| OpenMS 2.5.0

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/documentation/UTILS_MRMPairFinder.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    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 UTIL 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
+MRMPairFinder Util which can be used to evaluate labeled pair ratios on MRM features.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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 rt input 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_tolerance 0.01 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_tolerance 200.0 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_tolerance 5.0 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)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false