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<div class="title">ProteinInference </div> </div>
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<div class="textblock"><p>Computes a protein identification based on the number of identified peptides.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="4"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> ProteinInterference <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> (or other ID engines) </td><td valign="middle" align="center" rowspan="3"><a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FalseDiscoveryRate.html">FalseDiscoveryRate</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> </td></tr>
</table>
</center><dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000020">Experimental classes:</a></b></dt><dd>This TOPP-tool is not well tested and not all features might be properly implemented and tested!</dd></dl>
<p>This tool counts the peptide sequences that match a protein accession. From this count for all protein hits in the respective id run, only those proteins are accepted that have at least a given number of peptides sequences identified. The peptide identifications should be prefiltered with respect to false discovery rate and the score in general to remove bad identifications.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
ProteinInference -- Protein inference based on the number of identified peptides.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
ProteinInference <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'idXML')
-out <file>* Output file (valid formats: 'idXML')
-min_peptides_per_protein <num> Minimal number of peptides needed for a protein identification
(default: '2' min: '1')
-treat_charge_variants_separately If this flag is set, different charge variants of the same peptid
e sequence count as inidividual evidences.
-treat_modification_variants_separately If this flag is set, different modification variants of the same
peptide sequence count as individual evidences.
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool
(default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+ProteinInference</span><span class="node_description">Protein inference based on the number of identified peptides.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'ProteinInference'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_peptides_per_protein</span><span class="item_value">2</span>
<span class="item_description">Minimal number of peptides needed for a protein identification</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">treat_charge_variants_separately</span><span class="item_value">false</span>
<span class="item_description">If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">treat_modification_variants_separately</span><span class="item_value">false</span>
<span class="item_description">If this flag is set, different modification variants of the same peptide sequence count as individual evidences.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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