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<div class="title">FeatureFinderRaw </div> </div>
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<div class="textblock"><p>Identifies peptide features in raw (i.e. profile) LC-MS data.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FeatureFinderRaw <img class="formulaInl" alt="$ \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_FileConverter.html">FileConverter</a> </td><td valign="middle" align="center" rowspan="2"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FileFilter.html">FileFilter</a> </td></tr>
</table>
</center><p>FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.</p>
<p><b>Algorithm</b></p>
<p>The underlying algorithm of the tool is equivalent to that of SILACAnalyzer.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FeatureFinderRaw -- Determination of peak ratios in LC-MS data
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FeatureFinderRaw <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file>* Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided
data!) (valid formats: 'mzML')
-out <file> Set of all identified peptides. The m/z-RT positions correspond to the lightest peptide
in each group. (valid formats: 'featureXML')
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)
The following configuration subsections are valid:
- algorithm Parameters for the algorithm.
- sample Parameters describing the sample and its labels.
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
</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">+FeatureFinderRaw</span><span class="node_description">Determination of peak ratios in LC-MS data</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 'FeatureFinderRaw'</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">Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Set of all identified peptides. The m/z-RT positions correspond to the lightest peptide in each group.</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML</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 class="node"><span class="node_name">+++algorithm</span><span class="node_description">Parameters for the algorithm.</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">rt_threshold</span><span class="item_value">30</span>
<span class="item_description">Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">rt_min</span><span class="item_value">0</span>
<span class="item_description">Lower bound for the retention time [s].</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">intensity_cutoff</span><span class="item_value">1000</span>
<span class="item_description">Lower bound for the intensity of isotopic peaks in a SILAC pattern.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">intensity_correlation</span><span class="item_value">0.7</span>
<span class="item_description">Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">model_deviation</span><span class="item_value">3</span>
<span class="item_description">Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation ).</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="node"><span class="node_name">+++sample</span><span class="node_description">Parameters describing the sample and its labels.</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">charge</span><span class="item_value">2:4</span>
<span class="item_description">Range of charge states in the sample, i.e. min charge : max charge.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">peaks_per_peptide</span><span class="item_value">3:5</span>
<span class="item_description">Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. </span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<p><b>Parameter Tuning</b></p>
<p><em>input:</em></p>
<ul>
<li>in [*.mzML] - LC-MS dataset to be analyzed</li>
<li>ini [*.ini] - file containing all parameters (see discussion below)</li>
</ul>
<p><em>standard output:</em></p>
<ul>
<li>out [*.consensusXML] - contains the list of identified peptides</li>
</ul>
<p><em>optional output:</em></p>
<ul>
<li><p class="startli">out_clusters [*.consensusXML] - contains the complete set of data points passing the filters</p>
<p class="startli">The results of an analysis can be easily visualized within TOPPView. Simply load *.consensusXML and *.featureXML as layers over the original *.mzML.</p>
<p class="startli">Parameters in section <em>algorithm:</em></p>
</li>
<li><em>allow_missing_peaks</em> - Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Specify if such peptides should be included in the analysis.<ul>
<li><em>rt_threshold</em> - Upper bound for the retention time [s] over which a characteristic peptide elutes.</li>
<li><em>rt_min</em> - Lower bound for the retentions time [s].</li>
<li><em>intensity_cutoff</em> - Lower bound for the intensity of isotopic peaks in a SILAC pattern.</li>
<li><em>intensity_correlation</em> - Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.</li>
<li><em>model_deviation</em> - Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation ). </li>
</ul>
</li>
</ul>
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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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