MRMPairFinder

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:

stty: 'standard input': Inappropriate ioctl for device

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: 3.4.0-pre-HEAD-2025-01-17 Jan 27 2025, 12:59:34, Revision: 483d1ee
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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: 'featureXML')
                       
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

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

version3.4.0-pre-HEAD-2025-01-17 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