Commit d70a25c9 authored by Renne Thomas's avatar Renne Thomas
Browse files

undo the doc deletion

parent 5bc1c1e1
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<title>output, xsl path</title>
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<td align="left" valign="top"><h1>output, mzid</h1>
<h2>Syntax</h2>
<p>Value is "yes" or "no".</p>
<h2>Description</h2>
<p>Since the X!Tandem version PILEDRIVER (2015.04.01), it is possible to use the mzIdentML file format as output result files.
If it is set to "yes", this will produce output files with the .mzid extension.
Beware that mzIdentML files are not yet supported as input in X!TandemPipeline.
</p>
<hr align="left" width="200">
<span class="also">see also: <a href="opath.html">output, path</a>
</span>
<br><br><a href="index.html">X! TANDEM API description project</a>
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<title>spectrum, use noise suppression</title>
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<td align="left" valign="top"><h1>spectrum, use noise suppression</h1>
<h2>Syntax</h2>
<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
<h2>Notes</h2>
<ol>
<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
<li>A default value of <span class="v">no</span> is substituted if the parameter cannot be interpreted or is absent.</li>
</ol>
<h2>Description</h2>
<p>X! TANDEM uses several mechanisms to attempt to reduce the number of spectra considered in a list
of spectra. When this parameter is set to <span class="v">yes</span>, spectra that fit the pattern
of "noise" - spectra caused by the fragmentation of chemical noise peaks - are rejected without
further analysis. This feature can be very useful when dealling with large amounts of data from
automated LC/MS experiments. Some experimentation may be required to determine what settings
are appropriate for the noise detection filters (see the links below). Setting the parameter to
<span class="v">no</span> skips the noise filters and allows all spectra to be modelled.</p>
<hr align="left" width="200">
<span class="also">see also:<a href="smpmh.html">spectrum, minimum parent m+h</a> |
<a href="smp.html">spectrum, minimum peaks</a>
</span>
<br><br><a href="index.html">X! TANDEM API description project</a>
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