Corrects the precursor mz of high resolution data.

pot. predecessor tools	→ HighResPrecursorMassCorrector →	pot. successor tools
PeakPickerHiRes	→ HighResPrecursorMassCorrector →	MascotAdapter (or other ID engines)

This tool performs precursor m/z correction on picked (=centroided) high resolution data.

Three methods are available: 'nearest_peak', 'highest_intensity_peak' and 'feature'.

nearest_peak: Use nearest centroided MS1 peak for precursor mass correction.
highest_intensity_peak: Use highest intensity centroided MS1 peak in a given mass range for precursor mass correction.
feature: Use features for precursor mass correction, which allows for charge correction.

The method hightest_intensity_peak searches in a specific m/z-window of the precursor information for the peak with the highest intensity. Suggestioned value 1/maximal expected charge. E.g maximal expected charge 5, m/z-window = +/- 0.2 Da

See the corresponding parameter subsection for details.

The command line parameters of this tool are:

HighResPrecursorMassCorrector -- Corrects the precursor mass and charge determined by the instrument software
.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/TOPP_HighResPrecursorMassCorrector.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:
  HighResPrecursorMassCorrector <options>

Options (mandatory options marked with '*'):
  -in <file>*                                         Input file (centroided data) (valid formats: 'mzML')
  -out <file>*                                        Output file (valid formats: 'mzML')

Use features for precursor mass correction.:
  -feature:in <file>                                  Features used to correct precursor masses. (valid forma
                                                      ts: 'featureXML')
  -feature:mz_tolerance <num>                         The precursor mass tolerance. Used to determine matchin
                                                      g to feature mass traces. (default: '5.0')
  -feature:mz_tolerance_unit <choice>                 Unit of precursor mass tolerance (default: 'ppm') (vali
                                                      d: 'Da', 'ppm')
  -feature:rt_tolerance <num>                         Additional retention time tolerance added to feature 
                                                      boundaries. (default: '0.0')
  -feature:believe_charge                             Assume precursor charge to be correct.
  -feature:keep_original                              Make a copy of the precursor and MS2 (true) or discard 
                                                      the original (false).
  -feature:assign_all_matching                        Correct a precursor using all matching features (true) 
                                                      or only the nearest (false). Only evaluated if copies 
                                                      are created (feature:keep_original).

Use nearest centroided MS1 peak for precursor mass correction.:
  -nearest_peak:mz_tolerance <num>                    The precursor mass tolerance to find the closest MS1 
                                                      peak. (Disable method by setting value to 0.0) (default
                                                      : '0.0')
  -nearest_peak:mz_tolerance_unit <choice>            Unit of precursor mass tolerance (default: 'ppm') (vali
                                                      d: 'Da', 'ppm')

Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction:
  -highest_intensity_peak:mz_tolerance <num>          The precursor mass tolerance to find the highest intens
                                                      ity MS1 peak. Suggested value 1/max. expected charge. 
                                                      (Disable method by setting value to 0.0) (default: '0.0
                                                      ')
  -highest_intensity_peak:mz_tolerance_unit <choice>  Unit of precursor mass tolerance (default: 'ppm') (vali
                                                      d: 'Da', 'ppm')

  -out_csv <file>                                     Optional CSV output file for results on 'nearest_peak' 
                                                      or 'highest_intensity_peak' algorithm (see correspondin
                                                      g subsection) containing columns: RT, uncorrectedMZ, 
                                                      correctedMZ, deltaMZ. (valid formats: 'csv')
                                                      
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

+HighResPrecursorMassCorrectorCorrects the precursor mass and charge determined by the instrument software.

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

++1Instance '1' section for 'HighResPrecursorMassCorrector'

in Input file (centroided data)input file*.mzML

out Output fileoutput file*.mzML

out_csv Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ.output file*.csv

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

+++featureUse features for precursor mass correction.

in Features used to correct precursor masses.input file*.featureXML

mz_tolerance5.0 The precursor mass tolerance. Used to determine matching to feature mass traces.

mz_tolerance_unitppm Unit of precursor mass toleranceDa, ppm

rt_tolerance0.0 Additional retention time tolerance added to feature boundaries.

max_trace2 Maximum isotopic trace considered in matching a precursor to a feature.

believe_chargefalse Assume precursor charge to be correct.true, false

keep_originalfalse Make a copy of the precursor and MS2 (true) or discard the original (false).true, false

assign_all_matchingfalse Correct a precursor using all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original).true, false

+++nearest_peakUse nearest centroided MS1 peak for precursor mass correction.

mz_tolerance0.0 The precursor mass tolerance to find the closest MS1 peak. (Disable method by setting value to 0.0)

mz_tolerance_unitppm Unit of precursor mass toleranceDa, ppm

+++highest_intensity_peakUse centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction

mz_tolerance0.0 The precursor mass tolerance to find the highest intensity MS1 peak. Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)

mz_tolerance_unitppm Unit of precursor mass toleranceDa, ppm