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Proteome Discoverer 3.1 User Guide
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Ardia Platform > Software > Proteome Discoverer Software
Desktop 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

This chapter describes how to use 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
  • 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
  • Run large studies with automation
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