OpenMS  3.0.0
SpectraFilterParentPeakMower

Filters the top Peaks in the given spectra according to a given schema/thresholdset

pot. predecessor tools $ \longrightarrow $ SpectraFilter $ \longrightarrow $ pot. successor tools
PeakPickerWavelet any tool operating on MS peak data
(in mzML format)

The command line parameters of this tool are:

SpectraFilterParentPeakMower -- Applies thresholdfilter to peak spectra.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SpectraFilterParentPeakMower.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
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:
  SpectraFilterParentPeakMower <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

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

The following configuration subsections are valid:
 - algorithm   Algorithm parameter subsection.

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_SpectraFilterParentPeakMower.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+SpectraFilterParentPeakMowerApplies thresholdfilter to peak spectra.
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'SpectraFilterParentPeakMower'
in input file input file*.mzML
out output file output file*.mzML
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
+++algorithmAlgorithm parameter subsection.
window_size2.0 The size of the m/z window where the peaks are removed, +/- window_size.
default_charge2 If the precursor has no charge set, the default charge is assumed.
clean_all_charge_states1 Set to 1 if precursor ions of all possible charge states should be removed.
consider_NH3_loss1 Whether NH3 loss peaks from the precursor should be removed.
consider_H2O_loss1 Whether H2O loss peaks from the precursor should be removed.
reduce_by_factor0 Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0).
factor1000.0 Factor which is used to reduce the intensities if 'reduce_by_factor' is selected.
set_to_zero1 Reduce the intensities of the precursor and related ions to zero.