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Thermo Fisher Scientific LC Studies User guide

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Thermo
Compound Discoverer
User Guide for LC Studies
Software Version 3.2
XCALI-98278 Revision A October 2020
© 2020 Thermo Fisher Scientific Inc. All rights reserved.
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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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
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
Contents
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.
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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
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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).
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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.
/