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mstoolkit.html
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<!DOCTYPE html>
<html>
<head>
<title>MSToolKit</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="stylesheet" type="text/css" href="styles.css">
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-26136956-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
<script type="text/javascript">
// Main Menu
$( document ).ready(function() {
var pull = $('.btn');
menu = $('nav ul');
menuHeight = menu.height();
$(pull).on('click', function(e) {
e.preventDefault();
menu.slideToggle();
});
$(window).resize(function(){
var w = $(window).width();
if(w > 320 && menu.is(':hidden')) {
menu.removeAttr('style');
}
});
});
</script>
</head>
<body>
<div class="page-wrap">
<nav>
<div class="btn">
</div>
<img src="images/crux-logo.png" id="logo"></a>
<ul id="navitems">
<li><a href="index.html">Home</a></li>
<li><a href="download.html">Download</a></li>
<li><a href="fileformats.html">File Formats</a></li>
<li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
</ul>
</nav>
<div id="content">
<!-- START CONTENT -->
<h2>MSToolkit</h2>
<p>
MSToolkit is a library for handling mass spectrometry data in various file
formats. Crux is capable of using MSToolkit to parse spectrum files. The
ProteoWizard parser is used by default, but the MSToolkit parser can be used by
commands that support the <span class="code">spectrum-parser</span> parameter.
</p>
<p>
The following is a list of spectrum file formats supported by MSToolkit.
</p>
<ul>
<li>MS1/CMS1/BMS1</li>
<li><a href="file-formats/ms2-format.html">MS2</a>/CMS2/BMS2</li>
<li>ZS</li>
<li>UZS</li>
<li>MSMAT</li>
<li>RAW</li>
<li><a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">MZXML[.GZ]</a></li>
<li>MZ5</li>
<li><a href="http://www.psidev.info/mzml_1_0_0">MZML[.GZ]</a></li>
<li><a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a> (Mascot Generic Format)</li>
<li>SQLITE3</li>
<li>PSM</li>
</ul>
<!-- END CONTENT -->
</div>
</div>
<footer class="site-footer">
<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.
</p>
</div>
</div>
</footer>
</body>
</html>