FeatureFinderMetabo assembles metabolite features from singleton mass traces.
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Mass traces alone would allow for further analysis such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied by satellite C13 peaks and thus may render the analysis more difficult. FeatureFinderMetabo fulfills a further data reduction step by assembling compatible mass traces to metabolite features (that is, all mass traces originating from one metabolite). To this end, multiple metabolite hypotheses are formulated and scored according to how well differences in RT and m/z or intensity ratios match to those of theoretical isotope patterns.
If the raw data scans contain the scan polarity information, it is stored as meta value "scan_polarity" in the output file.
The command line parameters of this tool are:
FeatureFinderMetabo -- Assembles metabolite features from singleton mass traces. Version: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND Usage: FeatureFinderMetabo <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the --helphelp option. Options (mandatory options marked with '*'): -in <file>* Input centroided mzML file (valid formats: 'mzML') -out <file>* Output featureXML file with metabolite features (valid formats: 'featureXML') 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.
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5 |