HighResPrecursorMassCorrector

Corrects the precursor mz of high resolution data.

pot. predecessor tools	$\longrightarrow$ HighResPrecursorMassCorrector $\longrightarrow$	pot. successor tools
PeakPickerHiRes		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
.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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 formats: 'fea
                                              tureXML')
  -feature:mz_tolerance <num>                 The precursor mass tolerance. Used to determine matching to 
                                              feature mass traces. (default: '5')
  -feature:mz_tolerance_unit <choice>         Unit of precursor mass tolerance (default: 'ppm' valid: 'Da', 
                                              'ppm')
  -feature:rt_tolerance <num>                 Additional retention time tolerance added to feature boundaries
                                              . (default: '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 orig
                                              inal (false).
  -feature:assign_all_matching                Correct a precursor using all matching features (true) or only 
                                              the nearest (false). Only evaluated if copies are created (feat
                                              ure: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. (Dis
                                              able method by setting value to 0.0) (default: '0')
  -nearest_peak:mz_tolerance_unit <choice>    Unit of precursor mass tolerance (default: 'ppm' valid: '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 intensity MS1 
                                              peak (Da). Suggested value 1/max. expected charge. (Disable
                                              method by setting value to 0.0) (default: '0')

  -out_csv <file>                             Optional CSV output file for results on 'nearest_peak' or 'high
                                              est_intensity_peak' algorithm (see corresponding 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.

version2.3.0 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 Overwrite tool specific checks.true,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 The precursor mass tolerance. Used to determine matching to feature mass traces.

mz_tolerance_unitppm Unit of precursor mass toleranceDa,ppm

rt_tolerance0 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 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 The precursor mass tolerance to find the highest intensity MS1 peak (Da). Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)