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© 2016 Thermo Fisher Scientific Inc. All rights reserved.
Foundation, FreeStyle, and mzVault are trademarks, and Orbitrap, Thermo Scientific, TSQ Endura, TSQ
Quantiva, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
The following are registered trademarks in the United States and other countries: Adobe, Flash, and Reader are
registered trademarks of Adobe Systems Incorporated. Microsoft, Windows, Outlook, and Excel are registered
trademarks of Microsoft Corporation. NIST is a registered trademark of the National Institute of Standards
and Technology.
mzCloud is a registered trademark of HighChem, Ltd. in Slovakia.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, December 2016
Software version: (Thermo) Foundation 3.0 SP2 and later; FreeStyle 1.2 and later.
For Research Use Only. Not for use in diagnostic procedures.
Thermo Scientific FreeStyle User Guide iii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
License Activation and Deactivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Demonstration Animations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
What’s New in FreeStyle Version 1.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Chapter 2 Using the FreeStyle Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Workspaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Saving and Applying Layout Templates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Restoring the Default Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Workspace Options Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Workspace Processing Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Display Options Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Zoom Options Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Text and Graphic Annotation Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Views. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Arranging Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Using the Pointer to Update the Timebase or Rescale a Graph . . . . . . . . . . . 22
Info Bar Pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3 Working with Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Chromatogram-Specific Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Chromatogram Workspace Processing Toolbar . . . . . . . . . . . . . . . . . . . . . . . 27
Sequence Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Chromatogram Display Options Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Contents
Contents
iv FreeStyle User Guide Thermo Scientific
Chromatogram-Specific Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Active Traces View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Filtering Raw Data Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Using the Fill Down Feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Selecting the Field Columns to Display . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Moving a Row . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Copying and Pasting Rows. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Deleting Rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Chromatogram View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Viewing Chromatogram Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Adding and Deleting Chromatogram Traces . . . . . . . . . . . . . . . . . . . . . . . 47
Adding Plots to a Chromatogram View with the Auto Filter Feature . . . . . 48
Creating a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Comparing Chromatogram Traces in a Sequence. . . . . . . . . . . . . . . . . . . . 50
Displaying Extracted Ion Chromatogram Traces . . . . . . . . . . . . . . . . . . . . 51
Chromatogram View Header Information . . . . . . . . . . . . . . . . . . . . . . . . . 52
Normalizing and Scaling Chromatogram Traces . . . . . . . . . . . . . . . . . . . . 53
Peak List View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Selecting the Field Columns to Display . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Adding Peaks to the Peak List by Using Automatic Peak Detection . . . . . . 62
Manually Adding Peaks to and Deleting Peaks from the Peak List . . . . . . . 64
Chromatogram-Specific Pages in the Info Bar . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Sequence File Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Genesis Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
ICIS Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Avalon Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
PPD Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Detector Type Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Trace Type Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Filter Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Chapter 4 Working with Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Spectra-Specific Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Spectrum Workspace Processing Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Spectrum Display Options Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Multi Spectrum Display Options Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Contents
Thermo Scientific FreeStyle User Guide v
Spectra-Specific Views. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Displaying Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Averaging Spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Subtracting Background Spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Spectrum View Scan Header Information . . . . . . . . . . . . . . . . . . . . . . . . 100
Viewing Data-Dependent Scans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Multi Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Elemental Composition Results View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Library Search Result Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
mzVault Search Results View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
NIST Search Result View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Chemical Structure Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
NIST Chemical Structure View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
mzVault Chemical Structure View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Spectra-Specific Info Bar Pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Elemental Composition Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Determining Elemental Composition. . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Adding and Removing Elements in the Elements in Use Table . . . . . . . . 121
Isotope Simulation Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Simulating Isotopic Distributions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Library Search Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
mzVault Search Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Searching NIST or mzVault Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Comparing the Query Spectrum to the Library Spectrum . . . . . . . . . . . . 137
Managing Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Chapter 5 Working with CV Plots for FAIMS Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
CV Traces Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
CV Plot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Chapter 6 Viewing Experiment and Instrument Information. . . . . . . . . . . . . . . . . . . . . . . . .147
Workspace Options Toolbar – Report Area. . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Spectrum List Display Options Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Scan Header View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Spectrum List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Status Log View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Instrument Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Tune Method View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Sample Information View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
File Header View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Contents
vi FreeStyle User Guide Thermo Scientific
Chapter 7 Deconvolving and Deisotoping Spectra with the Xtract Algorithm . . . . . . . . .163
Xtract Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Deconvolved Spectrum View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Xtract Results View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Appendix A FreeStyle Default Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .177
Default Mass Precision Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Default Peak Detection Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Default Recently Used Files Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Default Raw Data Files Directory Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Default Elemental Composition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Factory Default Template Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Default Library Search Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Default Workspace Options Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Default Xtract Options Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Appendix B Scan Filters and Scan Headers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
Scan Filter Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Scan Headers and Scan Header Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . 194
Appendix C One- and Three-Letter Abbreviations for Amino Acid Residues . . . . . . . . . . . .197
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .201
Thermo Scientific FreeStyle User Guide v
P
Preface
This guide describes how to use the Thermo FreeStyle™ application to view and analyze raw
data.
Contents
•Related Documentation
•System Requirements
•License Activation and Deactivation
•Special Notices
•Contacting Us
To learn how to use the FreeStyle application, begin with the “Demonstration Animations” on
page 1. For a list of new features, see “What’s New in FreeStyle Version 1.2” on page 2.
To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
To open the FreeStyle application
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
FreeStyle > FreeStyle.
–or–
Click the FreeStyle icon, , on the desktop.
Preface
vi FreeStyle User Guide Thermo Scientific
Related Documentation
The FreeStyle application includes complete documentation. In addition to this guide, you
can also access the application Help.
To view the product manual
From the taskbar, choose Start > All Programs > Thermo FreeStyle > Manual >
FreeStyle User Guide.
To open the Help system from the FreeStyle window
Choose File > Help.
To view application-specific Help
If information about setting parameters is available for a specific view, page, dialog box, or
toolbar, click Help or press the F1 key for information about setting parameters.
System Requirements
The FreeStyle application requires a license. In addition, your system must meet the
minimum requirements as stated in the following table.
System Minimum requirements
Computer • 1.7 GHz dual core processor with 3.0 GB RAM
• CD/R-ROM or DVD drive
• 30 GB or greater available on drive C
• Video card and monitor capable of 1280 × 1024 resolution
Software • Adobe™ Flash™ Player 11 (to view the demonstration animations)
• Adobe Reader™ 10.1
• Microsoft .NET Framework 4.5.1
• Microsoft Office 2010
• Microsoft Windows 7 SP1 (64-bit)
• Thermo Foundation™ platform 3.0 SP2
Preface
Thermo Scientific FreeStyle User Guide vii
License Activation and Deactivation
Use the Thermo Scientific™ Product Licensing wizard to activate or deactivate the FreeStyle
application. To activate the FreeStyle application, you must have an activation code from
Thermo Fisher Scientific™. You must deactivate the FreeStyle application before you transfer
the license to another computer.
To open the Product Licensing wizard
1. Open the FreeStyle application.
2. Choose File > About FreeStyle to display the License Activation wizard.
3. Click Activate (Deactivate) to start the activation or deactivation processes, as applicable.
Special Notices
Make sure you follow the special notices presented in this guide. Special notices appear in
boxes; those concerning safety or possible system damage also have corresponding caution
symbols.
This guide uses the following types of special notices.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Preface
viii FreeStyle User Guide Thermo Scientific
Contacting Us
QR Code Email Telephone
Technical Support us.techsupport.analyze
@thermofisher.com
(U.S.) 1 (800) 532-4752
Customer Service and
Sales
us.customer-support.analyze
@thermofisher.com
(U.S.) 1 (800) 532-4752
Thermo Fisher Scientific
Global Contacts
To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us and then select the type of support you
need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.
To find product support, knowledge bases, and resources
Go to thermofisher.com/us/en/home/technical-resources.
To find product information
Go to
thermofisher.com/us/en/home/brands/thermo-scientific.
Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to
Technical Publications (techpubs-lcms@thermofisher.com).
Thermo Scientific FreeStyle User Guide 1
1
Introduction
Use the FreeStyle application to visualize and analyze data. With the FreeStyle application,
you can display chromatograms and spectra, detect chromatographic peaks, search mass
spectral libraries, simulate spectra, subtract background spectra, apply filters, annotate plots
with text and graphics, create and save layouts, and view the real-time status of various
instrument parameters as they change during data acquisition. You can also export spectral
data to the NIST™ application or mzCloud.org, calculate the elemental composition of a
component from its exact mass, and perform Xtract deconvolution.
Contents
• Demonstration Animations
• What’s New in FreeStyle Version 1.2
Demonstration Animations
By using demonstration animations, this guide shows you how to use the important features
of the FreeStyle application.
•To arrange views with the mouse
•To compare chromatogram traces
•To display extracted ion chromatograms
•To add peaks to the peak list by automatic peak detection
•To manually add peaks to and remove peaks from the peak list
•To display mass spectra
•To average spectra
•To subtract background spectra
•To determine the elemental composition of an ion
•To perform a library search
IMPORTANT Running these animations requires Adobe Flash Player.
1 Introduction
What’s New in FreeStyle Version 1.2
2FreeStyle User Guide Thermo Scientific
What’s New in FreeStyle Version 1.2
The following features are new in FreeStyle version 1.2:
• Local mass tolerance setting for active traces (see the Mass Tolerance parameter in the
“Active Traces View” on page 34)
• Auto Filter feature (see “Adding Plots to a Chromatogram View with the Auto Filter
Feature” on page 48)
• PPD peak detection algorithm (see “PPD Peak Detection Page” on page 77 and the
animation that demonstrates how to “To add peaks to the peak list by automatic peak
detection” on page 63)
• Elemental composition analysis for MS/MS data (see “Elemental Composition Page” on
page 111 and the animation that demonstrates how “To determine the elemental
composition of an ion” on page 120)
• Extracted ion chromatogram (EIC) option for simulated spectra (see “Isotope Simulation
Page” on page 122)
• Library searches of mzVault libraries (see “mzVault Search Page” on page 130 and the
animation that demonstrates how “To perform a library search” on page 137)
• Compensation voltage plots for FAIMS data (see “Working with CV Plots for FAIMS
Data” on page 141)
• File header information (see “File Header View” on page 158)
Thermo Scientific FreeStyle User Guide 3
2
Using the FreeStyle Window
Use the File menu, toolbars, views, and Info Bar pages to operate the FreeStyle application.
After you set up the appropriate views and settings for your data files, you can save the layout
to a template.
Contents
•File Menu
•Workspaces
• Saving and Applying Layout Templates
• Restoring the Default Settings
• Toolbars
•Views
• Info Bar Pages
Figure 1 shows the default FreeStyle window. The default window displays the Peak Detection
and Detector Type pages in the Info Bar to the left and the Chromatogram, Spectrum, and
Active Traces views in the Workspace area to the right. The mouse is pointing to the
workspace preview button for the hidden workspace—steroids04.
2 Using the FreeStyle Window
4FreeStyle User Guide Thermo Scientific
Figure 1. FreeStyle default window
To preview the chromatogram view for a workspace
Point to its preview button for a thumbnail view.
To display a workspace when multiple workspaces are open
• Click the target workspace tab.
–or–
• Click the workspace preview button for the target workspace at the bottom of the
FreeStyle window.
Toolbar
Info Bar page
Chromatogram
view
Spectrum
view
Toolbar tabs
Active Traces
view
File menu
Workspace preview button, ,
for the active workspace
(Workspace 1)
Status or error information
Toolbar areas
Workspace
view
Workspace preview button for
an inactive workspace
2 Using the FreeStyle Window
File Menu
Thermo Scientific FreeStyle User Guide 5
File Menu
Use the File menu (see Figure 2) in the upper left corner of the FreeStyle window to create a
new workspace, save a template, view the list of recently opened raw data files and folders, and
access the default settings. You can also select a recent raw data file to open as a new workspace
or select a recent folder to open and display its contents.
For more information about workspaces, see “Workspaces” on page 6. For more information
about templates, see “Saving and Applying Layout Templates” on page 9. For more
information about default settings, see Appendix A, “FreeStyle Default Settings.”
Figure 2. File menu
Table 1 describes the File menu commands.
Table 1. File menu commands (Sheet 1 of 2)
Item Description
Commands
Open RawFile Opens a dialog box where you can choose existing raw data files
(.raw) or sequence files (.sld) to open and create new workspaces. See
Workspaces.
Create Sequence Opens a dialog box where you can choose a set of raw data files to
open and create a sequence in a new workspace. See “Creating a
Sequence” on page 50.
Save as Default Automatically saves the current layout to the default template file.
See “Saving and Applying Layout Templates” on page 9.
Save As Opens a dialog box where you can save the current layout to a
template file with a different name. In the File Name box, type the
new name and click Save. See “Saving and Applying Layout
Te m pl a t es” on page 9.
Print Prints a report showing chromatogram and spectrum information for
the currently selected workspace.
Help Opens the FreeStyle Help window.
2 Using the FreeStyle Window
Workspaces
6FreeStyle User Guide Thermo Scientific
Workspaces
The FreeStyle application creates a workspace whenever you open a raw data file or a sequence
of raw data files. The Workspace view is the area of the FreeStyle window that displays the
workspace data (see Figure 1 on page 4). The application links all data in a workspace to a
single time base, which the Chromatogram View displays.
To create a workspace
1. Choose File > New Workspace.
The Open Raw File dialog box opens.
2. Do one of the following:
• Select a raw data file (.raw) and click Open to create a workspace.
–or–
• In the file type list in the lower right corner of the dialog box, change the file type to
Sequence Files (*.sld), locate and select a sequence file, and then click Open to
create a sequence and workspace.
The FreeStyle application displays the Sequence File page in the Info Bar at the left
side of the window (see “Sequence File Page” on page 66).
Report an Issue Opens a mail dialog box in the Microsoft Outlook™ application with
a default email address. You can enter a detailed description of the
issue, along with the steps to reproduce it, and send this information
to Thermo Fisher Scientific.
About FreeStyle Displays the FreeStyle version information and the release and
copyright dates, along with buttons to activate/deactivate the license
code (see “License Activation and Deactivation” on page vii), show
the version information of other Thermo Fisher Scientific
applications and instruments installed on your system, and display
the user license agreement.
Close Closes the File menu.
Buttons
Options Displays the current configuration of the default values. See
Appendix A, “FreeStyle Default Settings.”
Exit Exits the FreeStyle application.
Table 1. File menu commands (Sheet 2 of 2)
Item Description
2 Using the FreeStyle Window
Workspaces
Thermo Scientific FreeStyle User Guide 7
To create multiple workspaces
1. Choose File > New Workspace.
The Open Raw File dialog box opens.
2. Do one of the following:
• Select multiple raw data files and click Open.
–or–
• Drag the files into the FreeStyle window.
A separate workspace appears for each raw data file. In the default factory layout,
additional workspaces appear as horizontal tabs above the Chromatogram view.
To reposition the Workspace view
1. Right-click the workspace title bar or click the triangle icon, , on the right side of the
title bar to open the shortcut menu (see Figure 3).
Figure 3. Workspace shortcut menu
2. Do one of the following:
• Choose Floating in the shortcut menu to detach the Workspace view into a floating
window.
• Choose Dockable in the shortcut menu to return the Workspace view back to its
default position in the FreeStyle window.
–or–
• Choose Auto Hide in the shortcut menu or click the vertical pin icon, , on the
right side of the title bar (see Figure 4) to temporarily hide the Workspace view.
Tip To select multiple files, hold down the CTRL key when you select them. To
select a group of adjacent files, select the first file in the group, hold down the
SHIFT key, and then select the last file in the group.
Note Do not drag the files into the Active Traces View because this action adds
new traces to this view instead of adding new workspaces.
Workspace title bar
Shortcut menu
2 Using the FreeStyle Window
Workspaces
8FreeStyle User Guide Thermo Scientific
Figure 4. Workspace vertical pin icon
The Workspace view collapses as a tab near the right edge of the Info Bar (see
Figure 5).
Figure 5. Workspace tab
Placing the pointer over the tab displays the Workspace view again. When Auto Hide
is on, the pin icon is a horizontal pin, (see Figure 6). To turn off the Auto Hide
function, choose Auto Hide in the shortcut menu again to clear the check mark, or
click the pin icon to change it back to a vertical pin, .
Figure 6. Workspace horizontal pin icon
To close the Workspace view
Do one of the following:
• Choose Close in the shortcut menu (see Figure 3 on page 7).
• Click the Close icon, , on the right side of the title bar.
Pin icon
Workspace view tab when
Auto Hide is on
Info Bar
Pin icon
2 Using the FreeStyle Window
Saving and Applying Layout Templates
Thermo Scientific FreeStyle User Guide 9
Saving and Applying Layout Templates
A FreeStyle template contains the settings that define the workspace layout. The template
specifies what views are in the workspace, how the views are arranged, and what labeling the
views contain. The template also specifies which pages the Info Bar initially displays. For
future use, you can save the template as a new XML file, or save it as the default template.
The FreeStyle application stores all templates in the following folder:
drive:\Users\your name\AppData\Local\Thermo Scientific\FreeStyle\Templates\
To save the template as the default template
1. Click the Workspace Options toolbar tab to display the Workspace Options toolbar (see
Figure 7 on page 11).
2. Click Save As Default in the Layouts area.
The FreeStyle application saves the layout as the default template file,
DefaultTemplate.xml.
To apply the default template
1. Click the Worksp ac e Options tab to display the Workspace Options toolbar (see
Figure 7 on page 11).
2. Click Apply Default in the Layouts area.
To name the template and save it as an XML file
1. Click the Workspace Options toolbar tab to display the Workspace Options toolbar (see
Figure 7 on page 11).
2. Click Save As in the Layouts area to open the Save Settings dialog box.
3. Type a name for the template and click Save.
Note You can also choose File > Save As Default.
IMPORTANT Do not navigate to a different folder. The FreeStyle application reads
the template files only from the default template folder.
2 Using the FreeStyle Window
Restoring the Default Settings
10 FreeStyle User Guide Thermo Scientific
To apply a saved template
1. Click the Workspace Options toolbar tab to display the Workspace Options toolbar (see
Figure 7 on page 11).
2. Click Apply in the Layouts area to open the DataBrowser Templates dialog box.
3. Select a template and click OK.
Restoring the Default Settings
The FreeStyle application includes a dialog box with a set of pages containing initial default
settings upon installation. You can modify these settings as needed or restore them to the
factory default values.
For information about these settings, see Appendix A, “FreeStyle Default Settings.”
To open the Default Options Configuration dialog box
• On the Workspace Options toolbar, click Default Options.
–or–
a. Choose File to open the File menu (see “File Menu” on page 5).
b. In the lower right corner, click Options to display the Default Options
Configuration dialog box.
To restore the settings of a particular page to the factory default settings
1. Open the Default Options Configuration dialog box.
2. In the left pane of the dialog box, select the appropriate page of default settings.
3. In the upper right corner of the dialog box, click Revert to Factory Default Values.
To restore all settings to the factory default settings
1. Open the Default Options Configuration dialog box.
2. In the bottom left corner of the dialog box, click Revert All to Factory Default Values.
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