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<div class="title">PeakPickerHiRes </div> </div>
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<div class="textblock"><p>A tool for peak detection in profile data. Executes the peak picking with <a class="el" href="classOpenMS_1_1PeakPickerHiRes.html">high_res</a> algorithm.</p>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="4"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> PeakPickerHiRes <img class="formulaInl" alt="$ \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_BaselineFilter.html">BaselineFilter</a> </td><td valign="middle" align="center" rowspan="3">any tool operating on MS peak data <br/>
(in mzML format) </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_NoiseFilterGaussian.html">NoiseFilterGaussian</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_NoiseFilterSGolay.html">NoiseFilterSGolay</a> </td></tr>
</table>
</center><p>Reference:<br/>
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>
<p>The conversion of the "raw" ion count data acquired by the machine into peak lists for further processing is usually called peak picking or centroiding. The choice of the algorithm should mainly depend on the resolution of the data. As the name implies, the <a class="el" href="classOpenMS_1_1PeakPickerHiRes.html">high_res</a> algorithm is fit for high resolution (orbitrap or FTICR) data.</p>
<p><a class="el" href="TOPP_example_signalprocessing.html#TOPP_example_signalprocessing_parameters">Finding the right parameters for the</a> is explained in the TOPP tutorial.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
PeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PeakPickerHiRes <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 profile data file (valid formats: 'mzML')
-out <file>* Output peak file (valid formats: 'mzML')
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 Algorithm parameters 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">+PeakPickerHiRes</span><span class="node_description">Finds mass spectrometric peaks in profile mass spectra.</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 'PeakPickerHiRes'</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 profile 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;">out</span><span class="item_value"></span>
<span class="item_description">output peak file </span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</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">Algorithm parameters section</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">signal_to_noise</span><span class="item_value">1</span>
<span class="item_description">Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">ms1_only</span><span class="item_value">false</span>
<span class="item_description">If true, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
<p>For the parameters of the algorithm section see the algorithm documentation: <a class="el" href="classOpenMS_1_1PeakPickerHiRes.html">PeakPickerHiRes</a></p>
<p>In the following table you, can find example values of the most important algorithm parameters for different instrument types. <br/>
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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<td>  </td><td><b>Q-TOF</b> </td><td><b>LTQ Orbitrap</b> </td></tr>
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<td bgcolor="#EBEBEB"><b>signal_to_noise</b> </td><td>2 </td><td>0 </td></tr>
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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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