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<li><a href="index.html">Home</a></li>
<li><a href="download.html">Download</a></li>
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<!-- START CONTENT -->
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<img src="images/crux-logo.png" style="width:200px; float:left; padding:10px;">
<p>The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. The toolkit includes several search engines for both standard and cross-linked database search, as well as a variety of pre- and post-processing engines for assigning high-resolution precursor masses to spectra, assigning statistical confidence estimates to spectra, peptides and proteins, and performing label free quantification. Crux comes pre-complied for the Linux, Windows and MacOS operating systems. It is implemented as a single program that offers a wide variety of commands. If you use Crux in your research, please cite:
<br />
<span class="indentcitation">Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael
J. MacCoss and William Stafford
Noble. <a href="http://noble.gs.washington.edu/papers/park2008rapid.html">"Rapid
and accurate peptide identification from tandem mass spectra."</a>
<i>Journal of Proteome Research.</i> 7(7):3022-3027, 2008.</li></span>
<br /><br />
For a more up-to-date description of Crux, please read:<br />
<span class="indentcitation">Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas,
Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry
Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael
J. MacCoss and William Stafford
Noble. <a href="http://pubs.acs.org/doi/abs/10.1021/pr500741y">"Crux:
rapid open source protein tandem mass spectrometry
analysis."</a> <i>Journal of Proteome Research.</i>
13(10):4488-4491, 2014.</span>
</p>
<div class="chart-block" style="dislpay:none" align="center">
<p>Crux weekly usage by MS proteomics community over the last 32 weeks (in thousand runs).</p>
<div id="tooltip" class="hidden">
<strong>Week:</strong><span id="dateField">100</span><br/>
<strong>tide-search:</strong><span id="searchField">100</span><br/>
<strong>others:</strong><span id="othersField">100</span>
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<br />
<p/>
Crux is provided as a single executable that supports the following
commands:</p>
<table id="commandstable">
<tr>
<td colspan="2"><b>Primary commands</b></td>
</tr>
<tr>
<td><a href="commands/bullseye.html">bullseye</a></td>
<td>Assign high resolution precursor m/z values to MS/MS data using the Hardklör algorithm.
</tr>
<tr>
<td>
<a href="commands/tide-index.html">tide-index</a></td>
<td>
Create an index of all peptides in a fasta file, for use in subsequent
calls to <code>tide-search</code>.</td>
</tr>
<tr>
<td>
<a href="commands/tide-search.html">tide-search</a></td>
<td>
Search a collection of spectra against a sequence database, provided
either as a FASTA file or an index, returning a collection of
peptide-spectrum matches (PSMs). This is a fast search engine, but it
runs most quickly if provided with a peptide index built
with <code>tide-index</code>.</td>
</tr>
<tr>
<td>
<a href="commands/cascade-search.html">cascade-search</a></td>
<td>
An iterative procedure for incorporating information about peptide
groups into the database search and confidence estimation
procedure.</td></tr>
<tr>
<td>
<a href="commands/comet.html">comet</a></td>
<td>
Search a collection of spectra against a sequence database, returning
a collection of PSMs. This search engine runs directly on a protein
database in FASTA format.</td>
</tr>
<tr>
<td>
<a href="commands/percolator.html">percolator</a></td>
<td>
Re-rank and assign confidence estimates to a collection of PSMs using
the Percolator algorithm. Optionally, also produce protein rankings
using the Fido algorithm.</td></tr>
<tr>
<td>
<a href="commands/kojak.html">kojak</a></td>
<td>
Search a collection of spectra against a sequence database, finding
cross-linked peptide matches.</td></tr>
<tr>
<td>
<a href="commands/diameter.html">diameter</a></td>
<td>
Identify peptide sequences fromm data-independent acquisition
mass spectrometry data without requiring a spectral library</td></tr>
<tr>
<td>
<a href="commands/spectral-counts.html">spectral-counts</a></td>
<td>
Quantify peptides or proteins using one of three spectral counting
methods.</td></tr>
<tr>
<td>
<a href="commands/pipeline.html">pipeline</a></td>
<td>
Given one or more sets of tandem mass spectra as well as a protein
database, this command runs a series of Crux tools and reports all of
the results in a single output directory.
</td></tr>
<tr>
<td colspan="2"><b>Utilities</b></td>
</tr>
<tr>
<td>
<a href="commands/assign-confidence.html">assign-confidence</a></td>
<td>
Assign statistical confidence measures to each PSM in a given set.</td></tr>
<tr>
<td>
<a href="commands/generate-peptides.html">generate-peptides</a></td>
<td>
Extract from a given set of protein sequences a list of target and
decoy peptides fitting the specified criteria.</td>
</tr>
<tr>
<td>
<a href="commands/get-ms2-spectrum.html">get-ms2-spectrum</a></td>
<td>
Extract one or more fragmentation spectra, specified by scan number, from
an <code>MS2</code> file.</td>
</tr>
<tr>
<td><a href="commands/hardklor.html">hardklör</a></td>
<td>Identify isotopic distributions from high-resolution mass spectra.</td>
</tr>
<tr>
<td><a href="commands/make-pin.html">make-pin</a></td>
<td>Given a set of search results files, generate a pin file for input to
<code>crux percolator</code></td>
</tr>
<tr>
<td><a href="commands/param-medic.html">param-medic</a></td>
<td>Examine the spectra in a file to estimate the best precursor
and fragment error tolerances for database search.</td>
</tr>
<tr>
<td>
<a href="commands/predict-peptide-ions.html">predict-peptide-ions</a></td>
<td>
Given a peptide and a charge state, predict the m/z values of the
resulting fragment ions.</td>
</tr>
<tr>
<td>
<a href="commands/print-processed-spectra.html">print-processed-spectra</a></td>
<td>
Process spectra as for scoring xcorr and print the results to a file.</td></tr>
<tr>
<td>
<a href="commands/psm-convert.html">psm-convert</a></td>
<td>
Convert a file containing peptide-spectrum matches (PSMs) from one
format to another.</td></tr>
<tr>
<td>
<a href="commands/subtract-index.html">subtract-index</a></td>
<td>Subtract one index file from another, assuming both were generated
by tide-index.</td></tr>
<tr>
<td>
<a href="commands/localize-modification.html">localize-modification</a></td>
<td>Finds, for each peptide-spectrum match (PSM) in a given set, the most
most likely location along the peptide for a post-translational
modification (PTM). The mass of the PTM is inferred from the difference
between the spectrum neutral mass and the peptide mass.</td>
</tr>
<tr>
<td>
version</td>
<td>
Print the Crux version number to standard output, then exit.</td>
</tr>
</table>
<!-- END CONTENT -->
</div>
</div>
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<div id="centerfooter">
<div class="footerimportantlinks">
<img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
<ul>
<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>
<li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
<li><a href="release-notes.html">Release Notes</a></li>
<li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
<li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
<li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
</ul>
</div>
<div class="footerimportantlinks tutoriallinks">
<img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
<ul>
<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>
</ul>
</div>
<div id="footertext">
<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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