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

pot. predecessor tools	→ SpectraFilter →	pot. successor tools
PeakPickerHiRes	→ SpectraFilter →	any tool operating on MS peak data (in mzML format)

The command line parameters of this tool are:

SpectraFilterNLargest -- Keeps only the n largest peaks per spectrum.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SpectraFilterNLargest.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:
  SpectraFilterNLargest <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_SpectraFilterNLargest.html

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.

+SpectraFilterNLargestKeeps only the n largest peaks per spectrum.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SpectraFilterNLargest'

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.

n200 The number of peaks to keep