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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<html xmlns="http://www.w3.org/1999/xhtml">
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<title>Welcome — spectra-cluster toolsuite</title>
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<h1 class="logo logo-name">spectra-cluster toolsuite</h1>
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<p class="blurb">An MS/MS clustering framework</p>
<h3>Navigation</h3>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Welcome</a></li>
<li class="toctree-l1"><a class="reference internal" href="tools.html">Clustering tools / software</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/proteome_discoverer.html">Proteome Discoverer Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/clustering_basics.html">How to cluster MS/MS data</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/unidentified_analysis.html">Analysing proteomics samples using spectrum clustering</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis_results.html">Analysing clustering results</a></li>
</ul>
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<h3>Related Topics</h3>
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<li><a href="#">Documentation overview</a><ul>
<li>Next: <a href="tools.html" title="next chapter">Clustering tools / software</a></li>
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<h1>Welcome<a class="headerlink" href="#welcome" title="Permalink to this headline">¶</a></h1>
<p>The spectra-cluster toolsuite provides tools to facilitate the usage of
spectrum clustering for MS/MS based proteomics data analysis.</p>
<p>It is centered around our spectra-cluster algorithm which is used to build
the <a class="reference external" href="https://www.ebi.ac.uk/pride/cluster">PRIDE Cluster</a> resource (<a class="reference external" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968634/">Griss et al., Nat. Methods 2016</a>) and can process up to 100+ million MS/MS spectra.</p>
<div class="section" id="getting-started">
<h2>Getting started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h2>
<p>The simplest way to use the spectra-cluster algorithm is through our newly released <a class="reference external" href="http://ms.imp.ac.at/?goto=spectra-cluster">Proteome Discoverer Node</a>.</p>
<p>For a step-by-step instruction have a look at our <a class="reference internal" href="tutorials/proteome_discoverer.html"><span class="doc">Proteome Discoverer Tutorial</span></a>.</p>
<div class="admonition hint">
<p class="first admonition-title">Hint</p>
<p class="last">To get help simply post a question at <a class="reference external" href="http://qa.proteomics-academy.org">http://qa.proteomics-academy.org</a></p>
</div>
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<div class="section" id="content">
<h2>Content<a class="headerlink" href="#content" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Welcome</a></li>
<li class="toctree-l1"><a class="reference internal" href="tools.html">Clustering tools / software</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tools.html#developing-own-algorithms">Developing own algorithms</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/proteome_discoverer.html">Proteome Discoverer Tutorial</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#free-version-of-proteome-discoverer">Free version of Proteome Discoverer</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#installing-free-nodes">Installing free nodes</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#installing-the-spectra-cluster-node">Installing the spectra-cluster node</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#using-the-spectra-cluster-node">Using the spectra-cluster node</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#clustering-settings">Clustering settings</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/proteome_discoverer.html#clustering-results">Clustering results</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/clustering_basics.html">How to cluster MS/MS data</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorials/clustering_basics.html#preparing-your-data">Preparing your data</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/clustering_basics.html#searching-your-data">Searching your data</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/clustering_basics.html#merging-identification-data">Merging identification data</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/clustering_basics.html#running-the-clustering">Running the clustering</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/unidentified_analysis.html">Analysing proteomics samples using spectrum clustering</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorials/unidentified_analysis.html#exporting-data-from-proteome-discoverer-results">Exporting data from Proteome Discoverer results</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorials/unidentified_analysis.html#processing-clustering-results">Processing .clustering results</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis_results.html">Analysing clustering results</a></li>
</ul>
</div>
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