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<TITLE>Feature detection on centroided data</TITLE>
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<div class="title">Feature detection on centroided data </div> </div>
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<div class="textblock"><p>To quantify peptide features, TOPP offers the <b>FeatureFinder</b> tools. In this section the <b>FeatureFinderCentroided</b> is used, which works on centroided data only. There are other FeatureFinders available that also work on profile data.</p>
<p>For this example the file <em>LCMS-centroided.mzML</em> from the examples data is used (<em>File</em> > <em>Open</em> <em>example</em> <em>data</em>). In order to adapt the algorithm to our data, some parameters have to be set.</p>
<p><b>Intensity</b> <br/>
The algorithm estimates the significance of peak intensities in a local environment. Therefore, the HPLC-MS map is divided into n times n regions. Set the <em>intensity:bins</em> parameter to 10 if you are working on a whole map. If you are working on a small region only, you should set it to 1.</p>
<p><b>Mass</b> <b>trace</b> <br/>
For the mass traces, you have to define the number of adjacent spectra in which a mass has to occur (<em>mass_trace:min_spectra</em>). In oder to compensate for peak picking errors, missing peaks can be allowed (<em>mass_trace:max_missing</em>) and a tolerated mass deviation must be set (<em>mass_trace:mz_tolerance</em>).</p>
<p><b>Isotope</b> <b>pattern</b> <br/>
The expected isotopic intensity pattern is estimated from an averagene amino acid composition. The algorithm searches all charge states in a defined range (<em>isotopic_pattern:change_min</em> to <em>isotopic_pattern:change_max</em>). Just as for mass traces, a tolerated mass deviation between isotopic peaks has to be set (<em>isotopic_pattern:mz_tolerance</em>).</p>
<p>The image shows the centroided peak data and the found peptide features. The used parameters can be found in the TOPP tools dialog.</p>
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<img src="TOPPView_tools_ff_centroided.png" alt="TOPPView_tools_ff_centroided.png"/>
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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 11:19:25 using doxygen 1.8.5</font></TD>
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