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<div class="title">Feature grouping </div> </div>
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<div class="textblock"><p>In order to quantify differences across maps (label-free) or within a map (isotope-labeled), groups of corresponding features have to be found. The <b>FeatureLinker</b> TOPP tools support both approaches. These groups are represented by consensus features, which contain information about the constituting features in the maps as well as average position, intensity, and charge.</p>
<h1><a class="anchor" id="TOPP_example_featuregrouping_isotope_labeled"></a>
Isotope-labeled quantitation</h1>
<p><b>Goal:</b> You want to differentially quantify the features of an isotope-labeled HPLC-MS map.</p>
<p>The first step in this pipeline is to find the features of the HPLC-MS map. The FeatureFinder applications calculate the features from profile data or centroided data.</p>
<p>In the second step, the labeled pairs (e.g. light/heavy labels of ICAT) are determined by the <b>FeatureLinkerLabeled</b> application. <b>FeatureLinkerLabeled</b> first determines all possible pairs according to a given optimal shift and deviations in RT and m/z. Then it resolves ambiguous pairs using a greedy-algorithm that prefers pairs with a higher score. The score of a pair is the product of:</p>
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<li>feature quality of feature 1</li>
<li>feature quality of feature 2</li>
<li>quality measure for the shift (how near is it to the optimal shift)</li>
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<img src="TOPP_labeled_quant.png" alt="TOPP_labeled_quant.png"/>
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<h1><a class="anchor" id="TOPP_example_featuregrouping_labelfree"></a>
Label-free quantitation</h1>
<p><b>Goal:</b> You want to differentially quantify the features of two or more label-free HPLC-MS map.</p>
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<img src="TOPP_labelfree_quant.png" alt="TOPP_labelfree_quant.png"/>
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<dl class="section note"><dt>Note</dt><dd>This algorithm assumes that the retention time axes of all input maps are very similar. If you need to correct for retention time distortions, please have a look at <a class="el" href="TOPP_example_mapalignment.html">Map alignment</a> . </dd></dl>
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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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