| OpenMS 2.5.0

PrecursorMassCorrector

Corrects the precursor entries of MS/MS spectra, by using MS1 information.

pot. predecessor tools | PrecursorMassCorrector | pot. successor tools
- | MascotAdapter (or other ID engines)

Experimental classes:
  This TOPP-tool is not well tested and not all features might be properly implemented and tested!

This tool corrects the m/z entries of MS/MS spectra by using MS1 information. Therefore, MS1 spectra must be supplied as profile mode spectra. The isotope distribution of the peptide in the MS1 level information are then used to determine the exact position of the monoisotopic peak. If no isotope distribution can be found the original entry is kept. As a side effect of determining the exact position of the monoisotopic peak is that the charge state is also annotated.

This implementation uses the isotopewavelet featurefinder and sets the monoisotopic peak (and the charge) to the nearest feature.

The command line parameters of this tool are:

    PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information.

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

      PrecursorMassCorrector <options>

    Options (mandatory options marked with '*'):

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

      -out <file>*                           Output mzML file. (valid formats: 'mzML')

      -feature_in <file>                     Input featureXML file, containing features; if set, the MS/MS spectr

                                             a precursor entries

                                             will be matched to the feature m/z values if possible. (valid forma

                                             ts: 'featureXML')

      -precursor_mass_tolerance <tolerance>  Maximal deviation in Th which is acceptable to be corrected;

                                             this value should be set to the instruments selection window. (defa

                                             ult: '1.5' min: '0.0')

    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 (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
+PrecursorMassCorrector Corrects the precursor entries of MS/MS spectra, by using MS1 information.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'PrecursorMassCorrector'
in Input mzML file containing the spectra.input file*.mzML
out Output mzML file.output file*.mzML
feature_in Input featureXML file, containing features; if set, the MS/MS spectra precursor entries
will be matched to the feature m/z values if possible.input file*.featureXML
precursor_mass_tolerance 1.5 Maximal deviation in Th which is acceptable to be corrected;
this value should be set to the instruments selection window.0.0:∞
max_charge 3 Maximal charge that should be assumed for precursor peaks
intensity_threshold-1.0 Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details.
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