Util which can be used to evaluate pairs of MRM experiments.

Experimental classes:: This software is experimental and might contain bugs!

The command line parameters of this tool are:

MRMPairFinder -- Util which can be used to evaluate labeled pair ratios on MRM features.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MRMPairFinder.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:
  MRMPairFinder <options>

Options (mandatory options marked with '*'):
  -in <file>*          Input featureXML file containing the features of the MRM experiment spectra. (valid 
                       formats: 'featureXML')
  -pair_in <file>*     Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy 
                       rt (valid formats: 'csv')
  -out <file>*         Output consensusXML file were the pairs of the features will be written to. (valid 
                       formats: 'consensusXML')
  -feature_out <file>  Output featureXML file, only written if given, skipped otherwise. (valid formats: 'fea
                       tureXML')
                       
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.

+MRMPairFinderUtil which can be used to evaluate labeled pair ratios on MRM features.

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

++1Instance '1' section for 'MRMPairFinder'

in Input featureXML file containing the features of the MRM experiment spectra.input file*.featureXML

pair_in Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rtinput file*.csv

out Output consensusXML file were the pairs of the features will be written to.output file*.consensusXML

feature_out Output featureXML file, only written if given, skipped otherwise.output file*.featureXML

mass_tolerance0.01 Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features.0.0:∞

RT_tolerance200.0 Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file.0.0:∞

RT_pair_tolerance5.0 Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have.0.0:∞

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