IDExtractor

Extracts 'n' peptides randomly or best 'n' from idXML files.

Input and output format are 'idXML'. The tools allows you to extract subsets of peptides from idXML files.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

IDExtractor -- Extracts 'n' peptides randomly or best 'n' from idXML files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDExtractor.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  IDExtractor <options>

Options (mandatory options marked with '*'):
  -in <file>*                        Input file (valid formats: 'idXML')
  -out <file>*                       Output file (valid formats: 'idXML')
  -number_of_peptides <int>          Number of randomly chosen peptides (default: '10') (min: '1')
  -number_of_rand_invokations <int>  Number of rand invocations before random draw (basically a seed) (defaul
                                     t: '0') (min: '0')
  -best_hits                         If this flag is set the best n peptides are chosen.
                                     
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.

+IDExtractorExtracts 'n' peptides randomly or best 'n' from idXML files.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDExtractor'

in input fileinput file*.idXML

out output fileoutput file*.idXML

number_of_peptides10 Number of randomly chosen peptides1:∞

number_of_rand_invokations0 Number of rand invocations before random draw (basically a seed)0:∞

best_hitsfalse If this flag is set the best n peptides are chosen.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