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<div class="title">PrecursorMassCorrector </div> </div>
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<div class="textblock"><p>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</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 $" src="form_91.png"/> PrecursorMassCorrector <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">- </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> (or other ID engines) </td></tr>
</table>
</center><dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000019">Experimental classes:</a></b></dt><dd>This TOPP-tool is not well tested and not all features might be properly implemented and tested!</dd></dl>
<p>This tool corrects the m/z entries of MS/MS spectra by using MS1 information. Therefore, MS1 spectra must be supplied as profile mode spectra. The isotope distribution of the peptide in the MS1 level information are then used to determine the exact position of the monoisotopic peak. If no isotope distribution can be found the original entry is kept. As a side effect of determining the exact position of the monoisotopic peak is that the charge state is also annotated.</p>
<p>This implementation uses the isotopewavelet featurefinder and sets the monoisotopic peak (and the charge) to the nearest feature.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PrecursorMassCorrector <options>
Options (mandatory options marked with '*'):
-in <file>* Input mzML file containing the spectra. (valid formats: 'mzML')
-out <file>* Output mzML file. (valid formats: 'mzML')
-feature_in <file> Input featureXML file, containing features; if set, the MS/MS spectr
a precursor entries
will be matched to the feature m/z values if possible. (valid forma
ts: 'featureXML')
-precursor_mass_tolerance <tolerance> Maximal deviation in Th which is acceptable to be corrected;
this value should be set to the instruments selection window. (defa
ult: '1.5' min: '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 (defa
ult: '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">+PrecursorMassCorrector</span><span class="node_description">Corrects the precursor entries of MS/MS spectra, by using MS1 information.</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 'PrecursorMassCorrector'</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 mzML file containing the spectra.</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>
<span class="item_description">Output mzML file.</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">feature_in</span><span class="item_value"></span>
<span class="item_description">Input featureXML file, containing features; if set, the MS/MS spectra precursor entries <br>will be matched to the feature m/z values if possible.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_mass_tolerance</span><span class="item_value">1.5</span>
<span class="item_description">Maximal deviation in Th which is acceptable to be corrected;<br>this value should be set to the instruments selection window.</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:24px;">max_charge</span><span class="item_value">3</span>
<span class="item_description">Maximal charge that should be assumed for precursor peaks</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;">intensity_threshold</span><span class="item_value">-1</span>
<span class="item_description">Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details.</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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