OpenMS
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: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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.
version3.2.0-pre-nightly-2024-07-21 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