur application sets the IRC Flag to false. If the
qualifier ion peak/quantitation peak ratio is within range, the ion ratio confirmation test
passes and the application sets the IRC Flag to true. The response of all specified qualifier
ions must be within the respective ratio ranges for IRC to succeed.
In assessing a target ion ratio range, the Xcalibur application truncates the range at 0% to
avoid negative values.
Minimum Peak View or change the peak signal-to-noise criteria that needs to be equaled or exceeded for the
Height Xcalibur application to use the Nearest RT Peak Identification criteria. When identifying
components, the application ignores all chromatogram peaks that have signal-to-noise values
that are less than the S/N Threshold value. The valid range is 0.0 (all peaks) through 999.0.

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Table 56. Detection page parameters – User Identification Settings dialog box (Sheet 6 of 6)
Parameter Description
Buttons
Apply Apply the current peak detection parameters to the selected component of the selected sample in
the current sequence.

If one or more standard samples are changed, the Xcalibur application recalculates all
quantitation parameters, including peak areas and the calibration curve.
Apply To All Apply the current peak detection parameters to all samples that are currently displayed in the
sequence. For example, if you select the Standards option, the Xcalibur application applies the
current peak detection parameters only to the standards samples and not to any other samples. If
you select the All samples option, the application applies the current peak detection parameters
to all samples in the current sequence.

If one or more standard samples are changed, the Xcalibur application recalculates all
quantitation parameters, including peak areas and the calibration curve.

Flags Page – User Identification Settings Dialog Box

The Flags page of the User Identification Settings dialog box shows the current detection
flagging thresholds in use for the selected compound. These values are used in determining if
the peak detection is within user-specified limits. They do not alter the way calculations are
made. An entered value of 0.0 forces the flag to be false.
Table 57. Flags page parameters – User Identification Settings dialog box
Parameter Description
Area Threshold View or set a value for the current Area Threshold (AT) flag. The Xcalibur application sets
the AT flag in the results file if the quantified peak has an area that is lower than the entered
value.
Height Threshold View or set a value for the current Height Threshold (HT) flag. The Xcalibur application
sets the HT flag in the results file if the quantified peak has a height that is lower than the
entered value.

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Identification Page – User Identification Settings Dialog Box

Use the Identification page to change the current component name, mass range, scan filter,
and retention time for the selected component. You can then test the results of the new
settings by clicking Apply or OK. You can apply the new settings to all files in the Result grid
view by clicking Apply To All.

The Identification page helps to narrow the search parameters and to set filters so that the
peak detection algorithms have an easier time of locating the peaks. The compound of interest
is displayed in the Name box. This is a read-only field. To select a different compound, select
the name in the Component list on the right side of the display.
Table 58. Identification page parameters – User Identification Settings dialog box (Sheet 1 of 4)
Parameter Description
Name This box displays a list of component names for the active processing method.
Plot Type These three lists display the type of trace and optional trace math operation that is stored in
the processing method. Only certain combinations of plot types are possible as shown in the
following table:
1st Plot Type Math Operation 2nd Plot Type
Mass Range None n/a
Mass Range ± Mass Range
TIC n/a
TIC- Mass Range
TIC- Base Peak
Base Peak None n/a
Base Peak ± Mass Range
Analog 1, 2, 3, or 4 None n/a
Analog 1, 2, 3, or 4 ± Digital* 1, 2, 3, or 4
Digital 1, 2, 3, or 4 None n/a
Digital 1, 2, 3, or 4 ± Digital* 1, 2, 3, or 4

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Table 58. Identification page parameters – User Identification Settings dialog box (Sheet 2 of 4)
Parameter Description
Filter This box displays the current scan filter for the active file of extension .raw. 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 the list and edit the scan filter, or type a new scan filter
command string into the box using the scan filter format.

For example, the following scan filter:

c full ms [26.81-251]

finds all scans in a raw file that have the following properties:
centroid data
Scan Mode: Full
Scan Power: MS
Product Ion Mass Range: m/z 26.81 to 251.00

The Xcalibur application displays this box when you select a Base Peak trace for an MS
detector type. The box displays the range within which the application is to search for the
highest peak.

If you type a single m/z value in this box, that defines the base peak.

To change the base peak mass range, type the value in the box. A mass range from m/z=A to
m/z=B is entered in the format A-B.

The Xcalibur application displays this box when you select a Base Peak ± Mass Range trace
combination for an MS detector type. The box displays the mass range for the second, Mass
Range, trace type.

To change the range or to add a new range, type the range in the box. The format is
Low Mass - High Mass. For example, for the range m/z 123 through 456, type: 123 - 456.
Mass This box displays the masses stored in the processing method. This display area changes to
accommodate the type of data required. When a single mass range is required, there is a
single edit box displaying the current value. If two mass ranges are required (such as the case
of a trace defined as a Mass Range +/- Mass Range or Base Peak +/- Mass Range), this box is
replaced by two boxes (in the case of Base Peak +/- Mass Range, this box is replaced by the
BP and MR boxes). In the case of a TIC (no trace operator in use), Analog, or Digital traces,
this box is blank.
Keys This box displays specific flags stored in the processing method. This is a read-only field
used for reference.

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Table 58. Identification page parameters – User Identification Settings dialog box (Sheet 3 of 4)
Parameter Description
Retention Time
Retention Time The settings in this area define the expected retention time in minutes of the component
peak and the error window in seconds for the retention time.
Expected This box displays the expected peak width parameter (in seconds). This controls the
minimum width that a peak is expected to have if valley detection is enabled.

With valley detection enabled, any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the expected peak width, the
Xcalibur application terminates the peak at that point. It 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 box.
Window This box displays the allowable retention time window for the elution of the selected
component. The valid range is 1.0 to 999.0 seconds. To change the time window or to enter
a new time window, type the number of seconds in the (retention time) Window box.
Use as RT Reference This check box indicates whether or not the actual retention time (RT) of the active
component [as displayed in the Name combo box in the same view] was used to adjust the
expected retention time of another component. This check box is read-only.
View Width This box displays the current view width (in minutes). The valid range is dependent upon
the configured hardware. To change the view width, type the desired time in the View
Width text box.
Adjust Using This check box indicates whether or not the expected retention time (RT) of the active
component (as displayed in the Name box in the same view) is to be adjusted using the
actual retention time of the RT Reference, such as an internal standard. The Xcalibur
application displays the RT Reference in the Adjust Using box to the right of this check box.
This check box is read-only.
Adjust Using (box) This box displays the retention reference component that Xcalibur uses to adjust the
expected retention time of the active component (as displayed in the Name box in the same
view. The Xcalibur application uses the actual retention time of the RT Reference
component to correct the retention time of the active component. The application provides
the following correction to the expected retention time:

Adjusted RT Component Expected =

[RT Component Expected ´ RT Reference Actual] / RT Reference Expected.

This box is read-only.

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Table 58. Identification page parameters – User Identification Settings dialog box (Sheet 4 of 4)
Parameter Description
Detector Type
Type View detector type options. These are the detectors that you have configured using the
Instrument Configuration dialog box.
Peak Detection This list contains three options from which you can select an Xcalibur peak detection
Algorithm algorithm to recalculate the data using that algorithm.
Buttons
Apply This button applies the current peak detection parameters to the selected component of the
selected sample in the current sequence.
Apply to All This button applies the current peak detection parameters to all samples that are currently
displayed in the sequence. For example, if “Standards” are displayed, the current peak
detection parameters are applied to only the Standards samples and not to any other
samples. If “All” samples are displayed, the current peak detection parameters are applied to
all samples in the current sequence.

If one or more Standard samples are changed, the Xcalibur application recalculates all
quantitation parameters, including peak areas and the calibration curve.

If one or more Standard samples are changed, the Xcalibur application recalculates all
quantitation parameters, including peak areas and the calibration curve.

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Integration Page – User Identification Settings Dialog Box

Use the Integration page to change the current peak integration criteria for the selected
component. You can then test the results of the new criteria by clicking Apply or OK. You can
apply the new criteria to all files in the Result list by clicking Apply To All. These settings are
used by the Detection algorithm.

Depending on the peak detection algorithm that you are using, one of three Integration pages
is available:
• Genesis Integration Page Parameters
• ICIS Integration Page Parameters
• Avalon Integration Page Parameters

Genesis Integration Page Parameters

The following table lists the Genesis Integration page parameters.
Table 59. Genesis Integration page parameters – User Identification Settings dialog box (Sheet 1 of 2)
Parameter Description
Smoothing Points Determine the degree of data smoothing to be performed on the active component peak
prior to peak detection and integration. The valid range is any odd value between 1 (no
smoothing) through 15 (maximum smoothing). To smooth your component peak data
prior to integration, type a value in the Smoothing Points box. See also Avalon Integration
Page Parameters and ICIS Integration Page Parameters.
S/N Threshold View or change the current signal-to-noise threshold for peak integration. Peaks with
signal-to-noise less than this value are not integrated. Peaks with signal-to-noise greater than
this value are integrated. The valid range is 0.0 to 999.0. To change the current value, type a
new value in the S/N Threshold box.
Valley Detection Use the Xcalibur valley detection approximation method to detect unresolved peaks. This
Enabled 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, ensure that the check box is clear.
Expected Width View the expected peak width parameter (in seconds). This controls the minimum width
that a peak is expected to have if valley detection is enabled.

With valley detection enabled, any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the expected peak width, the
Xcalibur application terminates the peak at that point. The application always terminates a
peak when the signal reaches the baseline, independent of the value set for the expected peak
width. The valid range is 0.0 to 999.0 seconds. To change the current value, type a new
width in the Expected Width box.

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Table 59. Genesis Integration page parameters – User Identification Settings dialog box (Sheet 2 of 2)
Parameter Description
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, select the Constrain Peak
Width check box. The Peak Height (%) box and the Tailing Factor box are activated.
Peak Ht View or adjust 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 the
Constrain Peak Width check box is selected. The valid range is 0.0 to 100.0%. To enter this
height, type the appropriate value in the Peak Ht box.
Tailing Factor View or adjust a factor that controls how the Xcalibur data system integrates the tail of a
peak. This tailing factor is the maximum ratio of the trailing edge to the leading side of a
constrained peak. This box is active only when the Constrain Peak Width box is selected.
The valid range is 0.5 through 9.0.

ICIS Integration Page Parameters

The following table lists the ICIS Integration page parameters.
Table 60. ICIS Integration page parameters – User Identification Settings dialog box (Sheet 1 of 2)
Parameter Description
Smoothing Points Type the number of points used in the moving average used to smooth the data. The valid
range is any odd value from 1 through 15 points. The default value is 1 point. This value is
used by the ICIS peak detection algorithm.
Baseline Window Specify the number of scans over which to look 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, select the Constrain Peak
Width check box. The Peak Height (%) box and the Tailing Factor box are activated.

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Table 60. ICIS Integration page parameters – User Identification Settings dialog box (Sheet 2 of 2)
Parameter Description
Peak Ht View or adjust 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 the
Constrain Peak Width check box is selected. The valid range is 0.0 to 100.0%. To enter this
height, type the appropriate value in the Peak Ht box.
Tailing Factor View or adjust a factor that controls how the Xcalibur data system integrates the tail of a
peak. This tailing factor is the maximum ratio of the trailing edge to the leading side of a
constrained peak. This box is active only when the Constrain Peak Width check box is
selected. The valid range is 0.5 through 9.0.

Avalon Integration Page Parameters

The following table list the Avalon Integration page parameters.
Table 61. Avalon Integration page parameters – User Identification Settings dialog box (Sheet 1 of 3)
Parameter Description
Auto Calc Initial This button is active with the event list of the Avalon peak detection algorithm only if a raw file
Events is 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. Use this button to force Avalon to search for the best values of initial events that
detect peaks in the data. Any timed event in the event list is unchanged when you click 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, the user can specify timed events for these events in
the same event list.
Smoothing Points View or adjust the number of points that the Xcalibur data system uses for chromatogram
smoothing. The valid range for smoothing points is from 3 to 15. The number of smoothing
points must be odd. To change the number of smoothing points, type the new number of points
in the Smoothing Points box.
Event List
Event List To detect peaks, Avalon uses the settings for initial events and user-defined timed events in the
event list. To calculate values for initial events, click Auto Calc Initial Events.

The event list in the Avalon Event List dialog box contains two hidden columns of information
that are used by the algorithm and cannot be changed by the user: Event OP Code and Value2.

There are seven initial entry integration events, which are identified by the initial value setting in
the Time column. These are the default integration events required by the Avalon integration
algorithm. You can change the Value of an initial entry integration event, but you cannot delete
it or change its time value.
Time This column contains either the term initial value or a value of time in minutes.

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Table 61. Avalon Integration page parameters – User Identification Settings dialog box (Sheet 2 of 3)
Parameter Description
Event View descriptions of detection parameters for initial events and timed events.

You cannot change an event associated with an initial value.

Value View the values associated with initial events or timed events. The range of factors allowed for
each value is specific to each event.
Event List entry
Time View or change the currently highlighted entry from the Time column in the event list.
Event View the currently highlighted entry in the Event column of the event list.

An event cannot be changed that is listed with an Initial Value in the Time column. The
Threshold and Bunch Factor parameters are the most important ones in controlling peak
detection.
The Xcalibur application provides the following events:

Start/End Threshold: Directly related to the RMS noise in the chromatogram, this 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. Any peaks with a final area less than the area
threshold is not detected. 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 is specified as a percent of peak height overlap.

Negative Peaks: Automatically resets after a negative peak has been found.

Tension: Controls how closely the baseline should follow the overall shape of the
chromatogram. A lower tension traces the baseline to follow changes in the chromatogram more
closely. A high baseline tension follows the baseline less closely, over longer time intervals. Set in
minutes.

Tangent Skim: Using this event, you can tangent skim any peak clusters. By default, it chooses
the tallest peak in a cluster as the parent (solvent). You can also identify which peak in the cluster
is the parent. Tangent skim peaks are detected on either side (or both sides) of the parent peak.
Tangent skim automatically resets at the end of the peak cluster.
Value View or change the currently highlighted entry from the Value column in the event list. The
range of factors allowed for each value is specific to each event.

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Table 61. Avalon Integration page parameters – User Identification Settings dialog box (Sheet 3 of 3)
Parameter Description
Page Buttons
Add Add to add a time/event/value entry for a timed event in the event list. When you click Add,
both the event list and the chromatogram display update automatically with the added
specification in the currently selected chromatogram.
Delete Delete to remove a highlighted event from the event list. You cannot delete initial values.
Change Change to update a highlighted time/event/value entry in the event list. When you click
Change, both the event list and the chromatogram display update automatically with the
revised specification in the currently selected chromatogram. For initial events, only the values
(and not the events) can be changed.

View Sample Types Dialog Box

When opening Quan Browser, the Xcalibur data system first checks to confirm that the file
you select is valid. After verifying that all the files exist and can be opened, but before
displaying any data, the View Sample Types dialog box opens to prompt you to display only
“Standards and QC samples” or “All samples.”

A Don’t ask again check box is provided so that you do not have to see the dialog box again
after making your initial choice.

To reset the display of this dialog box and all other message type dialog boxes, choose
Options > Enable Warnings.
Table 62. View Sample Types dialog box parameters
Parameter Description
Viewing Options
Show Standards and QCs Display only Standards and QCs in the Quan Browser grid view. The Xcalibur
application does not display blanks and Unknowns. Select one of these tabs: Standards
or QCs.
Show All Sample Types Display Standards, QCs, Blanks, and Unknowns in the Quan Browser grid view. You
will be able to select from the following tabs: All, Standards, QCs, Blanks, or
Unknowns.
Don't Ask Again Decide whether you want to see the current message box or dialog box in the future.

For example, if you always select the Show All Sample Types option and never select the
Show Standards or QCs option, you might want to turn off the View Sample Types
dialog box.

To turn on the display of all message boxes and dialog boxes, choose Options > Enable
Warnings.

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Index
B External calibration file 12
External standards
Brackets/Groups In Use box 56
considering variables for 6–7
definition 6
C using, for quantitation 6
Cal Exclusion List dialog box 49
calibration F
modifying parameters 44
File menu for Quan Browser 70
replicates 11
Calibration Companion view 43
calibration curve G
editing samples 20 GoTo menu, Quan Browser 72
restoring a point 54 groups 12
using external standard (figure) 7
calibration file, setting 57
calibration settings
H
Curve page 47 Help menu, Quan Browser 72
Levels page 50
Calibration Settings dialog box 47, 86 I
Chromatogram view ICIS
editing samples 20 Advanced page
reviewing 37 User Identification Settings dialog box 32
working in 23 Integration page
Chromatogram view, about 18 User Identification Settings dialog box 31
chromatogram, integrating peaks manually 30 Identification page, User Identification Settings dialog box 27
Columns command 59 Include command 54
component list, setting 18 Include Sample Reports check box 61
continuing calibration method 12 Include Summary Reports check box 62
integration, chromatogram peaks manually 30
D internal standards (ISTDs)
Detection page, User Identification Settings dialog box 29 choosing 9
detection, limit 5 considering variables for 8
definition 7
using, for quantitation 8
E
editing L
a sample 20
LCQUAN
a sequence 19
acquiring and processing data with, overview 2
Exclusion List command 49

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quantitative analysis procedure 2 quantitative analysis

Levels page, Calibration Settings dialog box 50 definition 2
limit sources of error 7
of detection 5 using internal standards for 7
of quantitation 5
lower quantitation limit 5 R
Replace Calibration command 57
N replicates 11
nonoverlapped, bracket type 14 Reports dialog box, Select Samples button 62
Reset Scaling command 39
O Result List Column Hiding dialog box 59
Results grid
open, bracket type 13 changing the sort order 60
Options menu, Quan Browser 73 column headings 57, 59
overlapped, bracket type 14 definition 18
displaying columns 59
P editing a sequence 19
editing samples 20
Peak Detection Settings command, User Identification
hiding columns 59
Settings dialog box 25
working in 56
Peak Information dialog box 24, 120
peaks, integrating manually in chromatogram 30
Print Reports button 62 S
samples, editing in Quan Browser 20
Q Select Report Samples dialog box 62
Select Samples button 62
Quan Browser
sequences, editing in Quan Browser 19
Cal Exclusion List dialog box 49
Set Sorting Order command 60
Chromatogram view 18
component list 18 Show Calibration Curve command 39, 43
getting started 14 Show Peak Info command 24
opening files 14 Show Standards and QC commands 15
Peak Information dialog box 24 sort order 60
Quantitation Results Sorting Order dialog box 60 Spectrum at Peak Apex command 39
Reports dialog box 61 Spectrum at Peak Left Edge command 39
Result List Column Hiding dialog box 59 Spectrum at Peak Right Edge command 39
Results grid 18 Spectrum Companion view 38
Select Report Samples dialog box 62 Spectrum plot 39
User Identification Settings dialog box 25 standard
View Sample Types dialog box 15 clear 12
window features 17 update 12
Quan Browser views
Calibration Curve Plot view 81
Chromatogram Plot view 79 U
Component List view 78 unbracketed sequence 12
Results grid view 76 upper quantitation limit 5
Spectrum Plot view 80 User Identification Settings dialog box
Quan Browser window 66 Detection page 29
quantitation limits 5 ICIS Advanced page 32
quantitation range 5 ICIS Integration page 31
Quantitation Results Sorting Order dialog box 60 Identification page 27

158 Quantitative Analysis User Guide Thermo Scientific

 Index: V

reference 138
User Peak Detection Settings command 25

V
variables, discussion of
quantitation with external standards 6
quantitation with internal standards 8
View menu, Quan Browser 73
View Sample Types dialog box 15
View Spectrum Plot command 39

W
Warning dialog box 15
working in the Results grid 56

X
Xcal files 12

Z
Zoom menu, Quan Browser 74

Thermo Scientific Quantitative Analysis User Guide 159