Thermo Fisher Scientific MASS User guide

Thermo

Mass Frontier

User Guide

Software Version 8.0 SR1

XCALI-98160 Revision A December 2019

Fragment Ion Search (FISh), HighChem Fragmentation Library, Mass Frontier, Mass Frontier Server Manager,

Metabolika, MolGate, mzCloud, mzLogic, Spectral Tree, Wideband Activation, and ZoomScan are

trademarks; and Thermo Scientific 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

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SQL Server, DirectX, and Excel are registered trademarks of Microsoft Corporation. Intel is a registered

trademark of Intel Corporation.

ChemSpider is a registered trademark of ChemZoo Inc. KEGG is a registered trademark of Kanehisa, Minoru

(an individual). PubChem is a registered trademark of the U.S. National Library of Medicine. Wikipedia is a

registered trademark of the Wikimedia Foundation, Inc., a non-profit corporation.

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: December 2019

Software version: Mass Frontier 8.0 SR1; Server Manager 3.0

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

Thermo Scientific Mass Frontier User Guide iii

C

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

License Activation or Deactivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

New Modules, Features, and Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

New Features and Enhancements in Mass Frontier 8.0 SR1 . . . . . . . . . . . . . . 2

New Modules in Mass Frontier 8.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

New Features and Enhancements in Mass Frontier 8.0 . . . . . . . . . . . . . . . . . . 4

File Format Changes in Mass Frontier SR1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Supported File and Data Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Supported Chromatogram Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Supported MS Spectrum Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Background Subtraction Supported Chromatogram Formats . . . . . . . . . . . . . 8

Parameter File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Supported File Formats in Curator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Supported File Formats in Data Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Supported File Formats in Metabolika. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Supported File Formats in Structure Editor. . . . . . . . . . . . . . . . . . . . . . . . . . 12

Supported File Formats in Structure Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Supported File Formats in the Reaction Restrictions Dialog Box. . . . . . . . . . 13

Supported File Formats in Fragments & Mechanisms . . . . . . . . . . . . . . . . . . 13

Supported File Formats in Server Manager . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Startup Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Start Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Modules and Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Library Searches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Contents

iv Mass Frontier User Guide Thermo Scientific

Checking the Connection to the mzCloud Mass Spectral Database. . . . . . . . . . 21

Modifying the Layout of the Application Window . . . . . . . . . . . . . . . . . . . . . . 22

Following the Tutorials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Chapter 3 Chromatogram Processor Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Opening a Chromatogram Processor Window . . . . . . . . . . . . . . . . . . . . . . . . . 26

Showing or Hiding the Chromatogram Processor Views . . . . . . . . . . . . . . . . . . 28

Zoom and Scroll Controls for the Chromatogram and Spectrum Plots . . . . . . . 28

Using the Mouse Pointer to Zoom In on the X Axis . . . . . . . . . . . . . . . . . . . 28

Using the ALT Key to Scroll the X Axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Using the Mouse Pointer to Zoom In on the Y Axis . . . . . . . . . . . . . . . . . . . 29

Using the SHIFT Key to Scroll the Y Axis. . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Using the CTRL Key to Zoom In or Out of the Plot . . . . . . . . . . . . . . . . . . 29

Using the Zoom Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Window States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Interoperability of the Chromatogram Processor with Other Modules . . . . . . . 30

Chromatogram Processor Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

File Toolbar Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Edit Toolbar Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Actions Toolbar Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Search Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Send to Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

View Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Filter Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Display Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Zoom & Pan Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Annotate Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Reports Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Chromatogram Data View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

MS1 and Product Scans Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Components List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Chromatogram Data View Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Chromatogram Data View Column Options. . . . . . . . . . . . . . . . . . . . . . . . . 44

Sorting the Data in the Chromatogram Data View by a Single

Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Sorting the Data in the Chromatogram Data View by Two Columns . . . . . . 45

Filtering the Chromatogram Data View Columns. . . . . . . . . . . . . . . . . . . . . 45

Deleting Components from the Chromatogram Data View . . . . . . . . . . . . . 47

Command Processor View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

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Thermo Scientific Mass Frontier User Guide v

Chromatogram View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Chromatogram View – TIC Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Adding Fragment or Text Annotations to a Chromatogram . . . . . . . . . . . . . 49

TIC Page Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Chromatogram View – 2D Contour Page . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Customizing the Color Mapping of a 2D or 3D Plot . . . . . . . . . . . . . . . . . . 52

Chromatogram View – 3D Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Chromatogram View – Info Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Chromatogram View – Scan Filter List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

MS Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

MS Spectrum View – Spectral Tree Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

MS Spectrum View – Spectrum Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

MS Spectrum View – Data Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

MS Spectrum View – Info Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

MS Spectrum View – FISh Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Background Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Subtracting Background Noise from a Chromatogram . . . . . . . . . . . . . . . . . 65

Subtract Blank Filter View Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Baseline Correction and Noise Elimination Filter . . . . . . . . . . . . . . . . . . . . . . . 70

Opening the Baseline and Noise Elimination Filter View . . . . . . . . . . . . . . . 71

Using the Wizard Mode for Baseline Correction and Noise Elimination . . . . 71

Using the Details Mode for Baseline Correction and Noise Elimination . . . . 72

Contaminants Elimination Filter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Opening the Contaminants Elimination Filter View . . . . . . . . . . . . . . . . . . . 77

Contaminants Elimination Filter Parameters. . . . . . . . . . . . . . . . . . . . . . . . . 78

Add Custom Contaminant Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Peak Elimination Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Opening the Peak Elimination Filter View . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Peak Elimination Filter Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Smoothing Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Opening the Smoothing Filter View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Using the Wizard Mode for the Smoothing Filter . . . . . . . . . . . . . . . . . . . . . 83

Using the Details Mode for the Smoothing Filter . . . . . . . . . . . . . . . . . . . . . 84

Threshold Filter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Opening the Threshold Filter View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Using the Wizard Mode for the Threshold Filter. . . . . . . . . . . . . . . . . . . . . . 87

Using the Details Mode for the Threshold Filter . . . . . . . . . . . . . . . . . . . . . . 89

Component Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Joint Component Detection (JCD) Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . 93

Using the Wizard Mode for the JCD Algorithm . . . . . . . . . . . . . . . . . . . . . . 93

Using the Details Mode for the JCD Algorithm . . . . . . . . . . . . . . . . . . . . . . 96

Total Ion Extraction Component Detection (TECD) Algorithm . . . . . . . . . . 102

Direct Infusion Components Detection (DICD) Algorithm . . . . . . . . . . . . . . 104

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vi Mass Frontier User Guide Thermo Scientific

FISh Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Creating or Selecting the FISh Model for a FISh Analysis . . . . . . . . . . . . . . 107

Specifying the FISh Detection Options and Starting the Analysis . . . . . . . . 111

Viewing a FISh Chromatogram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

Component Library Searches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Identifying Components by Running a Components Library Search. . . . . . 119

Component Search Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Search Types for a Component Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

Search Parameters for Each Search Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

Library Parameter for a Component Search. . . . . . . . . . . . . . . . . . . . . . . . . 128

Search Results for a Component Search. . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Search Details Window for a Component Search . . . . . . . . . . . . . . . . . . . . 131

mzLogic Searches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Interoperability of the mzLogic View with Other Modules . . . . . . . . . . . . . 135

Running an mzLogic Component Search . . . . . . . . . . . . . . . . . . . . . . . . . . 135

mzLogic View Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Extracted Ion Chromatogram (XIC) Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Interoperability of the Extracted Ion Chromatogram Pane with Other

Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Viewing an Extracted Ion Chromatogram for a Detected Component . . . . 139

Using Extracted Ion Chromatograms for Verifying Component

Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Opening and Pinning the Extracted Ion Chromatogram Pane. . . . . . . . . . . 140

Extracted Ion Chromatogram Pane Parameters . . . . . . . . . . . . . . . . . . . . . . 141

Displaying an XIC by Selecting a Spectral Peak. . . . . . . . . . . . . . . . . . . . . . 142

Neutral Loss Chromatogram (NLC) Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Neutral Loss Chromatogram Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Adding and Deleting Neutral Loss Masses. . . . . . . . . . . . . . . . . . . . . . . . . . 144

Report Generation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

Grid Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

Spreadsheet Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Chapter 4 Data Manager Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .149

Interoperability of the Data Manager Module with Other Modules . . . . . . . . 150

Opening a Data Manager Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

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Thermo Scientific Mass Frontier User Guide vii

Data Manager Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

File Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Edit Group – Tree Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

Edit Group – Mechanisms Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

Library Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

Actions Group – Tree Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Zoom & Pan Group – Mechanisms View . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Common Options Group – Mechanisms View . . . . . . . . . . . . . . . . . . . . . . 156

Page Group – Mechanisms View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

View Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

mzCloud Tools Group – Tree Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Send to Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158

Tree View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Spectral Tree Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Spectrum Pane – Spectrum Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162

Spectrum Pane – Peaks Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Spectrum Pane – BDC Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Spectrum Pane – Metadata Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

Spectrum Pane – Compare Spectra Page . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Compound Structure or Precursor Structure Pane. . . . . . . . . . . . . . . . . . . . 165

Mechanism View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

Notifications Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Libraries Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

Compound or Precursor Structure Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Loading a Spectral Link from the mzCloud Database to the Clipboard . . . . . . 170

Copying Library Records. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170

Chapter 5 Curator Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .173

Interoperability of the Curator Module with Other Modules . . . . . . . . . . . . . 173

Opening a New Curator Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174

Curator – Spectral Tree Pane – Tree Processing Page . . . . . . . . . . . . . . . . . . . 176

Spectral Tree Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176

Breakdown Curves (BDC) Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177

Spectrum Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178

Peaks Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

TIC Profiles of Parallel Spectra Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Spectrum Info Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Curator Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Edit Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Processing Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

View Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182

Filter Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

Send to Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

Receive From Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

Curator Structure Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

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viii Mass Frontier User Guide Thermo Scientific

Editing the Contributor Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185

Curator Command Processor Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186

Curator Action Step Pane Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187

Toolbar for Each Curator Action Step. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

Curator Action Step Pane Shortcut Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 188

Action Step Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

Curator Action Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

Raw Spectra Exclusion Step. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190

Copy to Filtered Tree Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

Select Significant Spectra Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

Remove Resonance Peaks Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

Select Relevant Peaks Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Merge Replicate Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

Apply Changes to Raw Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

Assign Fragments (Raw, Filtered) Step. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

Copy to Recalibrated Tree Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Recalibrate Step. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Assign Fragments (Recalibrated) Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209

Assign Molecular Formulas Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209

Curator – Spectral Pane – Metadata Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210

Downloading Metadata for a Compound . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211

Chapter 6 Metabolika Pathways Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .215

Interoperability of the Metabolika Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Opening the Metabolika Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Metabolika Home Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217

File Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

Copy & Paste Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

Send Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219

Edit Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219

Zoom & Pan Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

Views Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

Metabolika Marks Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

Metabolika Settings Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

Common Options Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

Straight & Arc Options Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

Orthogonal Options Group. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

Page Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

Metabolika Drawing Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Draw Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Alignment Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224

Mode Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224

Metabolika Drawing and Viewing Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Zoom and Pan Tools. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Drawing Pane Shortcut Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

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Thermo Scientific Mass Frontier User Guide ix

Properties Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Metadata Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Errors Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Marks Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Mark Properties Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

Define Structure and Mark Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

Pathways Explorer Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

Chapter 7 Structure Editor Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .229

Interoperability of the Structure Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

Structure Editor Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230

Structure Editor Home Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231

Drawing Tools and Atom and Bond Properties Pane. . . . . . . . . . . . . . . . . . . . 232

Assigning an Unspecified Charge Site to a Structure . . . . . . . . . . . . . . . . . . . . 236

Structure Limitations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236

Chapter 8 Structure Grid Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .239

Interoperability of the Structure Grid Module with Other Modules . . . . . . . . 239

Opening a Structure Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

Adding Structures to a Structure Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

Filtering the Structures in a Structure Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

Structure Grid Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242

Metadata Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244

Card View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244

Table View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244

Customizing the Table View Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Using a Structure Grid as an XICs Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Using a Structure Grid as a Source of Structure Candidates for an

mzLogic Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246

Chapter 9 Batch Fragment Generation Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .247

Starting the Batch Fragment Generation Wizard. . . . . . . . . . . . . . . . . . . . . . . 247

Batch Fragment Generation Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

Specifying the Reaction Restrictions for a Batch Fragmentation . . . . . . . . . . . 250

Generating the Output Files for a Batch Fragmentation . . . . . . . . . . . . . . . . . 251

Chapter 10 Fragments & Mechanisms Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253

Assumptions for Generating the Fragmentation and Rearrangement

Pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254

Generating Fragments and Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256

Fragment Generation Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

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xMass Frontier User Guide Thermo Scientific

Reaction Restrictions Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

Reaction Restrictions Dialog Box Toolbar and Command Buttons . . . . . . . 261

Reaction Restrictions – Structure Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261

Reaction Restrictions – Base Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262

Reaction Restrictions – Ionization & Cleavage Page . . . . . . . . . . . . . . . . . . 264

Reaction Restrictions – H-Rearrangements Page . . . . . . . . . . . . . . . . . . . . . 267

Reaction Restrictions – Resonance Page . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

Reaction Restrictions – Additional Page . . . . . . . . . . . . . . . . . . . . . . . . . . . 269

Reaction Restrictions – Sizes Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271

Saving Reaction Restrictions to a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272

Importing Reactions Restrictions from a File. . . . . . . . . . . . . . . . . . . . . . . . 272

Working in a Fragments & Mechanisms Window. . . . . . . . . . . . . . . . . . . . . . 273

Fragments & Mechanisms Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274

Displaying the Fragmentation Pathways or Isobaric Fragments for an

m/z Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

Customizing the List of Isobaric m/z Values . . . . . . . . . . . . . . . . . . . . . . . . 279

Saving Fragments to a File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Saving Mechanisms to a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Copying Fragments or Mechanisms to the Clipboard . . . . . . . . . . . . . . . . . 279

Starting the Fragmentation of a Selected Fragment . . . . . . . . . . . . . . . . . . . 280

Sending Fragments to Other Modules from the Fragments &

Mechanisms Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

Previewing Unimolecular Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

Reaction Formalism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282

Working with Generated Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283

Linking Generated Fragments with a Spectrum. . . . . . . . . . . . . . . . . . . . . . 283

Automatically Assigning Generated Fragments to a User Library Entry . . . . 284

Eliminating Generated Fragments That Are Not Present in a Spectrum . . . 284

Simulating Fragmentation Processes in MS/MS Experiments . . . . . . . . . . . 286

Unexplained Spectral Peaks from Compound-Specific Fragmentation

Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

Limitations of the General Fragmentation Rules . . . . . . . . . . . . . . . . . . . . . . . 287

Chapter 11 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .289

Formula Generator Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Interoperability of the Formula Generator Tool . . . . . . . . . . . . . . . . . . . . . 290

Using the Formula Generator Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290

Formula Generator Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292

Molecular Formula Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 292

Isotope Pattern Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296

Interoperability of the Isotope Pattern Tool. . . . . . . . . . . . . . . . . . . . . . . . . 297

Using the Isotope Pattern Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297

Isotope Pattern Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299

Using the MolGate Search Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300

Periodic Table Tool. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302

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Thermo Scientific Mass Frontier User Guide xi

Chapter 12 Independent Library Searches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303

Running a Library Search from the Search Toolbar. . . . . . . . . . . . . . . . . . . . . 303

Libraries Panes for Any of the Search Types . . . . . . . . . . . . . . . . . . . . . . . . . . 305

Compound Classes Pane for Any of the Search Types . . . . . . . . . . . . . . . . . . . 305

Monoisotopic Mass Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305

Opening the Monoisotopic Mass Search Dialog Box. . . . . . . . . . . . . . . . . . 305

Query Pane for a Monoisotopic Mass Search. . . . . . . . . . . . . . . . . . . . . . . . 306

Monoisotopic Search Result Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307

Peak Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308

Opening the Peak Search Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308

Peak Search Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310

Peak Search Results Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311

Precursor Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313

Opening the Precursor Search Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . 313

Precursor Search Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315

Precursor Search Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316

Spectrum Searches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318

Opening the Spectrum Search Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . 318

Spectrum Search Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320

Select Peak Tolerance Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322

Query Spectrum Peak Filter Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 322

Spectrum Search Results Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323

Structure Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327

Starting a Structure Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327

Structure Search Dialog Box Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 329

Structure Search Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330

Search Result Window Toolbar and Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

Search Result Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

Result List Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

Library Entry Information Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

Library Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

Compound Structure Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

Precursor Structure Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

Chapter 13 Global Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .335

Configuring the Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335

General Configuration Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337

Layout Configuration Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338

Mass Accuracy and Precision Configuration Settings. . . . . . . . . . . . . . . . . . . . 342

Reaction Restrictions Configuration Settings. . . . . . . . . . . . . . . . . . . . . . . . . . 343

Chapter 14 Spectral Library Creation and Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . .345

Creating a New User Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345

Connecting the Application to the Library Service . . . . . . . . . . . . . . . . . . . . . 348

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Sharing Spectral Libraries Using the Client/Server Installation . . . . . . . . . . . . 350

Connecting the Client-only Mass Frontier Application to the Library

Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350

Installing or Restoring a Server Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351

Uninstalling or Deleting a Server Library. . . . . . . . . . . . . . . . . . . . . . . . . . . 351

Transferring Spectral Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352

Backing Up Spectral Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354

Restoring Spectral Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356

Reinstalling Spectral Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357

Migrating Spectral Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358

Chapter 15 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .361

Appendix A Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .365

Accuracy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365

Component. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366

HighChem Fragmentation Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367

Ion Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370

MolGate Structure Aggregator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370

mzCloud Spectral Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372

Resonance Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372

Spectral Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374

Unspecified Charge Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374

Post-processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .377

Thermo Scientific Mass Frontier User Guide xiii

P

Preface

This guide describes how to use the Thermo Mass Frontier™ application to manage, evaluate,

and interpret mass spectra.

Contents

•Related Documentation

•System Requirements

•License Activation or Deactivation

•Special Notices

•Contacting Us

To familiarize yourself with the Mass Frontier application, follow the tutorials that are

available from the application Help menu.

Related Documentation

The Mass Frontier 8.0™ SR1 application includes these manuals and tutorials as PDF files:

• Mass Frontier User Guide

• Mass Frontier Installation Guide

• Auto Annotation of Spectral Trees Using Fragments & Mechanisms Tutorial

• Curating Spectral Trees for Spectral Libraries Tutorial

• Saving Compounds to Spectral Libraries Tutorial

• Detecting Structurally-Related Compounds with the FISh Algorithm Tutorial

• Identifying Unknowns by Library Searching and mzLogic (HRAM) Tutorial

• Identifying Unknowns by Library Searching and mzLogic (Nominal Mass) Tutorial

• Creating Metabolika Pathways Tutorial

Preface

xiv Mass Frontier User Guide Thermo Scientific

To view the Mass Frontier manuals and tutorials

From the Start menu, click Help to view the available manuals and tutorials in PDF

format.

–or–

In the upper right corner of the application window, click the Help icon, . Then,

select a PDF from dropdown list.

To view user documentation from the Thermo Scientific website

1. Go to thermofisher.com.

2. In the Search box, type the name of the product, for example, Mass Frontier.

3. On the left, click Documents & Support.

4. From the results list, click the title to open the document in your web browser, save it, or

print it.

To return to the document list, click the browser Back button.

Preface

Thermo Scientific Mass Frontier User Guide xv

System Requirements

The following table lists the minimum and recommended system configuration requirements

for using the Mass Frontier 8.0 and Server Manager 3.0 applications.

Table 1 lists the hardware and software requirements for the processing computer.

Table 1. Hardware and software requirements for the processing computer

System Minimum requirements Recommended requirements

Hardware • Intel™ or compatible processor

with a minimum speed of 1 GHz

• 8 GB of RAM

• 30 GB of disk space

•DVD-ROM drive

• Monitor resolution display of

1024 x 768

• Intel or compatible quad-core

processor with a minimum speed

of 2.5 GHz

•32 GB of RAM

• 100 GB of solid-state drive (SSD)

disk space

• DirectX™ 12 or compatible GPU

•DVD-ROM drive

• Dual monitors with a resolution

display of 1920 x 1080 (1080p)

Software • Microsoft™ Windows™ 7

Professional SP1 (64-bit)

• Microsoft .NET Framework

4.5.2

• Microsoft Office 2010

• Adobe™ Acrobat™ Reader™ DC

• Windows 10 Professional (64-bit)

or Windows 10 Enterprise LTSB

2016 (64-bit) with latest updates

•.NET Framework 4.5.2

• Office 2016

• Acrobat Reader DC

System

settings

• To run processing workflows with online mass spectral database searches,

ensure the computer has unblocked access to the mass spectral databases

on the Internet.

• Ensure that the computer has the correct time and date settings and is

synchronized with Internet time.

• Set the Region and Language setting to English (United States).

Note Ensure that you have a Windows account with administrator rights to do the

following:

• Install the Mass Frontier and Server Manager applications.Forinformation on how

to install Mass Frontier software, refer to the Mass Frontier Installation Guide.

• Create, copy, and delete spectral libraries.

Preface

xvi Mass Frontier User Guide Thermo Scientific

License Activation or Deactivation

Use the Thermo Scientific product licensing wizard to activate or deactivate the license for the

Mass Frontier 8.0 SR1 application. To activate the license, you must have an activation code

from Thermo Fisher Scientific.

To activate or deactivate your license

1. Click Start tab to open the Start menu, and then choose About

The About Mass Frontier dialog box opens.

2. Click the License tab, and then click Activate License to start the activation or

deactivation process, as applicable.

3. Follow the instructions in the wizard. For additional instructions, click Help on the

bottom left.

After you activate a permanent license, the Deactivate button appears. When you need to

transfer the permanent license from one computer to another computer, click the Deactivate

button.

Special Notices

Make sure you understand the special notices, symbols, and caution labels in this guide. Most

of the special notices and cautions appear in boxes. Some symbols are also marked on the

instrument itself and can appear in color or in black and white. For complete definitions, see

the following table.

Note For software download and licensing questions, contact support at

ThermoMSLicensing@thermo.com.

IMPORTANT Depending on the features that you purchased in the Mass Frontier 8.0

software, your permanent license covers one of three options:

• Option 1: Mass Frontier 8.0 Base + Curator

• Option 2: Mass Frontier 8.0 Base

• Option 3: Curator Only

The license keys control the different features in the software and determine which ones

are active. For example, for option 2, all Mass Frontier 8.0 base modules are active when

you apply the license key, but the Curator module is inactive. You can purchase option 3

to activate the Curator module at a later date.

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.

Preface

Thermo Scientific Mass Frontier User Guide xvii

Contacting Us

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Contact Email Telephone QR Code

U.S. Technical Support us.techsupport.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

U.S. Customer Service

and Sales

us.customer-support.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

E.U. Technical Support eu.techsupport.cms@thermofisher.com

Global support To find global contact information or customize your request

1. Go to thermofisher.com.

2. Click Contact Us, select the country, and then select the type of support

you need.

3. At the prompt, if displayed, type the catalog number or product name.

4. Select the display location to view information for the best team to help

you with that product.

5. 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).

Preface

xviii Mass Frontier User Guide Thermo Scientific

Thermo Scientific Mass Frontier User Guide 1

1

Introduction

The Mass Frontier application is a software package for the management, evaluation, and

interpretation of mass spectra. To manage the large amount of mass spectral and

chromatographic data, the application provides various tools and features. The application

can interpret mass spectra even when it does not find a matching spectrum in your user

library, as it includes the HighChem Fragmentation Library™ and an interface to the online

mzCloud™ mass spectral database.

Contents

• New Modules, Features, and Enhancements

• File Format Changes in Mass Frontier SR1

• Supported File and Data Formats

New Modules, Features, and Enhancements

The Mass Frontier 8.0 application includes two new modules, Curator and Metabolika, and

new features and enhancements. And this service release includes additional new features and

enhancements.

•New Features and Enhancements in Mass Frontier 8.0 SR1

•New Modules in Mass Frontier 8.0

•New Features and Enhancements in Mass Frontier 8.0

For more information about file format changes in Mass Frontier 8.0, see “File Format

Changes in Mass Frontier SR1” on page 5.

1 Introduction

New Modules, Features, and Enhancements

2Mass Frontier User Guide Thermo Scientific

New Features and Enhancements in Mass Frontier 8.0 SR1

Table 2 describes the features and enhancements that are new in this service release.

Table 2. New features and enhancements in this service release

General

• The startup window includes the Modules & Tools toolbar.

• In addition to the existing fold and unfold whole tree icons, the spectral tree pane

includes a new compress current node icon and a new expand all node options icon.

Chromatogram Processor module

• Improved JCD—A new algorithm performs more detailed analysis of the relationship

between ions in each spectrum. It tries to determine the potential molecular ion, which

might not be the most intense ion in the MS1 spectrum. The new algorithm reduces

the number of noisy components (components of low intensity produced by oscillation

of XIC traces).

• Components list—The shortcut menu (right-click menu) includes a new command:

Show XIC m/z. This command adds the m/z values traces associated with the

component to the Extracted Ion Chromatogram pane.

• Components list—Supports multiple column sorting by using the SHIFT key.

• mzLogic search for a spectrum (mzLogic Search command )—Right-clicking a

spectrum and choosing mzLogic Search supports MS2 spectra and MSn (n > 2) spectra.

• mzLogic search for components (mzLogic toolbar command)—In addition to the

mzCloud libraries, mzLogic searches can now include local user libraries.

• FISh Modifications dialog box—The columns in the FISh Modification dialog box are

sortable.

• FISh—The FISh Filter: Input m/z List dialog box supports these additional file types:

CSV and TXT. This dialog box also supports manual entry of the m/z and accuracy

values.

Curator

• Fragmentation is directly performed in the Assign Fragments (Raw, Filtered) step.

• The Recalibration step includes the option to create a weighted regression curve based

on peak abundance (Use Abundance as Weight check box) and an automatic mode that

assigns the appropriate regression model for the data.

• The ChemSpider API in Download Metadata is new.

Data Manager

• A spectrum, spectral tree, or pathway can be pasted from the Clipboard to the New

library or a user library, even when the workspace is empty.

• The Show Neutral Loss (NL) command is now available in Data Manager in the

shortcut menu for the Spectrum page.

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