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<div class="title">MassTraceExtractor </div> </div>
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<div class="textblock"><p>MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile.</p>
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> MassTraceExtractor <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
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<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerHiRes.html">PeakPickerHiRes</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureFinderMetabo.html">FeatureFinderMetabo</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_TextExporter.html">TextExporter</a> </td></tr>
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</center><p>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 <a class="el" href="TOPP_FeatureFinderMetabo.html">FeatureFinderMetabo</a> tool offers both mass trace extraction and isotope pattern assembly. For proteomics data, please refer to the <a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> tool.</p>
<p><b>The command line parameters of this tool are:</b> </p>
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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.
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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