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<div class="title">OpenSwathDecoyGenerator </div> </div>
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<div class="textblock"><p>Generates decoys according to different models for a specific TraML</p>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> OpenSwathDecoyGenerator <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FileFilter.html">FileFilter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathAnalyzer.html">OpenSwathAnalyzer</a> </td></tr>
</table>
</center><p>This module generates "decoy" transitions from a set of real or "target" transitions. The idea is to use the decoy transitions in a statistical scoring process to estimate the false hits in an SRM / SWATH experiment.</p>
<p>There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.</p>
<p>Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
OpenSwathDecoyGenerator -- Generates decoys according to different models for a specific TraML
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
OpenSwathDecoyGenerator <options>
Options (mandatory options marked with '*'):
-in <file>* Input file ('traML') (valid formats: 'traML')
-out <file>* Output file (valid formats: 'traML')
-method <type> Decoy generation method ('shuffle','pseudo-reverse','reverse','shift') (def
ault: 'shuffle')
-decoy_tag <type> Decoy tag (default: 'DECOY_')
-min_transitions <int> Minimal number of transitions (default: '2')
-max_transitions <int> Maximal number of transitions (default: '6')
-theoretical Set this flag if only annotated transitions should be used and be corrected
to the theoretical mz.
-mz_threshold <double> MZ threshold in Thomson for fragment ion annotation (default: '0.8')
-exclude_similar Set this flag if decoy assays with similarity of the peptide sequence to
the target assays higher than the identity_threshold should be excluded.
If similarity_threshold is over 0, decoy assays with an absolute difference
of the decoy and target product mz smaller than similarity_threshold are
further excluded.
-similarity_threshold <double> Similarity threshold for absolute difference of the product mz of target
and decoy assays for exclusion in Dalton. Suggested value: 0.05 (default:
'-1')
-append Set this flag if non-decoy TraML should be appended to the output.
-remove_CNterm_mods Set this flag to remove decoy peptides with C/N terminal modifications (may
be necessary depending on the decoy generation method).
-identity_threshold <double> Shuffle: identity threshold for the shuffle algorithm (default: '0.7')
-max_attempts <int> Shuffle: maximum attempts to lower the sequence identity between target
and decoy for the shuffle algorithm (default: '10')
-mz_shift <double> Shift: MZ shift in Thomson for shift decoy method (default: '20')
-precursor_mass_shift <double> Mass shift to apply to the precursor ion (default: '0')
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>The algorithm parameters for the Analyzer filter are:</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">+OpenSwathDecoyGenerator</span><span class="node_description">Generates decoys according to different models for a specific TraML</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 'OpenSwathDecoyGenerator'</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 ('traML')</span><span class="item_tags">input file</span><span class="item_restrictions">*.traML</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">*.traML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">method</span><span class="item_value">shuffle</span>
<span class="item_description">decoy generation method ('shuffle','pseudo-reverse','reverse','shift')</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">decoy_tag</span><span class="item_value">DECOY_</span>
<span class="item_description">decoy tag</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_transitions</span><span class="item_value">2</span>
<span class="item_description">minimal number of transitions</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_transitions</span><span class="item_value">6</span>
<span class="item_description">maximal number of transitions</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">theoretical</span><span class="item_value">false</span>
<span class="item_description">set this flag if only annotated transitions should be used and be corrected to the theoretical mz.</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;">mz_threshold</span><span class="item_value">0.8</span>
<span class="item_description">MZ threshold in Thomson for fragment ion annotation</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">exclude_similar</span><span class="item_value">false</span>
<span class="item_description">set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded. If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded.</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;">similarity_threshold</span><span class="item_value">-1</span>
<span class="item_description">Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">append</span><span class="item_value">false</span>
<span class="item_description">set this flag if non-decoy TraML should be appended to the output.</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;">remove_CNterm_mods</span><span class="item_value">false</span>
<span class="item_description">set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method).</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;">identity_threshold</span><span class="item_value">0.7</span>
<span class="item_description">shuffle: identity threshold for the shuffle algorithm</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_attempts</span><span class="item_value">10</span>
<span class="item_description">shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mz_shift</span><span class="item_value">20</span>
<span class="item_description">shift: MZ shift in Thomson for shift decoy method</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_mass_shift</span><span class="item_value">0</span>
<span class="item_description">Mass shift to apply to the precursor ion</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;">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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