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get-ms2-spectrum.html
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<!DOCTYPE html>
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<title>get-ms2-spectrum</title>
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<!-- START CONTENT -->
<h1>get-ms2-spectrum</h1>
<h2>Usage:</h2>
<p><code>crux get-ms2-spectrum [options] <ms2 file></code></p>
<h2>Description:</h2>
<p>Extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output summary statistics for each spectrum.</p>
<h2>Input:</h2>
<ul>
<li><code>ms2 file</code> – File containing spectra to be searched.</li>
</ul>
<h2>Output:</h2>
<ul>
<li><code>stdout</code> – the requested spectrum or spectra in MS2 format.</li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<h3>get-ms2-spectrum options</h3>
<ul>
<li class="nobullet"><code>--stats T|F</code> – Rather than the spectrum, output summary statistics to standard output. Each statistic is placed on a separate line, in the format <name>:<value> (e.g. "TIC:1000.0").<br>The following statistics are reported for the entire spectrum:<ul><li>Precursor m/z</li><li>Total Ion Current</li><li>Base Peak Intensity</li><li>Number of peaks</li><li>Minimum m/z</li><li>Maximum m/z</li></ul>In addition, for each possible spectrum charge state, the following statistics are reported:<ul><li>Charge state</li><li>Neutral mass</li><li>Charged mass</li><li>M+H+ mass</li></ul> Default = <code>false</code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Search parameters</h3>
<ul>
<li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
<li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Input and output</h3>
<ul>
<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>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
</ul>
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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> awards R01 GM096306 and P41 GM103533.
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