| OpenMS 2.5.0

ERPairFinder

Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.

This tool allows to calculate ratios of labeled peptides based on single enhanced resolution scans (also called zoom scans). Zoom scans is a mode of some mass spectrometry instruments to allow scanning at a higher resolution, at the cost of low scan speed. It can be used to determine charge states of precursors on ion-trap or related instruments.

This tool works scan based. Each scan is examined using the IsotopeWavelet (see docs of that class) to fit an isotope distribution based on the averagine model. Known pairs are given by the pair_in input parameter, which allow to search for specific pairs. Light and heavy variant are search for, and the pairs are finally reported with their ratios.

If a pair is available in several scans, the intensities are summed up and the ratio is calculated from the sum of the isotope fits.

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

The command line parameters of this tool are:

    ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.

    Full documentation: http://www.openms.de/documentation/UTILS_ERPairFinder.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:

      ERPairFinder <options>

    Options (mandatory options marked with '*'):

      -in <file>*                            Input mzML file containing the ER spectra. (valid formats: 'mzML')

      -pair_in <file>*                       Pair-file in the format: m/z-light m/z-heavy charge rt (valid format

                                             s: 'txt')

      -out <file>*                           Output consensusXML file were the pairs of the feature are written

                                             into. (valid formats: 'consensusXML')

      -feature_out <file>                    Output featureXML file, only written if given, skipped otherwise.

                                             (valid formats: 'featureXML')

      -precursor_mass_tolerance <tolerance>  Precursor mass tolerance which is used for the pair finding and the

                                             matching of the given pair m/z values to the features. (default:

                                             '0.3' min: '0.0')

    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 (defa

                                             ult: '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
+ERPairFinder Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'ERPairFinder'
in Input mzML file containing the ER spectra.input file*.mzML
pair_in Pair-file in the format: m/z-light m/z-heavy charge rt input file*.txt
out Output consensusXML file were the pairs of the feature are written into.output file*.consensusXML
feature_out Output featureXML file, only written if given, skipped otherwise.output file*.featureXML
precursor_mass_tolerance 0.3 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 1.0:∞
max_charge 3 Maximal charge state features should be search for.1:∞
intensity_threshold-1.0 Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation.-1.0:∞
max_isotope 3 Max isotope of the isotope distribution to be considered 2:∞
expansion_range 5.0 The range that is used to extend the isotope distribution with null intensity peaks in Th.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