OpenMS  2.5.0
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'.

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/documentation/TOPP_HighResPrecursorMassCorrector.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:

  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' valid:

                                                      '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' 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 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' valid:

                                                      '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.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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_tolerance5.0 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