Corrects the precursor mz of high resolution data.

pot. predecessor tools	→ HighResPrecursorMassCorrector →	pot. successor tools
PeakPickerHiRes	→ HighResPrecursorMassCorrector →	CometAdapter (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/nightly/html/TOPP_HighResPrecursorMassCorrector.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

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

version3.6.0-pre-nightly-2026-03-06 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 peak offset from the monoisotopic peak to consider for correction. For example, with max_trace=2, the tool can reassign a precursor to the monoisotopic peak (M+0) even if it was originally assigned to M+1 or M+2 (corrections of approximately -1 or -2 Da). To allow larger corrections (e.g., -3 Da), increase this value accordingly.

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