| OpenMS 2.5.0

MassTraceExtractor

MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile.

pot. predecessor tools | MassTraceExtractor | pot. successor tools
PeakPickerHiRes | FeatureFinderMetabo
PeakPickerWavelet | TextExporter

This TOPP tool detects mass traces in centroided LC-MS maps and stores them as features in a FeatureMap. These features may be either used directly as input for an metabolite ID approach or further be assembled to aggregate features according to a theoretical isotope pattern. For metabolomics experiments, the FeatureFinderMetabo tool offers both mass trace extraction and isotope pattern assembly. For proteomics data, please refer to the FeatureFinderCentroided tool.

The command line parameters of this tool are:

    MassTraceExtractor -- Detects mass traces in centroided LC-MS data.

    Full documentation: http://www.openms.de/documentation/TOPP_MassTraceExtractor.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    Usage:

      MassTraceExtractor <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 mass traces (valid formats: 'featureXML', 'consensusXML')

      -out_type <type>   Output file type -- default: determined from file extension or content (valid: 'featureX

                         ML', 'consensusXML')

    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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_MassTraceExtractor.html