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glossary.html
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<!DOCTYPE html>
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<head>
<title>Crux glossary</title>
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<h2>Crux glossary</h2>
<h3>Mass spectrometry terminology</h3>
<ul>
<li><b>c-term peptide</b>: The last peptide in the protein,
occurring at the c-terminal end of the protein.</li>
<li><b>decoy peptide</b>: A shuffled, reversed or randomly
generated peptide sequence. Matches to decoy peptides are used
for two purposes: to estimate statistical confidence measures
such as the false discovery rate, and to train machine learning
methods to recognize correctly identified spectra.</li>
<li><b>modification</b>: A chemical modification of a single amino
acid, typically corresponding to the addition of a molecular
group to the amino acid side chain.</li>
<li><b>n-term peptide</b>: The first peptide in the protein,
occurring at the n-terminal end of the protein.</li>
<li><b>peptide</b>: A subsequence of a protein.</li>
<li><b>peptide-spectrum match (PSM)</b>: An observed spectrum
paired with a peptide sequence, along with a score quantifying
the quality of the match.</li>
<li><b>static modification</b>: A chemical modification of a
single amino that is expected to occur on every instance of that
amino acid. A common example is carbamidomethylation of
cysteine, which adds 57.02146 Da to the mass of every
cysteine.</li>
<li><b>target peptide</b>: A real peptide, usually drawn from a
protein database.</li>
<li><b>trypsin</b>: An enzyme used to cleave a protein into
peptides.</li>
<li><b>variable modification</b>: A chemical modification of a
single amino that is expected to occur on some instances of that
amino acid but not others. A common example is phosphorylation
of serine, threonine or tyrosine, which adds a mass of 79.966331
Da to each of those amino acids.</li>
</ul>
<h3>Analysis terminology</h3>
<ul>
<li><b>false discovery rate (FDR)</b>: Estimated proportion of
incorrectly identifications among a set of PSMs, peptides or
proteins.</li>
<li><b>support vector machine (SVM)</b>: A machine learning method
that learns to classify data objects into two groups.</li>
</ul>
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<li><a href="faq.html">Crux FAQ</a></li>
<li><a href="glossary.html">Glossary of terminology</a></li>
<li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
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<img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
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<li><a href="tutorials/install.html">Installation</a></li>
<li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
<li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
<li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
<li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
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<p>
The original version of Crux was written by Chris Park and Aaron Klammer
under the supervision
of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
MacCoss</a>
and <a href="http://noble.gs.washington.edu/~noble">Prof. William
Stafford Noble</a> in the Department of Genome Sciences at the
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
<br />The complete list of contributors
can be found <a href="contributors.html">here</a>.
<br />
<br />
Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
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