Thermo Fisher Scientific LC Studies User guide

Thermo

Compound Discoverer

User Guide for LC Studies

Software Version 3.2

XCALI-98278 Revision A October 2020

Compound Discoverer, Exactive, Foundation, FreeStyle, Mass Frontier, Metabolika, mzCloud, mzVault,

Normalized Collision Energy, Orbitrap ID-X, Q Exactive, ToxID, and TraceFinder are trademarks; Orbitrap,

Orbitrap Fusion, Orbitrap Lumos, Thermo Scientific, and Xcalibur are registered trademarks of Thermo

Fisher Scientific Inc. in the United States.

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registered trademarks of Adobe Systems Incorporated. Microsoft, Internet Explorer, Visual C++, Windows,

and Excel are registered trademarks of Microsoft Corporation. Xeon is a registered trademark of Intel

Corporation. ActiveReports is a registered trademark of GrapeCity, Inc.

KEGG is a registered trademark of Kanehisa, Minoru (an individual).

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 October 2020

Software version: Compound Discoverer 3.2.x

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

Thermo Scientific Compound Discoverer User Guide for LC Studies 3

C

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Accessing the Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Installation Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Creating and submitting a bug report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Chapter 1 Introduction to Compound Discoverer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

New features and enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Supported file formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Starting the application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Application toolbar, menus, and Start Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Application menu bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Application toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Terminology used in the Compound Discoverer application. . . . . . . . . . . . . . . 45

LC studies overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Auto-Hiding the Start Page, the Chromatograms view, and the Mass

Spectrum view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Showing, hiding, and rearranging the tabbed pages of the application . . . . . . . . 49

Tabbed pages list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Opening a hidden tabbed page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Tab groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Shortcut menu commands that control the layout of the tabbed pages . . . . . 52

Rearranging the tabbed pages and graphical views . . . . . . . . . . . . . . . . . . . . . 53

Chapter 2 Functional description of the data-processing features . . . . . . . . . . . . . . . . . . . .55

Chromatographic peak detection, alignment, and identification . . . . . . . . . . . . 55

Online compound databases and metabolism pathways. . . . . . . . . . . . . . . . . . . 56

Local spectral databases, mass lists, and metabolism pathways . . . . . . . . . . . . . . 57

Best scans for composition prediction and spectral matching. . . . . . . . . . . . . . . 57

Using mzLogic to score candidates for unknown compounds . . . . . . . . . . . . . . 58

Confidence score for an mzCloud hit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

FISh scoring for proposed structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Contents

4Compound Discoverer User Guide for LC Studies Thermo Scientific

Mass defect types and visualization techniques . . . . . . . . . . . . . . . . . . . . . . . . . 65

Neutral loss detection and visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Using quality control samples to compensate for batch effects . . . . . . . . . . . . . . 70

Batch normalization for single sequence runs. . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Batch normalization for multiple sequence runs (LC studies) . . . . . . . . . . . . . . 71

Stable isotope labeling experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Methods for imputing values for missing chromatographic peaks across a

set of input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Chapter 3 Creating a new study and setting up an analysis . . . . . . . . . . . . . . . . . . . . . . . . . .77

Available sample types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Directory structure for studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Creating a study template file that contains all the study information . . . . . . . . 80

Starting the New Study and Analysis Wizard. . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Defining the study type, naming the study, and optionally selecting a

study template and a processing workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Adding input files to a new study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Characterizing new input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Selecting the delimiters for parsing the file names . . . . . . . . . . . . . . . . . . . . . 89

Adding categorical study factors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Adding numeric study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Adding biological replicate study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Deleting study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Duplicating study factors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Editing study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Automatically assigning study factor values . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Manually selecting the study factor values . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Resetting the sample assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Selecting the sample types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Using the regular expression builder to extract the study factors . . . . . . . . . . . . 96

Setting up the sample groups and ratios for a new analysis. . . . . . . . . . . . . . . . 103

Preparing to submit a processing job to the job queue. . . . . . . . . . . . . . . . . . . 109

Accessing the wizard Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

Chapter 4 Editing existing studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111

Study files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

Opening an existing study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

Study page commands and tabs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Editing the study factors and the study description . . . . . . . . . . . . . . . . . . . . . 115

Adding input files to an existing study. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

Removing input files or updating their location. . . . . . . . . . . . . . . . . . . . . . . . 118

Editing the sample type and study factor values. . . . . . . . . . . . . . . . . . . . . . . . 123

Saving a study file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

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Thermo Scientific Compound Discoverer User Guide for LC Studies 5

Chapter 5 Setting up, running, and reprocessing analyses. . . . . . . . . . . . . . . . . . . . . . . . . .127

Setting up a new analysis from within an existing study. . . . . . . . . . . . . . . . . . 127

Starting a new analysis and selecting a processing workflow from

within an existing study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Customizing the processing workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

Selecting the input files for a new analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Naming the result file for a new analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Setting up the sample groups and ratios for a new analysis. . . . . . . . . . . . . . 132

Troubleshooting common analysis errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

Common analysis errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Submitting an analysis to the job queue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Common validation issues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Controlling the job queue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

Reviewing or reprocessing an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

Reviewing an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

Reprocessing an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Analysis pane parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Setting up isotope patterns for pattern scoring or pattern traces. . . . . . . . . . 148

Creating an isotope patterns list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

Extracting analog traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Extracting PDA traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Chapter 6 Creating and editing processing workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . .159

Processing workflow files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Workflows page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160

Opening the Workflows page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160

Workflows page command bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Workflows page shortcut menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Editing an existing processing workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

Fixing a workflow node that has a caution symbol. . . . . . . . . . . . . . . . . . . . 164

Fixing a workflow node that has an exclamation mark. . . . . . . . . . . . . . . . . 165

Adding a workflow node to a processing workflow . . . . . . . . . . . . . . . . . . . 166

Deleting a workflow node from a processing workflow . . . . . . . . . . . . . . . . 166

Editing the parameter settings for a workflow node . . . . . . . . . . . . . . . . . . . 166

The defined processing workflow templates for LC studies . . . . . . . . . . . . . . . 167

Targeted processing workflows for expected compounds . . . . . . . . . . . . . . . 167

Untargeted processing workflows for identifying unknown compounds . . . 176

Nomenclature for the provided processing workflow templates . . . . . . . . . . 180

Defined processing workflow templates. . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

Creating a completely new processing workflow for LC studies . . . . . . . . . . . . 185

Connecting the workflow nodes for an LC study. . . . . . . . . . . . . . . . . . . . . . . 189

Saving a processing workflow as a template . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

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6Compound Discoverer User Guide for LC Studies Thermo Scientific

Chapter 7 Workflow nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .197

Input and Output nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197

Export Spectra node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198

Input Files node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199

Spectrum Processing nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199

Align Retention Times node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200

Filter By Mass Defect node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

Filter By Scan Event node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204

Filter Centroids node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

Select Spectra node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208

Trace Creation nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215

Create Analog Trace node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Create FISh Trace node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

Create Mass Trace node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

Create Pattern Trace node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

Expected Compounds nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

FISh Scoring node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Find Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Generate Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Group Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232

Merge Features node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233

Compound Detection nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233

Analyze Labeled Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234

Detect Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

Fill Gaps node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238

Group Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

Peak Area Refinement nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

Apply Missing Value Imputation node . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

Apply QC Correction node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242

Apply SERRF QC Correction (beta) node . . . . . . . . . . . . . . . . . . . . . . . . . 244

Mark Background Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246

Normalize Areas node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247

Scale Areas node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

Compound Identification nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250

Assign Compound Annotations node (LC studies) . . . . . . . . . . . . . . . . . . . 250

Predict Compositions node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252

Search ChemSpider node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256

Search Mass Lists node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257

Search mzCloud node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

Search mzVault node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264

Pathway Mapping nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Map to BioCyc Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Map to KEGG Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

Map to Metabolika Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270

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Thermo Scientific Compound Discoverer User Guide for LC Studies 7

Compound Scoring nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271

Apply Spectral Distance node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272

Apply mzLogic node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273

Calculate Mass Defect node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274

Compound Class Scoring node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

Generate Molecular Networks node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276

Pattern Scoring node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Search Neutral Losses node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280

Post-Processing nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

Descriptive Statistics node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

Differential Analysis node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

Export Xcalibur Inclusion or Exclusion List node . . . . . . . . . . . . . . . . . . . . 282

Scripting Node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283

Chapter 8 Reviewing the analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .285

Opening, closing, and updating result files . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

Opening result files created in the current version of the application . . . . . . 286

Opening result files created in previous versions of the application . . . . . . . 287

Update modes for legacy result files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288

Closing a result file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Factory default layout for a result page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Modifying the result page layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Floating a result page view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Enlarging a result page view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Collapsible pane options for filtering, grouping, coloring, and

discriminating by . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292

Using the collapsible pane for a view to filter the data by the study

variable values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294

Using the collapsible pane for a view to filter the data by input file . . . . . . . 294

Using the collapsible pane for a view to group the data . . . . . . . . . . . . . . . . 294

Showing or hiding result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295

Custom color-coded tags for result table entries. . . . . . . . . . . . . . . . . . . . . . . . 295

Saving, restoring, and managing layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301

Editing compound annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304

Adding and deleting proposed structures for a compound . . . . . . . . . . . . . . . . 306

Replacing an annotation with a structure proposal . . . . . . . . . . . . . . . . . . . . . 307

Applying FISh scoring. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307

Using result filters for data reduction and creating filter sets . . . . . . . . . . . . . . 310

Viewing the result summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319

Shortcut menu commands for the result tables . . . . . . . . . . . . . . . . . . . . . . . . 322

Exporting the tabular results to an external file . . . . . . . . . . . . . . . . . . . . . . . . 327

Exporting the result table contents to a spreadsheet . . . . . . . . . . . . . . . . . . . 327

Exporting the result table contents to a text file . . . . . . . . . . . . . . . . . . . . . . 329

Exporting an Xcalibur inclusion or exclusion list from a result file. . . . . . . . 329

Exporting the contents of the compounds table to TraceFinder . . . . . . . . . 333

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8Compound Discoverer User Guide for LC Studies Thermo Scientific

Exporting spectral data to a new or existing mzVault library . . . . . . . . . . . . . . 333

Adding a compound to an existing mzVault library. . . . . . . . . . . . . . . . . . . 334

Creating a new mzVault library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335

Exporting compounds to a new or existing mass list . . . . . . . . . . . . . . . . . . . . 336

Exporting compounds from the Compounds table to a new mass list . . . . . 336

Exporting compounds from the Compounds table to an existing mass

list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336

Copying or saving graphical views for publication . . . . . . . . . . . . . . . . . . . . . . 338

Copying structures to the Clipboard for use in other applications . . . . . . . . . . 339

Chapter 9 Graphical views for a result file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .341

Chromatograms view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342

Mass Spectrum view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354

Result Charts view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362

Opening the Result Charts view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363

Using the copy, export, and zoom commands for the Result Charts

view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363

Displaying and pinning the Options Pane for the Result Charts view . . . . . 364

Histogram charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364

Bar charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370

Pie charts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373

Scatter plots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377

Trend Chart view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382

Isotopologues Distribution Chart view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389

Mass Defect Plot view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392

Principal Component Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393

Working interactively with the loadings plot . . . . . . . . . . . . . . . . . . . . . . . . 397

Interpreting the variance plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398

Principal Component Analysis view parameters. . . . . . . . . . . . . . . . . . . . . . 400

Descriptive Statistics view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400

Differential Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404

Partial Least Squares Discriminant Analysis view. . . . . . . . . . . . . . . . . . . . . . . 410

KEGG Pathways view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

BioCyc Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414

Metabolika Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417

Retention Time Corrections view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417

Compound Area Corrections view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419

Hierarchical Clustering Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423

mzLogic Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431

FISh Scoring Queue view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433

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Thermo Scientific Compound Discoverer User Guide for LC Studies 9

Chapter 10 Descriptive information for the result tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . .435

Common result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435

Adducts table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436

Chromatogram Peaks table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436

File Alignments table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437

FISh Trace Fragments table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438

Input Files table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439

Manual Peaks table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440

Merged Features table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440

Specialized Traces table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442

Study Information table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443

Structure Proposals table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444

Expected Compounds result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445

Expected Compounds table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445

Expected Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449

Expected Features table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452

Expected Formulas table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453

Related Structures table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455

Transformations table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456

Compound detection result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456

Compounds table (LC studies) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457

Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466

Features table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467

Filled Gaps table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468

Labeled Features table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469

Labeled Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

Similar Compounds Related table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Compound Identification result tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

ChemSpider Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

Mass List Search Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475

mzCloud Results table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476

mzVault Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479

Predicted Compositions table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480

Pathway Mapping result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482

BioCyc Pathways table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483

BioCyc Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484

KEGG Pathways table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485

Metabolika Pathways table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486

Metabolika Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488

Compound Scoring tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489

Compound Class Matches table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489

Matched Patterns table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491

Neutral Losses table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492

Differential analysis columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494

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10 Compound Discoverer User Guide for LC Studies Thermo Scientific

Descriptive statistics columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497

QC Correction columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498

Chapter 11 Creating and printing reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .499

Reporting workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499

Generating a report with an existing report template . . . . . . . . . . . . . . . . . . . . 501

Creating a new report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 504

Editing an existing report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512

Opening a report template. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514

Changing the logo image for a report template . . . . . . . . . . . . . . . . . . . . . . 514

Changing the time stamp format of a report template . . . . . . . . . . . . . . . . . 515

Adding items to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515

Adding main table columns to a report template . . . . . . . . . . . . . . . . . . . . . 516

Adding data graphs to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . 517

Adding related table columns to a report template. . . . . . . . . . . . . . . . . . . . 517

Editing the properties of subreport columns in a report template . . . . . . . . 519

Moving a subreport column to the main table of a report table . . . . . . . . . . 520

Modifying the properties of a section report item . . . . . . . . . . . . . . . . . . . . 522

Adding page breaks to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . 523

Deleting a pair of workspace sections on the report template page . . . . . . . . 523

Resizing the sections of a report template . . . . . . . . . . . . . . . . . . . . . . . . . . 523

Editing tools on the report template page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 524

Workspace sections and sizing bar on the report template page . . . . . . . . . . 525

Report template page toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527

Adding, aligning, and transposing columns in a report template using

the shortcut menu commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530

Adding a border to an item by using the Format Border command . . . . . . . 531

Descriptions of the shortcut menu commands for the report template

page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531

Section report items for a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532

Property settings for the sections and items in a report template . . . . . . . . . . . 535

Appearance properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536

Behavior properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539

Data properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541

Design properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544

Layout properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544

Miscellaneous properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545

Opening the property dialog boxes for the items in the Section

Reports pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546

Populating a rich text box by loading a file . . . . . . . . . . . . . . . . . . . . . . . . . 548

Selecting the paper type, print width, page orientation, and watermark

for a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 548

Previewing and printing a report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551

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Thermo Scientific Compound Discoverer User Guide for LC Studies 11

Chapter 12 Managing the lists and libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .557

Lists & Libraries manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 558

Expected Compounds view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 558

Expected Compounds view parameter descriptions . . . . . . . . . . . . . . . . . . . 559

Deleting, importing, or exporting expected compounds . . . . . . . . . . . . . . . 560

Adding and editing expected compounds with the Compound Editor. . . . . 561

Generating an Xcalibur inclusion list. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 563

Adducts view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565

Adducts view parameter descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566

Deleting, importing, and exporting adducts . . . . . . . . . . . . . . . . . . . . . . . . 566

Adding and editing adducts with the Adduct Editor . . . . . . . . . . . . . . . . . . 567

Ion Definitions view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568

Ion Definition view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569

Default list of ion definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570

Deleting an ion definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571

Importing ion definitions from an XML file . . . . . . . . . . . . . . . . . . . . . . . . 572

Exporting the ion definitions list to an XML File . . . . . . . . . . . . . . . . . . . . 572

Adding or editing ion definitions with the Ion Definition Editor . . . . . . . . 572

Transformations view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 574

Adding or editing transformations with the Transformation Editor. . . . . . . 577

Neutral Losses view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580

Neutral Loss Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 582

Default neutral loss entries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583

Mass Lists view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 584

Deleting or replacing mass list files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587

Importing a mass list from a CSV file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587

Importing a mass list from a massList file, an XML file, or an SDF

file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 588

Exporting a mass list file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 588

Mass Lists view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589

Creating and editing mass list files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 590

Adding and editing mass list compounds with the Compound Editor . . . . . 593

Spectral Libraries view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595

Metabolika Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 596

Deleting, importing, exporting, and replacing Metabolika pathways . . . . . . 598

Editing new and existing Metabolika pathways . . . . . . . . . . . . . . . . . . . . . . . . 598

Adding and editing Metabolika pathway structures . . . . . . . . . . . . . . . . . . . 603

Compound Classes view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605

Compound Classes view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607

Adding new files to the Compound Classes library . . . . . . . . . . . . . . . . . . . 608

Deleting, importing, and exporting compound class files. . . . . . . . . . . . . . . 609

Editing compound class files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 609

Edit Compound Class dialog box parameters . . . . . . . . . . . . . . . . . . . . . . . 610

Using the Fragment Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611

Loading a structure from a structure file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613

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12 Compound Discoverer User Guide for LC Studies Thermo Scientific

Finding a structure in the ChemSpider database . . . . . . . . . . . . . . . . . . . . . . . 613

Structure drawing tools and commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615

Structure editors toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615

Shortcut menu commands for the drawing area of the structure editors. . . . 616

Using the structure icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 617

Creating template structures and adding them to a drawing . . . . . . . . . . . . 617

Checking the validity of a structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618

Manipulating structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620

Selecting atoms and bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622

Moving structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Editing bond properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Editing atom properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Saving a structure to a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625

Copying and pasting InChi strings and MOL strings . . . . . . . . . . . . . . . . . . . 625

Chapter 13 Using the License Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .627

Opening the License Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627

License Manager command bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628

Activating the software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628

Deactivating the software license for transfer to another computer . . . . . . . . . 634

Installing or updating a processing workflow node . . . . . . . . . . . . . . . . . . . . . 636

Obtaining and installing the KEGG license. . . . . . . . . . . . . . . . . . . . . . . . . . . 637

Chapter 14 Compound Discoverer configuration options . . . . . . . . . . . . . . . . . . . . . . . . . . . .639

Opening the Configuration page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639

Selecting the maximum number of parallel processing jobs . . . . . . . . . . . . . . . 639

Selecting where to store temporary data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640

Turning off the auto-save feature for studies . . . . . . . . . . . . . . . . . . . . . . . . . . 641

Hiding the workflow node numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641

Setting up the global color palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642

Specifying the default mzCloud mass tolerance settings. . . . . . . . . . . . . . . . . . 649

Setting up a BioCyc account or subscription . . . . . . . . . . . . . . . . . . . . . . . . . . 650

Specifying the fragmentation databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652

Chapter 15 Common operations for manipulating data tables . . . . . . . . . . . . . . . . . . . . . . . .653

Moving up and down table rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653

Sorting data tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 654

Sorting table entries by one or more columns . . . . . . . . . . . . . . . . . . . . . . . 654

Sorting table entries by a column with a distribution map . . . . . . . . . . . . . . 654

Freezing table rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655

Grouping table rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656

Changing the position of table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657

Freezing table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659

Showing or hiding table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659

Contents

Thermo Scientific Compound Discoverer User Guide for LC Studies 13

Copying table entries to the clipboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661

Copying the contents of a single table cell to the Clipboard. . . . . . . . . . . . . 661

Copying the contents of a single table row to the Clipboard . . . . . . . . . . . . 662

Copying the contents of multiple rows to the Clipboard . . . . . . . . . . . . . . . 662

Filtering the tables on a study page or a list or library view . . . . . . . . . . . . . . . 662

Setting up a custom filter with multiple conditions . . . . . . . . . . . . . . . . . . . . . 669

Chapter 16 Exploring compound relations with the molecular networks viewer . . . . . . .675

Using the molecular networking feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 675

How the Generate Molecular Networks node works . . . . . . . . . . . . . . . . . . . . 676

Information displayed in the Similar Compounds table. . . . . . . . . . . . . . . . . . 678

Sending compounds to the molecular networks viewer . . . . . . . . . . . . . . . . . . 679

Marking selected compounds in the Compounds table . . . . . . . . . . . . . . . . . . 681

Working with the molecular networks viewer . . . . . . . . . . . . . . . . . . . . . . . . . 683

Panes at the left of the molecular networks viewer . . . . . . . . . . . . . . . . . . . . . . 691

Pane at the right of the molecular networks viewer . . . . . . . . . . . . . . . . . . . . . 696

Chapter 17 Testing communication to the online databases . . . . . . . . . . . . . . . . . . . . . . . . .697

Troubleshooting access to the online databases . . . . . . . . . . . . . . . . . . . . . . . . 697

Running the communication tests. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 698

Checking the URLs for the online databases in your browser . . . . . . . . . . . . . 699

Specifying the IP address of the proxy server . . . . . . . . . . . . . . . . . . . . . . . . . . 700

Setting the correct time and time zone on the processing computer. . . . . . . . . 701

Appendix A Experiment design for comparison statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . .703

Biological versus technical replicates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 703

Non-Nested versus nested experiment designs. . . . . . . . . . . . . . . . . . . . . . . . . 703

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .707

Contents

14 Compound Discoverer User Guide for LC Studies Thermo Scientific

Thermo Scientific Compound Discoverer User Guide for LC Studies 15

P

Preface

This guide describes how to use the Compound Discoverer™ application to qualitatively

process RAW data files with a targeted or untargeted workflow. A targeted workflow evaluates

the mass spectral data for the presence of specific compounds. An untargeted workflow

evaluates the mass spectral data, predicts the elemental composition of unknown compounds,

and searches mass spectral databases to identify these compounds.

To familiarize yourself with the Compound Discoverer application, follow the tutorials that

are available from the application Help menu.

Contents

•Accessing the Documentation

•System Requirements

•Installation Instructions

•Special Notices

•Creating and submitting a bug report

•Contacting Us

Accessing the Documentation

The Compound Discoverer application includes these manuals as PDF files:

• Compound Discoverer User Guide for LC Studies

• Compound Discoverer User Guide for GC Studies

•Compound Discoverer Tutorial for GC CI Workflows

•Compound Discoverer Tutorial for GC EI Workflows

•Compound Discoverer Tutorial for E & L Studies

•Compound Discoverer Metabolism Tutorial

•Compound Discoverer Metabolomics Tutorial

Preface

16 Compound Discoverer User Guide for LC Studies Thermo Scientific

•Compound Discoverer Stable Isotope Labeling Tutorial

•Compound Discoverer Reporting Quick Start Guide

The Compound Discoverer application also includes a context-sensitive Help system, which

means that you can access content-specific Help for each page or dialog box in the user

interface by pressing the F1 key on your computer keyboard. You can also open the Help

system to the Welcome page by choosing Help > Compound Discoverer Help from the

application menu bar.

For information about accessing the manuals, see these topics:

•Viewing the user guides and tutorials

•Downloading the user documentation for any Thermo Scientific product

Viewing the user guides and tutorials

To view the Compound Discoverer manuals

From the application window, choose Help > Manuals.

–or–

From the Microsoft™ Windows™ 10 taskbar, click the Start icon ( ), choose Thermo

Compound Discoverer 3.2, and select a manual.

The list of manuals includes two user guides (one for each study type), two tutorials for

GC studies, four tutorials for LC studies by field of study (vertical market), and one quick

start for reporting.

Preface

Thermo Scientific Compound Discoverer User Guide for LC Studies 17

Downloading the user documentation for any Thermo Scientific product

To download user documentation from the Thermo Scientific website

1. Go to thermofisher.com.

2. Point to Support, and then click Manuals under Product Documentation on the left.

3. On the Documents & Support page, type the product name in the search box, and then

click the Search icon.

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

print it.

Link to the Documents & Support page

Search box

Preface

18 Compound Discoverer User Guide for LC Studies Thermo Scientific

System Requirements

The Compound Discoverer 3.2 application can process data files produced by high-resolution

accurate-mass (HRAM) Thermo Scientific™ mass spectrometers, such as the Orbitrap

Fusion™, Q Exactive™, and Exactive™.

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

Hardware • 3.4 GHz dual-core processor

• 16 GB RAM

• 500 GB hard drive

• DVD-ROM and USB drive

• Display monitor resolution of 1920 1080

Software • Microsoft Windows 7 Pro SP1 (64-bit) or Windows 10 64-bit

operating system

• Microsoft .NET Framework 4.7.2

• Microsoft .NET Core Runtime 2.1.19

• Microsoft Office 2013

• PDF reader

System settings • To run processing workflows with online mass spectral database

searches, the computer must have unblocked access to the mass

spectral databases on the Internet.

• The computer must have the correct time and date settings and be

synchronized with Internet time.

• The Region and Language setting for the operating system must

be set to English (United States).

Preface

Thermo Scientific Compound Discoverer User Guide for LC Studies 19

Table 2 lists the recommended hardware configurations for enhanced performance using the

Compound Discoverer application.

To check the access to the mass spectral databases, the time and date settings, and the Internet

time, see Chapter 17, “Testing communication to the online databases.”

To verify that the system meets the minimum requirements, see these topics:

•Checking the computer specifications

•Checking the text size

•Checking the format setting for region and language

Checking the computer specifications

To check the computer specifications

1. From the Windows Explorer directory, right-click OSDisk (Drive:) (the directory for the

hard drive where the operating system is installed) and choose Properties.

The OSDisk (Drive:) Properties dialog box opens. This dialog box lists the file system

(NTFS or FAT) and the free disk drive space.

2. In the Windows search box, type System. Then, click System Information.

The System Information page opens. This page lists the operating system; the processor

type, speed, and number of cores; the installed RAM; and the system type (32-bit or

64-bit).

Table 2. Recommended hardware configurations for enhanced performance

System Recommended configurations

Hardware • Dual 8-core processor (for example, 2x Intel™ Xeon™ Gold 6134

CPU @ 3.20 GHz)

• 64 GB RAM

• 1 TB SSD (solid-state disk) hard drive for OS

• 2nd 3 TB (conventional disk) hard drive for data storage

• DVD-ROM and USB drive

• Two 27 in. UHD monitors: Display monitor resolution of

3840 2160 pixels

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20 Compound Discoverer User Guide for LC Studies Thermo Scientific

Checking the text size

To check the font DPI for a Windows 7 system

1. From the Windows taskbar, choose Start > Control Panel.

2. On the Adjust Your Computer’s Settings page, do the following:

a. For View By, select Category.

b. Under Appearance and Personalization, click Adjust Screen Resolution.

The Screen Resolution page opens.

3. Click Make Text and Other Items Larger or Smaller.

4. On the left panel, click Set Custom Text Size (DPI).

The Custom DPI Setting dialog box opens.

Figure 1. Custom DPI Setting dialog box

5. Make sure that the DPI setting is 96 pixels per inch.

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Thermo Fisher Scientific LC Studies User guide

Thermo Fisher Scientific LC Studies User guide

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