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	→ RNPxlXICFilter →	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/release/3.4.1/html/TOPP_RNPxlXICFilter.html
Version: 3.4.1 May 19 2025, 14:24:34, Revision: 8aec8ec
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

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

version3.4.1 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