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 |