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<div class="title">OpenSwathAnalyzer </div> </div>
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<div class="textblock"><p>Executes a peak-picking and scoring algorithm on MRM/SRM data.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> OpenSwathAnalyzer <img class="formulaInl" alt="$ \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_OpenSwathChromatogramExtractor.html">OpenSwathChromatogramExtractor</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathFeatureXMLToTSV.html">OpenSwathFeatureXMLToTSV</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MRMMapper.html">MRMMapper</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathConfidenceScoring.html">OpenSwathConfidenceScoring</a> </td></tr>
</table>
</center><p>The idea of the MRM peak-picker is to analyze a series of chromatograms together with the associated meta information (stored in TraML format) in order to determine likely places of elution of a peptide in MRM/SRM.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
OpenSwathAnalyzer -- Picks peaks and finds features in an SRM experiment.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
OpenSwathAnalyzer <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 containing the chromatograms. (valid formats: 'mzML')
-tr <file>* Transition file (valid formats: '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: 'featureXML')
-no-strict Run in non-strict mode and allow some chromatograms to not be mapped.
-swath_files <files> [applies only if you have full MS2 spectra maps] Swath files that were used
to extract the transitions. If present, SWATH specific scoring will be used.
(valid formats: 'mzML')
-min_upper_edge_dist <double> [applies only if you have full MS2 spectra maps] Minimal distance to the
edge to still consider a precursor, in Thomson (only in SWATH) (default:
'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 (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>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">+OpenSwathAnalyzer</span><span class="node_description">Picks peaks and finds features in an SRM experiment.</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 'OpenSwathAnalyzer'</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 containing the chromatograms.</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</span><span class="item_tags">input file</span><span class="item_restrictions">*.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">*.featureXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">no-strict</span><span class="item_value">false</span>
<span class="item_description">run in non-strict mode and allow some chromatograms to not be mapped.</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;">swath_files</span><span class="item_value">[]</span>
<span class="item_description">[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions. If present, SWATH specific scoring will be used.</span><span class="item_tags">input 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">[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)</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 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 item_advanced"><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 item_advanced"><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 item_advanced"><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 item_advanced"><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 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;">stop_report_after_feature</span><span class="item_value">-1</span>
<span class="item_description">Stop reporting after feature (ordered by quality; -1 means do not stop).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">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). For this to work, the TraML input file needs to contain normalized RT values.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_normalization_factor</span><span class="item_value">1</span>
<span class="item_description">The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">quantification_cutoff</span><span class="item_value">0</span>
<span class="item_description">Cutoff below which peaks should not be used for quantification any more</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:32px;">write_convex_hull</span><span class="item_value">false</span>
<span class="item_description">Whether to write out all points of all features into the featureXML</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:32px;">add_up_spectra</span><span class="item_value">1</span>
<span class="item_description">Add up spectra around the peak apex (needs to be a non-even integer)</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">spacing_for_spectra_resampling</span><span class="item_value">0.005</span>
<span class="item_description">If spectra are to be added, use this spacing to add them up</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++TransitionGroupPicker</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">sgolay_frame_length</span><span class="item_value">15</span>
<span class="item_description">The number of subsequent data points used for smoothing.<br>This number has to be uneven. If it is not, 1 will be added.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">sgolay_polynomial_order</span><span class="item_value">3</span>
<span class="item_description">Order or the polynomial that is fitted.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">gauss_width</span><span class="item_value">50</span>
<span class="item_description">Gaussian width in seconds, estimated peak size.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">use_gauss</span><span class="item_value">true</span>
<span class="item_description">Use gauss for smoothing (other option is sgolay)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">peak_width</span><span class="item_value">40</span>
<span class="item_description">Estimated peak width in seconds.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">signal_to_noise</span><span class="item_value">1</span>
<span class="item_description">Signal to noise.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">sn_win_len</span><span class="item_value">1000</span>
<span class="item_description">Signal to noise window length.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">sn_bin_count</span><span class="item_value">30</span>
<span class="item_description">Signal to noise bin count.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">stop_after_feature</span><span class="item_value">-1</span>
<span class="item_description">Stop finding after feature (ordered by intensity; -1 means do not stop).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">stop_after_intensity_ratio</span><span class="item_value">0.0001</span>
<span class="item_description">Stop after reaching intensity ratio</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">background_subtraction</span><span class="item_value">none</span>
<span class="item_description">Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.</span><span class="item_tags"></span><span class="item_restrictions">none,smoothed,original</span></div> <div class="node"><span class="node_name">++++DIAScoring</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">dia_extraction_window</span><span class="item_value">0.05</span>
<span class="item_description">DIA extraction window in Th.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">dia_centroided</span><span class="item_value">false</span>
<span class="item_description">Use centroded DIA 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:40px;">dia_byseries_intensity_min</span><span class="item_value">300</span>
<span class="item_description">DIA b/y series minimum intensity to consider.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">dia_byseries_ppm_diff</span><span class="item_value">10</span>
<span class="item_description">DIA b/y series minimal difference in ppm to consider.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">dia_nr_isotopes</span><span class="item_value">4</span>
<span class="item_description">DIA nr of isotopes to consider.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">dia_nr_charges</span><span class="item_value">4</span>
<span class="item_description">DIA nr of charges to consider.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++EMGScoring</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">interpolation_step</span><span class="item_value">0.2</span>
<span class="item_description">Sampling rate for the interpolation of the model function.</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;">tolerance_stdev_bounding_box</span><span class="item_value">3</span>
<span class="item_description">Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.</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;">max_iteration</span><span class="item_value">500</span>
<span class="item_description">Maximum number of iterations using by Levenberg-Marquardt algorithm.</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;">deltaAbsError</span><span class="item_value">0.0001</span>
<span class="item_description">Absolute error used by the Levenberg-Marquardt algorithm.</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;">deltaRelError</span><span class="item_value">0.0001</span>
<span class="item_description">Relative error used by the Levenberg-Marquardt algorithm.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">+++++statistics</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:48px;">mean</span><span class="item_value">1</span>
<span class="item_description">Centroid position of the model.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:48px;">variance</span><span class="item_value">1</span>
<span class="item_description">Variance of the model.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++++Scores</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">use_shape_score</span><span class="item_value">true</span>
<span class="item_description">Use the shape score</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;">use_coelution_score</span><span class="item_value">true</span>
<span class="item_description">Use the coelution score</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;">use_rt_score</span><span class="item_value">true</span>
<span class="item_description">Use the retention time score</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;">use_library_score</span><span class="item_value">true</span>
<span class="item_description">Use the library score</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;">use_elution_model_score</span><span class="item_value">true</span>
<span class="item_description">Use the elution model (EMG) score</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;">use_intensity_score</span><span class="item_value">true</span>
<span class="item_description">Use the intensity score</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;">use_nr_peaks_score</span><span class="item_value">true</span>
<span class="item_description">Use the number of peaks score</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;">use_total_xic_score</span><span class="item_value">true</span>
<span class="item_description">Use the total XIC score</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;">use_sn_score</span><span class="item_value">true</span>
<span class="item_description">Use the SN (signal to noise) score</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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