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/doxygen/release/3.0.0/html/TOPP_PrecursorMassCorrector.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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 format
                                         s: '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. (defau
                                         lt: '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

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

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '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_tolerance1.5 Maximal deviation in Th which is acceptable to be corrected;
this value should be set to the instruments selection window.0.0:∞

max_charge3 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)

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