PSMFeatureExtractor

PSMFeatureExtractor computes extra features for each input PSM.

Experimental classes:

Parts of this tool are still work in progress and usage and input requirements or output might change. (multiple_search_engine, Mascot support)

pot. predecessor tools	→ PSMFeatureExtractor →	pot. successor tools
PeptideIndexer		PercolatorAdapter

PSMFeatureExtractor is search engine sensitive, i.e. it's extra features vary, depending on the search engine. Thus, please make sure the input is compliant with TOPP SearchengineAdapter output. Also, PeptideIndexer compliant target/decoy annotation is mandatory. Currently supported search engines are Comet, X!Tandem, MSGF+. Mascot support is available but in beta development.

Note

if you have extra features you want to pass to percolator, use the extra flag and list the MetaData entries containing the extra features.

The command line parameters of this tool are:

PSMFeatureExtractor -- Computes extra features for each input PSM.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_PSMFeatureExtractor.html
Version: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  PSMFeatureExtractor <options>

Options (mandatory options marked with '*'):
  -in <files>*                 Input file(s) (valid formats: 'idXML', 'mzid')
  -out <file>*                 Output file in mzid or idXML format (valid formats: 'idXML', 'mzid')
  -out_type <type>             Output file type -- default: determined from file extension or content. (valid
                               : 'idXML', 'mzid')
  -extra <MetaData parameter>  List of the MetaData parameters to be included in a feature set for precolator
                               .
  -multiple_search_engines     Combine PSMs from different search engines by merging on scan level.
                               
Common TOPP options:
  -ini <file>                  Use the given TOPP INI file
  -threads <n>                 Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>            Writes the default configuration file
  --help                       Shows options
  --helphelp                   Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

• Name The identifier used in configuration files and on the command line.
• Default value The value used if the parameter is not explicitly specified.
• Description A short explanation describing the purpose and behavior of the parameter.
• Tags Additional metadata associated with the parameter.
• Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+PSMFeatureExtractorComputes extra features for each input PSM.

version3.6.0-pre-nightly-2026-03-12 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PSMFeatureExtractor'

in[] Input file(s)input file*.idXML, *.mzid

out Output file in mzid or idXML formatoutput file*.idXML, *.mzid

out_type Output file type -- default: determined from file extension or content.idXML, mzid

extra[] List of the MetaData parameters to be included in a feature set for precolator.

multiple_search_enginesfalse Combine PSMs from different search engines by merging on scan level.true, false

skip_db_checkfalse Manual override to skip the check if same settings for multiple search engines were applied. Only valid together with -multiple_search_engines flag.true, false

concatfalse Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level. Only valid together with -multiple_search_engines flag.true, false

imputefalse Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed. Only valid together with -multiple_search_engines flag.true, false

limit_imputationfalse Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score. Only valid together with -multiple_search_engines flag.true, false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false