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 mz correction on picked (=centroided) high resolution data.

The command line parameters of this tool are:

HighResPrecursorMassCorrector -- Corrects the precursor mass and charge determined by the instrument software
.
Version: 2.0.0 Jul 29 2015, 20:40:22, Revision: GIT-NOTFOUND

Usage:
  HighResPrecursorMassCorrector <options>

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

Use features for precursor mass correction.:
  -feature:in <file>                        Features used to correct precursor masses. (valid formats: 'featu
                                            reXML')
  -feature:mz_tolerance <num>               The precursor mass tolerance. Used to determine matching to featu
                                            re 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                   Whether precursor charge is assumed correct.
  -feature:keep_original                    Whether a copy of the precusor and MS2 should be made (true) or 
                                            if the original should be discarded (false).
  -feature:assign_all_matching              Whether a precursor should be corrected to all matching features 
                                            (true) or only the nearest (false). Only evaluated if copies are
                                            created (feature:keep_original).

  -out <file>*                              Output file (valid formats: 'mzML')
  -out_csv <file>                           Optional csv output file containing columns: precursor rt, uncorr
                                            ected mz, corrected mz, delta mz
                                            (valid formats: 'csv')

Use nearest MS1 peak for precursor mass correction.:
  -nearest_peak:mz_tolerance <num>          The precursor mass tolerance. Used to determine matching to next 
                                            MS1 peak. (default: '0')
  -nearest_peak:mz_tolerance_unit <choice>  Unit of precursor mass tolerance (default: 'ppm' valid: 'Da', 
                                            'ppm')

                                            
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.

version2.0.0 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 containing columns: precursor rt, uncorrected mz, corrected mz, delta mz
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 Whether precursor charge is assumed correct.true,false

keep_originalfalse Whether a copy of the precusor and MS2 should be made (true) or if the original should be discarded (false).true,false

assign_all_matchingfalse Whether a precursor should be corrected to all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original).true,false

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

mz_tolerance0 The precursor mass tolerance. Used to determine matching to next MS1 peak.

mz_tolerance_unitppm Unit of precursor mass toleranceDa,ppm