OpenMS
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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 |
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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/release/3.3.0/html/TOPP_RNPxlXICFilter.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 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: