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<div class="title">FeatureFinderCentroided </div> </div>
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<div class="contents">
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<div class="textblock"><p>The feature detection application for quantitation (centroided).</p>
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<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FeatureFinderCentroided <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
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<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> <br/>
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(or another feature grouping tool) </td></tr>
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<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_SeedListGenerator.html">SeedListGenerator</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MapAlignerPoseClustering.html">MapAlignerPoseClustering</a> <br/>
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(or another alignment tool) </td></tr>
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</center><p>Reference:<br/>
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Weisser <em>et al.</em>: <a href="http://dx.doi.org/10.1021/pr300992u">An automated pipeline for high-throughput label-free quantitative proteomics</a> (J. Proteome Res., 2013, PMID: 23391308).</p>
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<p>This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.</p>
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<p>The algorithm identifies pronounced regions of the data around so-called <code>seeds</code>. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions.</p>
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<p>How to find suitable parameters and details of the different algorithms implemented are described in the <a class="el" href="TOPP_example_featuredetection.html">TOPP tutorial</a>.</p>
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<p>Specialized tools are available for some experimental techniques: <a class="el" href="TOPP_SILACAnalyzer.html">SILACAnalyzer</a>, <a class="el" href="TOPP_ITRAQAnalyzer.html">ITRAQAnalyzer</a>.</p>
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<p><b>The command line parameters of this tool are:</b> </p>
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<pre class="fragment">
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FeatureFinderCentroided -- Detects two-dimensional features in LC-MS data.
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Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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FeatureFinderCentroided <options>
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This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
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on or use the --helphelp option.
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Options (mandatory options marked with '*'):
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-in <file>* Input file (valid formats: 'mzML')
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-out <file>* Output file (valid formats: 'featureXML')
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-seeds <file> User specified seed list (valid formats: 'featureXML')
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-ini <file> Use the given TOPP INI file
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-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
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-write_ini <file> Writes the default configuration file
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--helphelp Shows all options (including advanced)
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The following configuration subsections are valid:
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- algorithm Algorithm section
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You can write an example INI file using the '-write_ini' option.
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Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
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Have a look at the OpenMS documentation for more information.
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</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
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<div class="item item_required">required parameter</div>
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<div class="item item_advanced">advanced parameter</div>
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<div class="node"><span class="node_name">+FeatureFinderCentroided</span><span class="node_description">Detects two-dimensional features in LC-MS data.</span></div>
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<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
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<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 'FeatureFinderCentroided'</span></div>
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<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
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<span class="item_description">input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
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<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">seeds</span><span class="item_value"></span>
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<span class="item_description">User specified seed list</span><span class="item_tags">input 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>
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<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>
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<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>
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<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>
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<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>
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<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">Algorithm section</span></div>
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<div class="item"><span class="item_name" style="padding-left:32px;">debug</span><span class="item_value">false</span>
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<span class="item_description">When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++intensity</span><span class="node_description">Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">bins</span><span class="item_value">10</span>
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<span class="item_description">Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.<br>This parameter should be decreased, if the algorithm is used on small regions of a map.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="node"><span class="node_name">++++mass_trace</span><span class="node_description">Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">mz_tolerance</span><span class="item_value">0.03</span>
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<span class="item_description">Tolerated m/z deviation of peaks belonging to the same mass trace.<br>It should be larger than the m/z resolution of the instument.<br>This value must be smaller than that 1/charge_high!</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">min_spectra</span><span class="item_value">10</span>
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<span class="item_description">Number of spectra that have to show a similar peak mass in a mass trace.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">max_missing</span><span class="item_value">1</span>
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<span class="item_description">Number of consecutive spectra where a high mass deviation or missing peak is acceptable.<br>This parameter should be well below 'min_spectra'!</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">slope_bound</span><span class="item_value">0.1</span>
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<span class="item_description">The maximum slope of mass trace intensities when extending from the highest peak.<br>This parameter is important to seperate overlapping elution peaks.<br>It should be increased if feature elution profiles fluctuate a lot.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++isotopic_pattern</span><span class="node_description">Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">charge_low</span><span class="item_value">1</span>
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<span class="item_description">Lowest charge to search for.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">charge_high</span><span class="item_value">4</span>
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<span class="item_description">Highest charge to search for.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">mz_tolerance</span><span class="item_value">0.03</span>
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<span class="item_description">Tolerated m/z deviation from the theoretical isotopic pattern.<br>It should be larger than the m/z resolution of the instument.<br>This value must be smaller than that 1/charge_high!</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:40px;">intensity_percentage</span><span class="item_value">10</span>
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<span class="item_description">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">intensity_percentage_optional</span><span class="item_value">0.1</span>
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<span class="item_description">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">optional_fit_improvement</span><span class="item_value">2</span>
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<span class="item_description">Minimal percental improvement of isotope fit to allow leaving out an optional peak.</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">mass_window_width</span><span class="item_value">25</span>
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<span class="item_description">Window width in Dalton for precalculation of estimated isotope distributions.</span><span class="item_tags"></span><span class="item_restrictions">1:200</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">abundance_12C</span><span class="item_value">98.93</span>
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<span class="item_description">Rel. abundance of the light carbon. Modify if labeled.</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">abundance_14N</span><span class="item_value">99.632</span>
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<span class="item_description">Rel. abundance of the light nitrogen. Modify if labeled.</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="node"><span class="node_name">++++seed</span><span class="node_description">Settings that determine which peaks are considered a seed</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">min_score</span><span class="item_value">0.8</span>
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<span class="item_description">Minimum seed score a peak has to reach to be used as seed.<br>The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.<br>If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="node"><span class="node_name">++++fit</span><span class="node_description">Settings for the model fitting</span></div>
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<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">epsilon_abs</span><span class="item_value">0.0001</span>
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<span class="item_description">Absolute epsilon used for convergence of the fit.</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:40px;">epsilon_rel</span><span class="item_value">0.0001</span>
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<span class="item_description">Relative epsilon used for convergence of the fit.</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:40px;">max_iterations</span><span class="item_value">500</span>
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<span class="item_description">Maximum number of iterations of the fit.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="node"><span class="node_name">++++feature</span><span class="node_description">Settings for the features (intensity, quality assessment, ...)</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">min_score</span><span class="item_value">0.7</span>
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<span class="item_description">Feature score threshold for a feature to be reported.<br>The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">min_isotope_fit</span><span class="item_value">0.8</span>
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<span class="item_description">Minimum isotope fit of the feature before model fitting.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">min_trace_score</span><span class="item_value">0.5</span>
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<span class="item_description">Trace score threshold.<br>Traces below this threshold are removed after the model fitting.<br>This parameter is important for features that overlap in m/z dimension.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">min_rt_span</span><span class="item_value">0.333</span>
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<span class="item_description">Minimum RT span in relation to extended area that has to remain after model fitting.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">max_rt_span</span><span class="item_value">2.5</span>
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<span class="item_description">Maximum RT span in relation to extended area that the model is allowed to have.</span><span class="item_tags"></span><span class="item_restrictions">0.5:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">rt_shape</span><span class="item_value">symmetric</span>
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<span class="item_description">Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.</span><span class="item_tags"></span><span class="item_restrictions">symmetric,asymmetric</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">max_intersection</span><span class="item_value">0.35</span>
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<span class="item_description">Maximum allowed intersection of features.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">reported_mz</span><span class="item_value">monoisotopic</span>
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<span class="item_description">The mass type that is reported for features.<br>'maximum' returns the m/z value of the highest mass trace.<br>'average' returns the intensity-weighted average m/z value of all contained peaks.<br>'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.</span><span class="item_tags"></span><span class="item_restrictions">maximum,average,monoisotopic</span></div> <div class="node"><span class="node_name">++++user-seed</span><span class="node_description">Settings for user-specified seeds.</span></div>
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<div class="item"><span class="item_name" style="padding-left:40px;">rt_tolerance</span><span class="item_value">5</span>
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<span class="item_description">Allowed RT deviation of seeds from the user-specified seed position.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">mz_tolerance</span><span class="item_value">1.1</span>
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<span class="item_description">Allowed m/z deviation of seeds from the user-specified seed position.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">min_score</span><span class="item_value">0.5</span>
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<span class="item_description">Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="node"><span class="node_name">++++debug</span><span class="node_description"></span></div>
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<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">pseudo_rt_shift</span><span class="item_value">500</span>
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<span class="item_description">Pseudo RT shift used when .</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div></div>
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<p>For the parameters of the algorithm section see the algorithms documentation: <br/>
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<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">centroided</a> <br/>
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In the following table you can find example values of the most important parameters for different instrument types. <br/>
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These parameters are not valid for all instruments of that type, but can be used as a starting point for finding suitable parameters.</p>
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<p><b>'centroided' algorithm</b>: </p>
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<table class="doxtable">
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<td>  </td><td><b>Q-TOF</b> </td><td><b>LTQ Orbitrap</b> </td></tr>
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<td><b>intensity:bins</b> </td><td>10 </td><td>10 </td></tr>
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<td><b>mass_trace:mz_tolerance</b> </td><td>0.02 </td><td>0.004 </td></tr>
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<td><b>isotopic_pattern:mz_tolerance</b> </td><td>0.04 </td><td>0.005 </td></tr>
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<p>For the <em>centroided</em> algorithm centroided data is needed. In order to create centroided data from profile data use the <a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a>. </p>
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</div></div><!-- contents -->
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<TABLE width="100%" border="0">
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<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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