Thermo Fisher Scientific FreeStyle Software User guide

Thermo

FreeStyle

User Guide

Software Version 1.2

XCALI-97891 Revision A December 2016

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

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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Thermo Fisher Scientific FreeStyle Software User guide

Thermo Fisher Scientific FreeStyle Software User guide

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