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<div class="title">PeakPickerWavelet </div> </div>
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<div class="textblock"><p>A tool for peak detection in profile data. Executes the peak picking with the algorithm described in described in Lange et al. (2006) Proc. PSB-06. </p>
<center></center><center><table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="4"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> PeakPickerWavelet <img class="formulaInl" alt="$ \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> The conversion of the ''raw'' ion count data acquired by the machine into peak lists for further processing is usually called peak picking. 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 data whereas in case of low-resoluted data the <a class="el" href="classOpenMS_1_1PeakPickerCWT.html">wavelet</a> algorithm offers the ability to resolve highly convoluted and asymmetric signals, separation of overlapping peaks and nonlinear optimization.</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">
PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PeakPickerWavelet <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">+PeakPickerWavelet</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 'PeakPickerWavelet'</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;">write_peak_meta_data</span><span class="item_value">false</span>
<span class="item_description">Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file.Attention: this can blow up files,as 7 arrays are stored per spectrum!</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;">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.</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;">centroid_percentage</span><span class="item_value">0.8</span>
<span class="item_description">Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">peak_width</span><span class="item_value">0.15</span>
<span class="item_description">Approximate fwhm of the peaks.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">estimate_peak_width</span><span class="item_value">false</span>
<span class="item_description">Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored.</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;">fwhm_lower_bound_factor</span><span class="item_value">0.7</span>
<span class="item_description">Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded.</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;">fwhm_upper_bound_factor</span><span class="item_value">20</span>
<span class="item_description">Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded.</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;">optimization</span><span class="item_value">no</span>
<span class="item_description">If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional.</span><span class="item_tags"></span><span class="item_restrictions">no,one_dimensional,two_dimensional</span></div> <div class="node"><span class="node_name">++++thresholds</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">peak_bound</span><span class="item_value">10</span>
<span class="item_description">Minimal peak intensity.</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:40px;">peak_bound_ms2_level</span><span class="item_value">10</span>
<span class="item_description">Minimal peak intensity for MS/MS peaks.</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:40px;">correlation</span><span class="item_value">0.5</span>
<span class="item_description">minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">noise_level</span><span class="item_value">0.1</span>
<span class="item_description">noise level for the search of the peak endpoints.</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:40px;">search_radius</span><span class="item_value">3</span>
<span class="item_description">search radius for the search of the maximum in the signal after a maximum in the cwt was found</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++wavelet_transform</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">spacing</span><span class="item_value">0.001</span>
<span class="item_description">spacing of the cwt.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++optimization</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">iterations</span><span class="item_value">15</span>
<span class="item_description">maximal number of iterations for the fitting step</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:40px;">delta_abs_error</span><span class="item_value">9.99999974737875e-05</span>
<span class="item_description">if the absolute error gets smaller than this value the fitting is stopped.</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:40px;">delta_rel_error</span><span class="item_value">9.99999974737875e-05</span>
<span class="item_description">if the relative error gets smaller than this value the fitting is stopped</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">+++++penalties</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:48px;">position</span><span class="item_value">0</span>
<span class="item_description">penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized </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:48px;">left_width</span><span class="item_value">1</span>
<span class="item_description">penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized.</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:48px;">right_width</span><span class="item_value">1</span>
<span class="item_description">penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized.</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:48px;">height</span><span class="item_value">1</span>
<span class="item_description">penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">+++++2d</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:48px;">tolerance_mz</span><span class="item_value">2.2</span>
<span class="item_description">mz tolerance for cluster construction</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:48px;">max_peak_distance</span><span class="item_value">1.2</span>
<span class="item_description">maximal peak distance in mz in a cluster</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++deconvolution</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">deconvolution</span><span class="item_value">false</span>
<span class="item_description">If you want heavily overlapping peaks to be separated set this value to "true"</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;">asym_threshold</span><span class="item_value">0.3</span>
<span class="item_description">If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.</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:40px;">left_width</span><span class="item_value">2</span>
<span class="item_description">1/left_width is the initial value for the left width of the peaks found in the deconvolution step.</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:40px;">right_width</span><span class="item_value">2</span>
<span class="item_description">1/right_width is the initial value for the right width of the peaks found in the deconvolution step.</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:40px;">scaling</span><span class="item_value">0.12</span>
<span class="item_description">Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">+++++fitting</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:48px;">fwhm_threshold</span><span class="item_value">0.7</span>
<span class="item_description">If the fwhm of a peak is higher than fwhm_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.</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:48px;">eps_abs</span><span class="item_value">9.99999974737875e-06</span>
<span class="item_description">if the absolute error gets smaller than this value the fitting is stopped.</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:48px;">eps_rel</span><span class="item_value">9.99999974737875e-06</span>
<span class="item_description">if the relative error gets smaller than this value the fitting is stopped.</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:48px;">max_iteration</span><span class="item_value">10</span>
<span class="item_description">maximal number of iterations for the fitting step</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="node"><span class="node_name">++++++penalties</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:56px;">position</span><span class="item_value">0</span>
<span class="item_description">penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.</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:56px;">height</span><span class="item_value">1</span>
<span class="item_description">penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.</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:56px;">left_width</span><span class="item_value">0</span>
<span class="item_description">penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.</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:56px;">right_width</span><span class="item_value">0</span>
<span class="item_description">penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++SignalToNoiseEstimationParameter</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">max_intensity</span><span class="item_value">-1</span>
<span class="item_description">maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime).</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:40px;">auto_max_stdev_factor</span><span class="item_value">3</span>
<span class="item_description">parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev</span><span class="item_tags"></span><span class="item_restrictions">0:999</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">auto_max_percentile</span><span class="item_value">95</span>
<span class="item_description">parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">auto_mode</span><span class="item_value">0</span>
<span class="item_description">method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method</span><span class="item_tags"></span><span class="item_restrictions">-1:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">win_len</span><span class="item_value">200</span>
<span class="item_description">window length in Thomson</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:40px;">bin_count</span><span class="item_value">30</span>
<span class="item_description">number of bins for intensity values</span><span class="item_tags"></span><span class="item_restrictions">3:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">stdev_mp</span><span class="item_value">3</span>
<span class="item_description">multiplier for stdev</span><span class="item_tags"></span><span class="item_restrictions">0.01:999</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">min_required_elements</span><span class="item_value">10</span>
<span class="item_description">minimum number of elements required in a window (otherwise it is considered sparse)</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:40px;">noise_for_empty_window</span><span class="item_value">1e+20</span>
<span class="item_description">noise value used for sparse windows</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<p>For the parameters of the algorithm section see the algorithm documentation: <br/>
<a class="el" href="classOpenMS_1_1PeakPickerCWT.html">PeakPickerCWT</a> <br/>
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>
<table class="doxtable">
<tr bgcolor="#EBEBEB">
<td>  </td><td><b>Q-TOF</b> </td><td><b>LTQ Orbitrap</b> </td></tr>
<tr>
<td bgcolor="#EBEBEB"><b>signal_to_noise</b> </td><td>2 </td><td>0 </td></tr>
<tr>
<td bgcolor="#EBEBEB"><b>peak_width ("wavelet" only)</b> </td><td>0.1 </td><td>0.012 </td></tr>
</table>
<p>In order to impove the results of the peak detection on low resolution data <a class="el" href="TOPP_NoiseFilterSGolay.html">NoiseFilterSGolay</a> or <a class="el" href="TOPP_NoiseFilterGaussian.html">NoiseFilterGaussian</a> and <a class="el" href="TOPP_BaselineFilter.html">BaselineFilter</a> can be applied. For high resolution data this is not necessary. </p>
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
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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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