Executes a peak-picking and scoring algorithm on MRM/SRM data.
| potential predecessor tools | OpenSwathAnalyzer | potential successor tools |
| OpenSwathChromatogramExtractor | OpenSwathFeatureXMLToTSV | |
| MRMMapper | OpenSwathConfidenceScoring |
The idea of the MRM peak-picker is to analyze a series of chromatograms together with the associated meta information (stored in TraML format) in order to determine likely places of elution of a peptide in MRM/SRM.
The command line parameters of this tool are:
OpenSwathAnalyzer -- Picks peaks and finds features in an SRM experiment.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
OpenSwathAnalyzer <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file>* Input file containing the chromatograms. (valid formats: 'mzML')
-tr <file>* Transition file (valid formats: 'TraML')
-rt_norm <file> RT normalization file (how to map the RTs of this run to the ones stored in
the library) (valid formats: 'trafoXML')
-out <file>* Output file (valid formats: 'featureXML')
-no-strict Run in non-strict mode and allow some chromatograms to not be mapped.
-swath_files <files> [applies only if you have full MS2 spectra maps] Swath files that were used
to extract the transitions. If present, SWATH specific scoring will be used.
(valid formats: 'mzML')
-min_upper_edge_dist <double> [applies only if you have full MS2 spectra maps] Minimal distance to the
edge to still consider a precursor, in Thomson (only in SWATH) (default:
'0')
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 parameters section
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.
Have a look at the OpenMS documentation for more information.
The algorithm parameters for the Analyzer filter are:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |