FeatureFinderMetabo assembles metabolite features from singleton mass traces.
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Mass traces alone would allow for further analyzes such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied with 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, mass traces all stemming 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.
The command line parameters of this tool are:
FeatureFinderMetabo -- Assembles metabolite features from singleton mass traces.
Version: 1.10.0 Mar 7 2013, 08:30:22, Revision: unknown
Usage:
FeatureFinderMetabo <options>
This tool has algoritm parameters which can only be used via an INI file and are not accessible from the command line!
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 OpenMS documentation for more information.