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xlink-assign-ions.html
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<!DOCTYPE html>
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<title>xlink-assign-ions</title>
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<!-- START CONTENT -->
<h1>xlink-assign-ions</h1>
<h2>Usage:</h2>
<p><code>crux xlink-assign-ions [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file></code></p>
<h2>Description:</h2>
Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.
<h2>Input:</h2>
<ul>
<li><code>peptide A</code> – The sequence of peptide A.</li>
<li><code>peptide B</code> – The sequence of peptide B.</li>
<li><code>pos A</code> – Position of cross-link on peptide A</li>
<li><code>pos B</code> – Position of cross-link on peptide B</li>
<li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
<li><code>charge state</code> – The charge state of the peptide.</li>
<li><code>scan number</code> – Scan number identifying the spectrum.</li>
<li><code>ms2 file</code> – File containing spectra to be searched.</li>
</ul>
<h2>Output:</h2>
<ul>
<li><code>stdout</code> – tab-delimited text in which each row is a peak in the observed spectrum, and the columns are <ol><li>The m/z value.</li><li>The observed intensity.</li><li>The matched intensity.</li><li>The calculated m/z value of the theoretical peak.</li><li>The mass associated with the observed peak.</li><li>The mass difference (in ppm) between the observed and theoretical peaks.</li><li>The ion type, specified as b or y, followed by the charge state in parentheses.</li><li>The amino acid sequence of the fragment.</li></li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<h3>Search parameters</h3>
<ul>
<li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
<li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
<li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.0005079</code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Input and output</h3>
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<li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
<li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
<li class="nobullet"><code>--precision <integer></code> – Set the precision for scores written to sqt and text files. Default = <code>8</code>.</li>
</ul>
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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
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Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> awards R01 GM096306 and P41 GM103533.
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