Custom database support - Proteome Discoverer Software - Custom database support - 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

The Proteome Discoverer application has three “general” parsing rules to support custom sequence database formats. The generic parsing rules are applied only if no other parsing rule matches the given FASTA title line.

  • Custom parsing rule A
  • Custom parsing rule B
  • Custom parsing rule C
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