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<div class="title">Decharger </div> </div>
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<div class="textblock"><p>Decharges a feature map by clustering charge variants of a peptide to zero-charge entities. </p>
<center></center><center><table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> Decharger <img class="formulaInl" alt="$ \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_FeatureFinderCentroided.html">FeatureFinderCentroided</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_ProteinQuantifier.html">ProteinQuantifier</a> </td></tr>
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</center><p>The Decharger uses an ILP approach to group charge variants of the same peptide, which usually occur in ESI ionization mode. The resulting zero-charge peptides, which are defined by RT and mass, are written to consensusXML. Intensities of charge variants are summed up. The position of the zero charge variant is the average of all clustered peptides in each dimension (m/z and RT). It is also possible to include adducted species to the charge ladders (see 'potential_adducts' parameter). Via this mechanism it is also possible to use this tool to find pairs/triples/quadruples/... in labeled data (by specifing the mass tag weight as an adduct). If mass tags induce an RT shift (e.g. deuterium labeled data) you can also specify this also in the adduct list. This will allow to tighten the RT search window, thus reducing false positive results.</p>
<p>This tool is described in the following publication:</p>
<p>Bielow C, Ruzek S, Huber CG, Reinert K. Optimal decharging and clustering of charge ladders generated in ESI-MS. J Proteome Res 2010; 9: 2688.<br/>
DOI: 10.1021/pr100177k</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
Decharger -- Decharges and merges different feature charge variants of the same peptide.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
Decharger <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>* Input file (valid formats: 'featureXML')
-out_cm <file>* Output consensus map (valid formats: 'consensusXML')
-out_fm <file> Output feature map (valid formats: 'featureXML')
-outpairs <file> Output file (valid formats: 'consensusXML')
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 Feature decharging algorithm section
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">+Decharger</span><span class="node_description">Decharges and merges different feature charge variants of the same peptide.</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 'Decharger'</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">*.featureXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out_cm</span><span class="item_value"></span>
<span class="item_description">output consensus map</span><span class="item_tags">output file</span><span class="item_restrictions">*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_fm</span><span class="item_value"></span>
<span class="item_description">output feature map</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;">outpairs</span><span class="item_value"></span>
<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.consensusXML</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">Feature decharging algorithm section</span></div>
<div class="node"><span class="node_name">++++FeatureDeconvolution</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">charge_min</span><span class="item_value">1</span>
<span class="item_description">Minimal possible charge</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">charge_max</span><span class="item_value">10</span>
<span class="item_description">Maximal possible charge</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">charge_span_max</span><span class="item_value">4</span>
<span class="item_description">Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">q_try</span><span class="item_value">feature</span>
<span class="item_description">Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').</span><span class="item_tags"></span><span class="item_restrictions">feature,heuristic,all</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">retention_max_diff</span><span class="item_value">1</span>
<span class="item_description">Maximum allowed RT difference between any two features if their relation shall be determined</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">retention_max_diff_local</span><span class="item_value">1</span>
<span class="item_description">Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">mass_max_diff</span><span class="item_value">0.5</span>
<span class="item_description">Maximum allowed mass difference [in Th] for a single feature.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">potential_adducts</span><span class="item_value">[H+:0.9]</span>
<span class="item_description">Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge, e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">max_neutrals</span><span class="item_value">0</span>
<span class="item_description">Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">max_minority_bound</span><span class="item_value">2</span>
<span class="item_description">Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant. E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct</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_rt_overlap</span><span class="item_value">0.66</span>
<span class="item_description">Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)</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;">intensity_filter</span><span class="item_value">false</span>
<span class="item_description">Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.</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:40px;">default_map_label</span><span class="item_value">decharged features</span>
<span class="item_description">Label of map in output consensus file where all features are put by default</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">verbose_level</span><span class="item_value">0</span>
<span class="item_description">Amount of debug information given during processing.</span><span class="item_tags"></span><span class="item_restrictions">0:3</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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