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<div class="title">EICExtractor </div> </div>
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<div class="textblock"><p>Extracts EICs from an MS experiment, in order to quantify analytes at a given position</p>
<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 $" src="form_91.png"/> EICExtractor <img class="formulaInl" alt="$ \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_FileConverter.html">FileConverter</a> </td><td valign="middle" align="center" rowspan="1">statistical tools, e.g., Excel, R, ... </td></tr>
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</center><p>Use this instead of FeatureFinder, if you have bad features which are not recognized (much noise etc) or if you want to quantify non-peptides.</p>
<p>The EDTA file will specify where to search for signal. Retention time is in seconds [s]. 'int' and 'charge' are ignored but need to be present. However, you MUST specify a 'rank' column. Rows with equal rank are summed up in intensity (e.g. useful if you have charge variants you want to sum up to enhance quantitation robustness). Each rank represents a so called Master Compound, which constists of one or more sub compounds. If you do not require ranks, give each row a unique number, e.g. start numbering from 1 to n.</p>
<p>The intensity reported is the MAXIMUM intensity of all peaks each within the given tolerances for this row's position.</p>
<p>Example:<br/>
</p>
<pre>
RT m/z int charge rank
19.2 431.8599024 0 0 1
21 678.7729237 0 0 2
25 660.7629237 0 0 2
59.2 431.8599024 0 0 3
</pre><p>Here, rows 2 and 3 will be summed up, as they have the same rank.</p>
<p>As output, two files in text format are given. The detail file gives RT and m/z deltas from expected to identified signal position etc, the sum file represents the master compounds.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
EICExtractor -- Extracts intensities from dedicates positions in a LC/MS map
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
EICExtractor <options>
Options (mandatory options marked with '*'):
-in <file>* Input raw data file (valid formats: 'mzML')
-pos <file>* Input config file stating where to find signal (valid formats: 'edta')
-rt_tol RT tolerance in [s] for finding max peak (whole RT range around RT middle) (default:
'3')
-mz_tol M/z tolerance in [ppm] for finding a peak (default: '10')
-rt_collect # of scans up & down in RT from highest point for ppm estimation in result (default:
'1')
-out <file>* Output quantitation file (summed intensities by master compounds) (valid formats: 'txt
')
-out_detail <file>* Output quantitation file (valid formats: 'txt')
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">+EICExtractor</span><span class="node_description">Extracts intensities from dedicates positions in a LC/MS map</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 'EICExtractor'</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 raw data 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;">pos</span><span class="item_value"></span>
<span class="item_description">Input config file stating where to find signal</span><span class="item_tags">input file</span><span class="item_restrictions">*.edta</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_tol</span><span class="item_value">3</span>
<span class="item_description">RT tolerance in [s] for finding max peak (whole RT range around RT middle)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mz_tol</span><span class="item_value">10</span>
<span class="item_description">m/z tolerance in [ppm] for finding a peak</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_collect</span><span class="item_value">1</span>
<span class="item_description"># of scans up & down in RT from highest point for ppm estimation in result</span><span class="item_tags"></span><span class="item_restrictions"> </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 quantitation file (summed intensities by master compounds)</span><span class="item_tags">output file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out_detail</span><span class="item_value"></span>
<span class="item_description">Output quantitation file</span><span class="item_tags">output file</span><span class="item_restrictions">*.txt</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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