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<div class="title">OpenSwathChromatogramExtractor </div> </div>
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<div class="textblock"><p>Extracts chromatograms (XICs) from a file containing spectra.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> OpenSwathChromatogramExtractor <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FileFilter.html">FileFilter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathAnalyzer.html">OpenSwathAnalyzer</a> </td></tr>
</table>
</center><p>This module extracts ion traces (extracted ion chromatograms or XICs) from a file containing spectra. The masses at which the chromatograms should be extracted are stored in a TraML file and the result is stored in a mzML file holding chromatograms. This tool is designed to extract chromatogams from SWATH (data independent acquisition) data (see ref[1]), thus it will extract the masses found in the product ion section of the TraML transitions, returning as many chromatograms as input transitions were provided.</p>
<p>For SWATH data, the "is_swath" flag which will check the precursor isolation window of the first scan and assume all scans in that file were recorded with this precursor window (thus making it necessary to provide one input file per SWATH window). The module will then only extract transitions whose precursors fall into the corresponding isolation window.</p>
<p>For the extraction method, two convolution functions are available: top-hat and bartlett. While top-hat will just sum up the signal within a quadratic window, bartlett will weigh the signal in the center of the window more than the signal on the edge.</p>
<p>[1] Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. <br/>
<a href="http://dx.doi.org/10.1074/mcp.O111.016717">Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. </a> <br/>
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
OpenSwathChromatogramExtractor -- Extract chromatograms (XIC) from a MS2 map file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
OpenSwathChromatogramExtractor <options>
Options (mandatory options marked with '*'):
-in <files>* Input files separated by blank (valid formats: 'mzML')
-tr <file>* Transition file ('TraML' or 'csv') (valid formats: 'csv', 'traML')
-rt_norm <file> RT normalization file (how to map the RTs of this run to the ones stored
in the library) (valid formats: 'trafoXML')
-out <file>* Output file (valid formats: 'mzML')
-min_upper_edge_dist <double> Minimal distance to the edge to still consider a precursor, in Thomson
(default: '0')
-extraction_window <double> Extraction window used (in Thomson, to use ppm see -ppm flag) (default:
'0.05' min: '0')
-rt_extraction_window <double> Only extract RT around this value (-1 means extract over the whole range,
a value of 500 means to extract around +/- 500 s of the expected elution
). (default: '-1')
-is_swath Set this flag if the data is SWATH data
-ppm Extraction_window is in ppm
-extraction_function <name> Function used to extract the signal (default: 'tophat' valid: 'tophat',
'bartlett')
Options to control the modeling of retention time transformations from data:
-model:type <name> Type of model (default: 'linear' valid: 'linear', 'b_spline', 'interpolat
ed')
-model:symmetric_regression Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y +
x', instead of on 'y' vs. 'x'.
-model:num_breakpoints <number> Only for 'b_spline' model: Number of breakpoints of the cubic spline in
the smoothing step. The breakpoints are spaced uniformly on the retention
time interval. More breakpoints mean less smoothing. Reduce this number
if the transformation has an unexpected shape. (default: '5' min: '2')
-model:interpolation_type <name> Only for 'interpolated' model: Type of interpolation to apply. (default:
'cspline')
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>The algorithm parameters for the Analyzer filter are:</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">+OpenSwathChromatogramExtractor</span><span class="node_description">Extract chromatograms (XIC) from a MS2 map file.</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 'OpenSwathChromatogramExtractor'</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 files separated by blank</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;">tr</span><span class="item_value"></span>
<span class="item_description">transition file ('TraML' or 'csv')</span><span class="item_tags">input file</span><span class="item_restrictions">*.csv,*.traML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_norm</span><span class="item_value"></span>
<span class="item_description">RT normalization file (how to map the RTs of this run to the ones stored in the library)</span><span class="item_tags">input file</span><span class="item_restrictions">*.trafoXML</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 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;">min_upper_edge_dist</span><span class="item_value">0</span>
<span class="item_description">Minimal distance to the edge to still consider a precursor, in Thomson</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">extraction_window</span><span class="item_value">0.05</span>
<span class="item_description">Extraction window used (in Thomson, to use ppm see -ppm flag)</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_extraction_window</span><span class="item_value">-1</span>
<span class="item_description">Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">is_swath</span><span class="item_value">false</span>
<span class="item_description">Set this flag if the data is SWATH data</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">ppm</span><span class="item_value">false</span>
<span class="item_description">extraction_window is in ppm</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">extraction_function</span><span class="item_value">tophat</span>
<span class="item_description">Function used to extract the signal</span><span class="item_tags"></span><span class="item_restrictions">tophat,bartlett</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">+++model</span><span class="node_description">Options to control the modeling of retention time transformations from data</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">type</span><span class="item_value">linear</span>
<span class="item_description">Type of model</span><span class="item_tags"></span><span class="item_restrictions">linear,b_spline,interpolated</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">symmetric_regression</span><span class="item_value">false</span>
<span class="item_description">Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">num_breakpoints</span><span class="item_value">5</span>
<span class="item_description">Only for 'b_spline' model: Number of breakpoints of the cubic spline in the smoothing step. The breakpoints are spaced uniformly on the retention time interval. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.</span><span class="item_tags"></span><span class="item_restrictions">2:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">interpolation_type</span><span class="item_value">cspline</span>
<span class="item_description">Only for 'interpolated' model: Type of interpolation to apply.</span><span class="item_tags"></span><span class="item_restrictions"> </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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