OpenMS
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:

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: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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
+MRMPairFinderUtil which can be used to evaluate labeled pair ratios on MRM features.
version3.2.0-pre-nightly-2024-07-21 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