MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile.
pot. predecessor tools | ![]() ![]() | 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. Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: MassTraceExtractor <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 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: 'featureXML', '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. Have a look at the OpenMS documentation for more information.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |