OpenMS: MassTraceExtractor

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

pot. predecessor tools	$\longrightarrow$ MassTraceExtractor $\longrightarrow$	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: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  MassTraceExtractor <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 mass traces (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.