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fileformats.html
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<!DOCTYPE html>
<html>
<head>
<title>Crux File Formats</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="stylesheet" type="text/css" href="styles.css">
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-V7XKGGFPYX"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-V7XKGGFPYX');
</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 -->
<div id="content">
<h2>File formats</h2>
<table id="fileFormatsTable">
<tr>
<td> </td>
<td>bullseye</td>
<td>tide-index</td>
<td>tide-search</td>
<td>comet</td>
<td>percolator</td>
<td>spectral-counts</td>
</tr>
<tr>
<td>
<a href="file-formats/ms2-format.html">MS1</a>
</td>
<td>in</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/ms2-format.html">MS2</a>
(<a href="example-files/demo.ms2">sample</a>) / CMS2
</td>
<td>in/out</td>
<td> </td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a>
</td>
<td>in/out</td>
<td> </td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://www.psidev.info/mzml_1_0_0">mzML</a>,
<a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">mzXML</a>
</td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
Thermo .raw files
(Windows only)
</td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
<td> </td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://proteowizard.sourceforge.net/formats.shtml">Other
proprietary vendor formats</a> (Windows only)
</td>
<td> </td>
<td> </td>
<td>in</td>
<td> </td>
<td> </td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/fasta-format.html">FASTA</a>
(<a href="file-formats/sample.fasta">sample</a>)
</td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
database index
</td>
<td> </td>
<td>out</td>
<td>in</td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/txt-format.html">Tab-delimited text</a>
(<a href="example-files/search.target.txt">sample</a>)
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in/out</td>
<td>in/out</td>
</tr>
<tr>
<td>
<a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">
pepXML</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in/out</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="https://github.com/percolator/percolator/wiki/Interface">PIN</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td> </td>
<td>in</td>
<td> </td>
</tr>
<tr>
<td>
<a href="https://github.com/percolator/percolator/wiki/Interface">POUT</a>
</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td>out</td>
<td> </td>
</tr>
<tr>
<td>
<a href="http://www.psidev.info/mzidentml">mzIdentML</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>out</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/sqt-format.html">SQT</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/features.html">Feature file</a>
</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td>in/out</td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/parameter-file.html">Crux parameters</a>
(<a href="example-files/default.params">sample</a>)
</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
</tr>
</table>
</div>
<!-- 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>