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print-processed-spectra.html
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print-processed-spectra.html
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<!DOCTYPE html>
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<title>print-processed-spectra</title>
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<!-- START CONTENT -->
<h1>print-processed-spectra</h1>
<h2>Usage:</h2>
<p><code>crux print-processed-spectra [options] <ms2 file> <output file></code></p>
<h2>Description:</h2>
<p>Pre-process each spectrum in a given file in preparation for computing XCorr. The pre-processing steps are described in detail in this paper:</p><blockquote>J. K. Eng, B. Fischer, J. Grossman and M. J. MacCoss. <a href="http://pubs.acs.org/doi/abs/10.1021/pr800420s">"A fast SEQUEST cross correlation algorithm process the peaks as for computing."</a> <em>Journal of Proteome Research</em>. 7(10):4598-4602, 2008.</blockquote><p>The output of this program is equivalent to the spectrum shown in Figure 1D of the above paper.</p>
<h2>Input:</h2>
<ul>
<li><code>ms2 file</code> – File containing spectra to be searched.</li>
<li><code>output file</code> – File where spectrum will be written.</li>
</ul>
<h2>Output:</h2>
<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
<ul>
<li><code>output file</code> – The name of the file in which the processed spectra will be printed in MS2 format.</li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<h3>print-processed-spectra options</h3>
<ul>
<li class="nobullet"><code>--stop-after remove-precursor|square-root|remove-grass|ten-bin|xcorr</code> – Stop after the specified pre-processing step. Default = <code>xcorr</code>.</li>
<li class="nobullet"><code>--output-units mz|bin</code> – Specify the output units for processed spectra. Default = <code>bin</code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Input and output</h3>
<ul>
<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>
<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>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
<li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
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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
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>
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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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