Util to estimate probability of peptide hits.

pot. predecessor tools	→ IDDecoyProbability →	pot. successor tools
CometAdapter (or other ID engines)		-
PeptideIndexer		-

Experimental classes:: This util is deprecated and might behave not as expected!

So far an estimation of the false score distribution with a gamma distribution and the correct score distribution with a gaussian distribution is performed. The probabilities are calculated using Bayes law, similar to PeptideProphet. This implementation is much simpler than that of PeptideProphet.

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:

IDDecoyProbability -- Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDDecoyProbability.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:
  IDDecoyProbability <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <file>         Identification input of combined forward decoy search (reindex with PeptideIndexer first
                     ) (valid formats: 'idXML')
  -fwd_in <file>     Identification input of forward run (valid formats: 'idXML')
  -rev_in <file>     Identification input of decoy run (valid formats: 'idXML')
  -out <file>*       Identification output with forward scores converted to probabilities (valid formats: 
                     'idXML')
                     
                     
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)

The following configuration subsections are valid:
 - decoy_algorithm   Algorithm parameter subsection

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_IDDecoyProbability.html

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.

+IDDecoyProbabilityEstimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.

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

++1Instance '1' section for 'IDDecoyProbability'

in Identification input of combined forward decoy search (reindex with PeptideIndexer first)input file*.idXML

fwd_in Identification input of forward runinput file*.idXML

rev_in Identification input of decoy runinput file*.idXML

out Identification output with forward scores converted to probabilitiesoutput file*.idXML

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

+++decoy_algorithmAlgorithm parameter subsection

number_of_bins40 Number of bins used for the fitting, if sparse datasets are used, this number should be smaller

lower_score_better_default_value_if_zero50.0 This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)

For the parameters of the algorithm section see the algorithms documentation:
decoy_algorithm