Determine the overrepresented annotations associated with up- or down-regulated proteins in the Volcano Plot - Proteome Discoverer Software - Determine the overrepresented annotations associated with up- or down-regulated proteins in the Volcano Plot - Proteome Discoverer Software - Proteome Discoverer Software
Proteome Discoverer 3.1 User Guide
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Ardia Platform > Software > Proteome Discoverer Software
Document Type
User Guide
Software version
3.1
Proteome Discoverer
Welcome to the Proteome Discoverer Help application
Accessing documentation
System requirements
Special notices
Contact us
Overview
Introduction to the Proteome Discoverer application
The Proteome Discoverer application
Study management
Search engines
Customizable workflows
Quantification support
Reporter ion quantification
Precursor ion quantification
Label-free quantification
Statistics for differential expression
Protein annotation
Data filtering and validation
Integration with FreeStyle
Multidimensional separation experiments
Supported inputs and outputs
FASTA databases
Supported files
ProSightPD software
XlinkX algorithm
Proteome Discoverer task flow overview
Open and close the application
View the Start page
Access Help
Configuring Proteome Discoverer
Managing the application licenses
Open the License Manager
Activate the software license
Enter the product ID and the activation code
Complete license activation on a computer that is connected to the internet
Complete license activation on an offline computer
Deactivate the software license on computer that connects to the Internet
Deactivate the software license on an offline computer
License Manager command bar
Set the location for temporary files
Change the location of the spectral library files
Specify the number of workflows to execute in parallel
Configure Mascot search engine parameters
Configuring the Mascot search engine
Connect to the Mascot server
Configure Mascot parameters
Configure the Mascot node
Configure the Mascot protein-scoring calculation
Troubleshoot failed Mascot searches
Configure MSPepSearch
Configure the Sequest HT search engine
Configure the Sequest HT protein-scoring calculation
Review the Sequest HT protein-scoring configuration parameters
Configure the CHIMERYS search engine
Connect to the CHIMERYS server
Connect to the CHIMERYS User Portal
Using FASTA databases
Custom Filter dialog box parameters
View FASTA files
Download FASTA files to Proteome Discoverer
Download a FASTA file from the Annotation Server
Import a FASTA file from a local drive
Update a FASTA file from the Annotation Server
Edit the workflow Annotation server settings
Export FASTA files
Delete FASTA files
FASTA files view parameters
Download from the Protein Annotation server dialog box parameters
Find protein sequences and references
Filter a protein reference search
Refine a filtered protein reference search
Delete conditions in filtered protein reference searches
Custom Filter dialog box parameters
Compile a FASTA database
Exclude individual protein references and sequences from a FASTA database
Managing FASTA indexes
Specify the location and number of stored FASTA Indexes
Display the FASTA Indexes view
Specify the columns to display in the FASTA Indexes view
Manually create a FASTA index
FASTA Index creator dialog box parameters
Control automatic FASTA index removal
Deactivate automatic FASTA index removal
Activate automatic FASTA index removal
Delete a FASTA index
Restore a deleted FASTA index
Change the number and location of stored FASTA indexes
Reset the stored FASTA index changes
FASTA indexes view parameters
FASTA Indexes View Field Chooser dialog box parameters
FASTA Indexes Options dialog box parameters
Add or modify FASTA parsing rules
FASTA Parsing Rules View parameters
Add or modify a regular expression
Change or rename a regular expression
Test a parsing rule
Working with spectrum library searches
Display spectrum libraries
Select the columns to display
Add a spectrum library
Map unrecognized modifications
Create a predicted spectrum library
Predict a Spectrum Library parameters
Download a spectrum library
Export a spectrum library
Delete a spectrum library
Spectrum Libraries View parameters
Chemical modifications
Open the Chemical Modifications view
Chemical Modifications View parameters
Add chemical modifications
Update an existing chemical modification
Delete chemical modifications
Import Chemical Modifications
Customizing cleavage reagents
Cleavage enzyme specificities
Work with cleavage reagents
Cleavage Reagents View parameters
Work with Annotation Aspects
Annotation Aspect Editor parameters
Annotation Aspects View parameters
Open the Annotation Aspects view
Add an annotation aspect
Edit user-defined annotation aspects
Remove an annotation group
Deactivate a user-defined annotation aspect
Activate a user-defined annotation aspect
Remove user-defined annotation aspects
Export a user-defined annotation aspect
Import a user-defined annotation aspect
CHIMERYS Inclusion Files
Add CHIMERYS Inclusion Files
Remove CHIMERYS Inclusion Files
Quantification methods and quantification channels
Reporter ion quantification
Precursor ion quantification
Working with quantification methods
Create a quantification method
Use the Method Editor for reporter ion quantification
Use the Method Editor for precursor ion quantification
Add a new label rather than modifying an existing label
Import a quantification method
Export a quantification method
Remove a quantification method
Deactivate a quantification method
Restore quantification method template defaults
Configuring General Preferences
Configure study and analysis preferences
Edit the Annotation Source URLs
Administration Page Configuration parameters
General configuration parameters
Annotation Server configuration parameters
CHIMERYS configuration parameters
CHIMERYS on Ardia Server configuration parameters
Comet configuration parameters
Display Settings node configuration parameters
IMP-ptmRS node configuration parameters
INFERYS Spectrum Library Prediction
Mascot configuration parameters
Minora Feature Detector node configuration parameter
MSF Files node configuration parameter
MSPepSearch node configuration parameters
Percolator configuration parameters
Sequest configuration parameters
Spectrum Files RC configuration parameters
Temporary Files configuration parameters
Spectrum Library Files location parameters
Parallel Job Execution parameters
Discoverer Daemon configuration parameters
FASTA indexes configuration parameters
Create New Quantification Method dialog box parameters
Creating and working with studies
Create a study
Working with an existing study
Open an existing study
Add or change basic study information
Add or change the quantification method
Add study factors to the study
Add categorical study factors
Add numerical study factors
Add biological replicate study factors
Add input files
Samples and Files
Add one or more input files
Fractions and fractionated samples
Add fractions
Create subsets of the fractions
Assign the order of fractions
Import result files
Specify the quantification method for input files
Setting the sample type for the TMT quantification
Setting factor values for the samples
Set values for multiple sample cells at the same time
Filter multiple samples at the same time
Set custom filters for multiple samples at the same time
Creating a custom study definition file
Triple Knockout TMT 11plex example
Copy the exact text of the Quantification Method directly from the application
Export a study definition file
Save a study
Copying a study to another computer
Find missing input files
Update quantification methods
Retain study names or result file names on the Start Page
Delete a study name or a result file name from the Start Page
Clear the Start Page
Study Window parameters
Working with analyses and workflows
Working with analyses
Analyses
The Analysis window
Create an analysis
Add input files to an analysis
Using multiple processing steps in an analysis
Add or delete a consensus step in an analysis
Save an analysis as a template
Create an analysis template from analysis results
Open an existing analysis
Reprocessing an existing analysis
Reprocess an existing search by using different parameters
Reprocess existing results by using a new consensus workflow
Analysis Window parameters
Using workflows
Workflows overview
Using the Workflow Editor
The Workflow Editor
Working with the stand-alone Workflow Editor
Working with the integrated Workflow Editor
View the workflow that generated a result file
Workflow Editor Parameters
Create a workflow
Open a custom workflow template
Open a custom workflow template in an existing analysis
Save a workflow as a custom template
Delete a workflow template
Correct workflow errors
Working with grouping and quantification
The Grouping & Quantification page
Generate custom quantification ratios semiautomatically
Generate custom quantification ratios manually
Generate custom quantification ratios based on quan channels
Perform searches
Perform a search in each file separately
Understanding analysis validation messages
Working with the search results
View the workflow and the analysis from the results
Search analysis results
Add result files to a study for reprocessing
Add result files to a new study or existing study
Add result files to an existing study
Interpreting search results with the results file
The result file and the .pdResultView file
Open a result file
Close a result file
Remove search results
Organizing results
Display the pages of the result file
Display the columns on the result pages
Display associated tables
Move a column
Move rows to the top
Fix the position of a column
Expand column headers
Sort the data in a column
Create and apply layouts
Load an existing layout
Create a layout
Save a modified layout
Manage the contents of the layout list
Apply a layout to a result file during data processing
Check items on the pages of a result file
Selecting items to export
Copying items in a result file
The Proteins page
Annotation Column Listing
The ProteinCard Page
Open the ProteinCard page
Master column
Proteins page columns
The Protein Groups page
Protein Groups page columns
The Peptide Groups page
Modifications of peptides on the Peptide Groups page
Charts available on the Peptide Groups page
Peptide Groups Page Columns
The PSMs page
PSMs
The Delta Score column
Charts available on the PSMs page
PSMs page columns
The MS/MS Spectrum Info page
MS/MS Spectrum Info page columns
The Quan Spectra page
The Input Files page
Charts available on the Input Files page
Input Files page columns
The Specialized Traces page
Charts available on the Specialized Traces page
Specialized Traces page columns
The Study Information page
Study Information page columns
The Modification Sites page
Modifications Site page columns
The Peptide Isoforms page
The Peptide Isoforms page columns
The Consensus Features page
Charts available on the Consensus Features page
Consensus Features page columns
The LCMS Features page
Charts available on the LCMS Features page
LCMS Features page columns
The Result Statistics page
Result Statistics page columns
The Mass Recalibrations page
Charts available on the Mass Recalibrations page
Mass Recalibrations page columns
The Decoy Protein Groups page
Decoy Protein Groups page columns
The Decoy Proteins page
Decoy Proteins page columns
The Decoy Peptide Groups page
Decoy Peptide Groups page columns
The Decoy PSMs page
Decoy PSMs page columns
The Annotated Modifications page, Found Modifications page, and Unknown Modifications page
Display the Annotated Modifications page
Display the Found Modifications page
Display the Unknown Modifications page
Columns on the Annotated Modifications page, Found Modifications page, and Unknown Modifications page
The Amino Acids page
Columns on the Amino Acids page
Custom color-coded tags for result table entries
Define custom tags with the Custom Tags Editor
Add or remove custom tags
Filter a result table by the custom tags
Import or export custom tags
Validating results
Validating raw quantification values
Validating raw quantification values in reporter ion quantification
Validating raw quantification values in precursor ion quantification
Calculating and validating raw quantification values in label-free quantification
Peptide and protein false discovery rate
Target false discovery rate
Peptide confidence indicators
Interpreting search results with views and charts
Displaying graphical views
Using data distribution maps
Generate data distribution maps
Display data distribution maps
Sort the data in distribution map columns
Using Pathway Maps
Use the Protein Identification Details view
Open the Protein Identification Details view
Display a protein’s PTMs
Control the display of the probability of a PTM occurring on a site
Display UniProt PTM annotations of the protein
Copy the colored bar on the Sequence page
Save the colored bar on the Sequence page
Export the Modification List page to Excel
Coverage Page
Sequence Page
Modification List page
Sequence Coverage column
Parameters on the Coverage page of the Protein Identification Details view
ProteinCard page
Use the ProteinCard page
Use the Peptide Spectrum Match Identification Details view
Peptide Spectrum Match Identification Details view parameters
Displaying fragment ions
Display different fragment ions in the Fragment Matches pane and the Fragment Spectrum pane
Display neutral loss ions
Display the precursor ions
Display fragment ions according to the charge state in the ion table
Specify the units to use to display the fragment ion masses in the ion table
Using the Report Item Distribution charts
Display the Scatter Plot view
Display an S plot
Parameters in the Scatter Plots view
Display a Histogram
Parameters on the Histogram view
Display the Bar Chart
Parameters in the Bar Charts view
Display the Pie Chart
Parameters in the Pie Charts view
Display the Venn Diagram
Parameters on the Venn Diagrams view
Displaying the Volcano Plot
Displaying the Principal Component Analysis (PCA) Plot
Displaying the Sample Abundances Chart
Font dialog box
Using the Chromatogram Traces view
View a feature trace in the Chromatogram Traces view
Add a plot in the Chromatogram Traces view
Align chromatogram traces in the Chromatogram Traces view
Compare chromatograms
Map the trace color to an input file
Decrease or increase the number of legends displayed
Group the data by the study variables or individual samples
Filter the data by one or more study variables
Filter the data by one or more files
Chromatogram Traces view parameters
Chromatogram Traces view shortcut menu.
Use the Fragment Match Spectrum view
Use the Mirror Plot to visually verify spectrum library matches
Generate a mirror plot
Use the Mirror Plot to view the INFERYS Predicted spectrum for the target peptide sequence
Fragment Match Spectrum view parameters
Use the Mirror Plot to view the INFERYS Predicted spectrum for multiple target peptide sequences from the same source spectrum
Use the Precursor Isotope Pattern view
Precursor Isotope Pattern view parameters
Use the Sequence Comparison view
Sequence Comparison view parameters
Using the Result Summaries
Samples & Files page
Samples & Files page parameters
Analysis Settings page
Display the Analysis Settings page
Analysis Settings page parameters
Validation page
Validation page
Display the Validation page
Validation page parameters
FDR Calculation for Protein Groups, Proteins, and Peptide Groups
FDR Calculation for PSMs
Quantification page
Quantification page parameters
Configuration page
Configuration page parameters
Copy information from the Result Summaries pane to the clipboard
Copy information from all the Result Summaries pages
Copy information from one of the Result Summaries pages
Copy information from a subpage of one of the Result Summaries pages
Display the Mass Recalibration view
Parameters in the Mass Recalibration view
Shortcut menu commands in the Mass Recalibration view
View result files using FreeStyle
View the files from a result in the FreeStyle application
Open the FreeStyle application
Filtering results data
Display filters
The Display Filter pane
Working with display filters
Create a display filter
Temporarily disable filters (method 1)
Temporarily disable filters (method 2)
Work with filter sets
Save a filter set
Load a filter set
View the filter settings in the Result Summaries pane
Save a filter set in a result file
Apply stored filters to a result file
Add a filter with wild cards
Display Filter pane parameters
Interpreting quantitative results
Display the Trend Chart
Trend Chart Parameters
Display the Sample Abundances chart
Parameters in the Sample Abundances view
Work with Heat Maps
Heat Map Parameters
Displaying data distribution maps for quantification
Sample information used to calculate and display quantification results
Sample information used to display identifications and quantifications among files and samples
Display data distribution maps
Display the Quantification Channel Values chart
Displaying quantification channel values for reporter ion quantification
Display the Quantification Channel Values chart for PSMs, MS/MS Spectrum Info input, and quantification spectra for reporter ion quantification
Display the Quantification Channel Values chart for proteins and peptide groups for reporter ion quantification
Displaying quantification channel values for precursor ion quantification
Display the Quantification Channel Values chart for PSMs and quantification spectra for precursor ion quantification
Display the Quantification Channel Values chart for proteins and peptide groups for precursor ion quantification
Display Quantification Channel Values chart for label-free quantification
Display the Quantification Spectrum chart
Display the Quantification Spectrum chart for reporter ion quantification
Display the Quantification Spectrum chart for precursor ion quantification
Display the Quantification Spectrum chart for label-free quantification
Display the Quan Spectra page
Quan Spectra Page parameters
Display Quantification Ratio Distribution charts
Display the Volcano Plot
Parameters in the Volcano Plots view
Shortcut menu commands in the Volcano Plots view
Display the principal component analysis plot
Scores Plot
Loadings Plot
Variances Plot
Parameters in the PCA Plots View of the Report Item Distribution Chart
Shortcut menu commands in the PCA Plots view
Displaying the File Alignment view
Parameters in the File Alignment view
Shortcut menu commands in the File Alignment view
Display the Enrichment Chart
Display the Enrichment Chart
Determine the overrepresented annotations associated with up- or down-regulated proteins in the Volcano Plot
Determine the overrepresented annotations associated with coregulating proteins in the heat map
Enrichment Chart parameters
Exporting data
Export options
Export data from the result file
Export Spectra
Export Spectra dialog box parameters
Exporting Spectra without a PSM match
Export annotated spectra
PSMs table in the output HTML file
Export Annotated Spectra dialog box parameters
Fragment Match Options dialog box
Export search results to a Tab-Delimited TXT file
Export search results to a tab-delimited TXT file
Export to Text (Tab Delimited) dialog box parameters
Export search results to Excel workbooks
Export to Excel dialog box parameters
Export search results in PepXML format
Export to PepXML dialog box parameters
Export search results in ProtXML format
Export to ProtXML dialog box parameters
Export search results in mzIdentML format
Export to MzIdentML dialog box parameters
Export search results in mzTab format
Export protein references to a FASTA file
Export to FASTA dialog box parameters
Export mass lists
Export Mass List dialog box parameters
Exporting crosslinked search results to xiNET
Copy or Save a view to an image
Export study information to a study definition file
Export CHIMERYS Inclusion File
Using the Proteome Discoverer Daemon utility
Create processing and consensus workflows on the remote server
Create Daemon user and token
Start the Daemon utility in a window
Select the server
Run the Daemon utility from the window
Monitor job execution in the Daemon utility
Proteome Discoverer Daemon utility window parameters
Log in to a remote server
Running the Daemon utility from the Xcalibur data system
Overview of the Proteome Discoverer Daemon Analysis
Prepare to run the Daemon utility in Xcalibur
Run the Daemon utility from a parameter file
Create a processing method that calls the Daemon utility from the Xcalibur data system
Specify the sample types to be sent to Proteome Discoverer Daemon
By File processing with a processing method that calls the Daemon utility
By File processing with multiple processing methods
Process MudPIT samples by using a processing method
Run the Daemon utility from the command line
Using the Proteome Discoverer interface
Proteome Discoverer Toolbar
Status bar
File menu
View menu
Administration menu
Tools menu
Window menu
Help menu
Shortcut menus
Results report shortcut menu
Graph shortcut menu
Workflow editor shortcut menu
Job queue
Display the job queue
Promote a job
Abort a job
Remove a job from the job queue
Refresh the job queue
Open a results report from the job queue
Open a study from the job queue
Display long messages in the job queue
Job queue parameters
Manipulate search results views and Workflow Editor panes
Customizing the interface
Customizing menus
Add and Remove shortcut keys
Add a shortcut key from a command
Remove a shortcut key from a command
Restore shortcut key defaults
Display information about a command
Display full or partial menus
Specify the menu deployment method
Customizing the toolbar
Control toolbar visibility
Hide a toolbar from the main toolbar
Display a toolbar in the main toolbar
Add a Toolbar
Delete a toolbar
Renaming a Toolbar
Reposition a toolbar
Restore toolbar defaults
Customize toolbar icons, fonts, and tooltips display
Resize icons in toolbars
Modify icons and menu commands
Customize ToolTips
Hide ToolTips
Customize dialog box parameters
Customize keyboard dialog box parameters
Set global default fragment match options
Set the global default colors and fonts
Options dialog box parameters
Fragment match options page parameters
Fragment match colors and fonts page parameters
Processing workflow editor nodes reference
Data Input nodes
Spectrum Files node
Spectrum Files RC node
Spectrum Retrieval nodes
Spectrum Selector node
Feature Detection & Quantification nodes
Minora Feature Detector node
Reporter Ions Quantifier node
Spectrum Processing nodes
Noise Peak Filter node
Non-Fragment Filter node
Precursor Detector node
Spectrum Grouper node
Spectrum Normalizer node
Top N Peaks Filter node
Xtract Node
Spectrum Filter nodes
Scan Event Filter node
Spectrum Confidence Filter node
Spectrum Properties Filter node
Sequence Database Search nodes
Mascot node
Sequest HT node
CHIMERYS node
CHIMERYS On Ardia Server
Comet node
Spectral Library Search nodes
MSPepSearch node
PSM Validation nodes
Fixed Value PSM Validator node
INFERYS Rescoring node
Percolator node
Target Decoy PSM Validator node
PTM Analysis nodes
IMP-ptmRS node
Data Export nodes
Spectrum Exporter node
Post-Processing Nodes
PSM and Protein Grouper node
Consensus workflow editor nodes reference
Data Input nodes
MSF Files node
Using the MSF Files Node to Change Title Line Parsing
Bottom-Up analysis nodes
PCM Grouper node
PSM Grouper node
Peptide Validator node
Peptide and Protein Filter node
Protein FDR Validator node
Protein Grouping node
Protein Scorer node
Quantification nodes
Feature Mapper node
Fragment Ions Quantifier node
Precursor Ions Quantifier node
Reporter Ions Quantifier node
Annotation nodes
Peptide in Protein Annotation node
Protein Annotation node
Protein Marker node
PTM Analysis nodes
Modification Sites node
Peptide Isoform Grouper node
Post-Processing nodes
Data Distributions node
Display Settings node
Result Exporter node
Result Statistics node
Understanding protein grouping
Protein grouping algorithm
Number of unique Peptides Column on the Proteins page
PSMs identified by multiple workflow nodes
Technical and biological replicates
What are replicates?
Specifying replicates in a study
Non-nested experiments
Nested experiments
Using biological replicates in the Proteome Discoverer application
Custom script integration
Scripting Node overview
General mechanism of the Scripting Node
Use the Scripting Node in a workflow
Integrate your script into a Post-Processing Scripting Node
Reading the node_args.json file into the script
The node_args.json file parameter descriptions
Guidelines for R Developers
Reading the exported tables and columns into the script
Guidelines for R Developers
Writing results as new columns to an existing table
The node_response.json file parameter descriptions
Guidelines for R Developers
Create new tables and connecting them to existing tables
Guidelines for Developers
Install or update a scripting workflow node
Register standalone scripting nodes
Scripting Node parameters
Table name and column name listing
Understanding quantification algorithms
Calculate p-values and adjusted p-values for quantification results
Calculate p-values for replicate data by using biological replicate study factors
Create nested designs
Create non-nested designs
Grouping similar files for label free
Calculate p-values for replicate data without using biological replicate study factors
Ensuring that p-values are calculated
Impute missing values
Treating missing quantification channels for quantification methods
Accepting spectra with missing quantification channels
Rejecting the quantification results
Replacing the missing quantification channels
Understanding how quantification results are calculated
Calculating PSM abundances
Using Reporter Ion Isotopic Distribution Values to Correct for Impurities
Excluding PSMs with high levels of coisolation
Classifying quantification results
Classification flow chart
Calculating peptide group abundances
Classifying peptide groups
Calculating protein abundances
Normalizing peptide groups and protein abundances
Normalization Mode parameter
Scaling Mode parameter
Excluded Peptide Modification parameter
Using sample information to calculate and display quantification results
Calculating group abundances
Calculating peptide group and protein ratios
Calculating ratios using the Summed Abundance approach
Calculating ratios using the Pairwise Ratio approach
Calculating abundance CVs and ratio variability
Calculating protein group ratios
Understanding how quantification methods work in Proteome Discoverer
Specifying the quantification channels
Checking the quantification method
How the ptmRS Node calculates sequence and site probabilities
PSM Display Logic
Minora Feature Detection
Retention-time alignment and feature mapping
Troubleshooting quantification
Troubleshoot reporter ion quantification
Troubleshoot precursor ion quantification
Filtering reporter ion quantification data with signal-to-noise values
Using signal-to-noise values as quantification channel values
Filtering quantification data with average reporter ion signal-to-noise values
Identifying isotope patterns in precursor ion quantification
Understanding how the CHIMERYS algorithm quantifies data produced by Data Independent Acquisition
Overview of the CHIMERYS workflow
Default DIA workflows in Proteome Discoverer
Viewing DIA results
FASTA file and annotation database topics
FASTA databases
NCBI
UniRef100
UniProtKB/SwissProt and UniProtKB/TrEMBL
Custom database support
Custom parsing rule A
Custom parsing rule B
Custom parsing rule C
Adding protein sequences and references to a FASTA database file
FASTA database utilities dialog box parameters
Add Protein References page
Compile FASTA Database page
Find Protein References page
Chemistry references
Amino acid mass values
Enzyme cleavage properties
Fragment ions
Creating workflows for specific purposes
Creating Reporter Ion Quantification Workflows
Creating Precursor Ion Quantification Workflows
Creating Label-Free Workflows
Creating INFERYS Rescoring Workflows
Creating CHIMERYS Workflows
Adding PTM Analysis to a Workflow
Supporting Analyses of Datasets with Multiple Fragmentation Methods
Including Precursor Detector node
Including Spectra Export in a Workflow
Adding Columns for Marking Proteins in Results
Incorporating Mass Recalibration
Searching for Quantification Modifications with Mascot
Performing TMT Quantification on HCD and CID Scans
Creating a Multiconsensus Report
Searching Spectrum Libraries
Filtering Results in a Workflow
Calculating FDRs
Assigning Confidence to PSMs in Large Data Sets
Assigning Confidence to PSMs in Smaller Data Sets
Assigning Confidence to Proteins
Filtering PSMs with the Fixed Value PSM Validator Node
Filtering PSMs with the Peptide and Protein Filter Node
Filtering Proteins
Filtering PSMs with MSF Node Parameters
Filter PSMs with the Maximum Delta Cn parameter
Filter PSMs with the Maximum Rank parameter
Filter PSMs with the Maximum Delta Mass parameter
Filter PSMs with the Score and Threshold parameters
Specify the list of score names to filter by
Adding Protein Annotation to a Workflow
Displaying Species Names for Proteins and Peptide Groups
Post-Processing Workflows
Proteome Discoverer powered by Ardia
Proteome Discoverer powered by Ardia overview
Licensing the Ardia features in the Proteome Discoverer software
Register on the Ardia Server
Sign in to the Ardia Platform
Deregister from the Ardia Server
Configure CHIMERYS on Ardia Server
Open remote results
Access remote files and results within a study
Publish analyses to the Ardia Platform
Configure automated processing
Server Configuration for automated processing
Create templates for automated processing
Run the automated processing
Run large studies with automation
Processing-only analysis workflows
Using Results Path for studies
Create a multiconsensus workflow
Copyright
Open the result of interest. Select the Proteins tab. Choose View > Distribution Charts , or select Distribution Charts Select the Volcano Plot tab. For more information about Volcano Plots, see Display the Volcano Plot . In the Comparison dropdown list, choose a relevant ratio. Right-click the Volcano Plot, and choose Check All Up-Regulated Points or Check All Down-Regulated Points . The Volcano Plot The Enrichment Chart updates to show the overrepresented terms for the selected annotation category. Volcano plot with updated Enrichment Chart
in the toolbar.