RNPxlXICFilter

Filters MS2 spectra based on XIC intensities in control and treatment. Used in RNPxl experiments to reduce candidate spectra.

potential predecessor tools	→ RNPxlXICFilter →	potential successor tools
PeakPickerHiRes		NuXL

The command line parameters of this tool are:

RNPxlXICFilter -- Remove MS2 spectra from treatment based on the fold change between control and treatment.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_RNPxlXICFilter.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:
  RNPxlXICFilter <options>

Options (mandatory options marked with '*'):
  -control <file>*    Input mzML file (valid formats: 'mzML')
  -treatment <file>*  Input mzML file (valid formats: 'mzML')
  -fold_change        Fold change between XICs (default: '2.0')
  -rt_tol             RT tolerance in [s] for finding max peak (whole RT range around RT middle) (default: 
                      '20.0')
  -mz_tol             M/z tolerance in [ppm] for finding a peak (default: '10.0')
  -out <file>*        Output of the treatment file after XIC filtering. (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)

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.

+RNPxlXICFilterRemove MS2 spectra from treatment based on the fold change between control and treatment.

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

++1Instance '1' section for 'RNPxlXICFilter'

control input mzML fileinput file*.mzML

treatment input mzML fileinput file*.mzML

fold_change2.0 fold change between XICs

rt_tol20.0 RT tolerance in [s] for finding max peak (whole RT range around RT middle)

mz_tol10.0 m/z tolerance in [ppm] for finding a peak

out output of the treatment file after XIC filtering.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