MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
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FileFilter | OpenSwathAnalyzer |
This tool reads an mzML containing chromatograms (presumably measured on an SRM instrument) and a TraML file that contains the data that was used to generate the instrument method to measure said data. It then maps the transitions in the TraML file to the chromatograms found in the mzML file and stores the mapping by replacing the "id" paramter in the mzML with the "id" of the transition in the TraML file. It removes chromatograms for which it cannot find a mapping and throws an error if more than one transitions maps to a chromatogram. In strict mode (default) it also throws an error it not all chromatograms could be found in the TraML file.
The thus mapped file can then be used in a downstream analysis.
The command line parameters of this tool are:
MRMMapper -- MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: MRMMapper <options> Options (mandatory options marked with '*'): -in <file>* Input file containing chromatograms (converted mzXML file) (valid formats: 'mzML') -tr <file>* Transition file (valid formats: 'TraML') -out <file>* Output file containing mapped chromatograms (valid formats: 'mzML') -precursor_tolerance <double> Precursor tolerance when mapping (in Th) (default: '0.1') -product_tolerance <double> Product tolerance when mapping (in Th) (default: '0.1') -no-strict Run in non-strict mode and allow some chromatograms to not be mapped. 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 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 |