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<div class="title">TOFCalibration </div> </div>
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<div class="textblock"><p>Performs an external calibration for tof spectra.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> TOFCalibration <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="2">- </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_InternalCalibration.html">InternalCalibration</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a> </td></tr>
</table>
</center><p>Given one or more calibrant spectra containing flight times, the instrument's calibration constants and the expected masses the quadratic function <img class="formulaInl" alt="$y_i = a + bx_i + cx_i^2$" src="form_96.png"/> is fitted, where <img class="formulaInl" alt="$x_i$" src="form_97.png"/> is the ith flight time. If there are more than one calibrant spectra the coefficients <img class="formulaInl" alt="$a$" src="form_98.png"/>, <img class="formulaInl" alt="$b$" src="form_99.png"/> and <img class="formulaInl" alt="$c$" src="form_100.png"/> are averaged. The fitted function is then used to convert the flight times of the given experiment to m/z-values.</p>
<p>You can choose to calibrate picked or raw data. If you use picked data, set the flag peak_data. If you have raw data an additional peak picking step for the calibrant spectra is needed, the parameters for the peak picker can be set in the ini-file.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
TOFCalibration -- Applies time of flight calibration.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
TOFCalibration <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 peak or raw data file (valid formats: 'mzML')
-out <file>* Output file (valid formats: 'mzML')
-ext_calibrants <file>* Input file containing the external calibrant spectra (peak or raw data)
(valid formats: 'mzML')
-ref_masses <file>* Input file containing reference masses of the external calibrant spectra (one per
line) (valid formats: 'txt')
-tof_const <file>* File containing TOF conversion constants. These can be either two or three constan
ts
per set, depending on the conversion type. Either one set for all calibrant spect
ra
(tab separated), or one for each spectrum.
For a detailed description, please have a look at the doxygen documentation.(one
set, tab separated, per line) (valid formats: 'csv')
-peak_data Set this flag, if you have peak data, not raw data (the picking parameters are
accessible only from the INI file).
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 section for peak picking
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">+TOFCalibration</span><span class="node_description">Applies time of flight calibration.</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 'TOFCalibration'</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 peak or raw 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 file </span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">ext_calibrants</span><span class="item_value"></span>
<span class="item_description">input file containing the external calibrant spectra (peak or raw data)<br></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;">ref_masses</span><span class="item_value"></span>
<span class="item_description">input file containing reference masses of the external calibrant spectra (one per line)</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">tof_const</span><span class="item_value"></span>
<span class="item_description">File containing TOF conversion constants. These can be either two or three constants<br>per set, depending on the conversion type. Either one set for all calibrant spectra <br>(tab separated), or one for each spectrum.<br>For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)</span><span class="item_tags">input file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">peak_data</span><span class="item_value">false</span>
<span class="item_description">set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file).</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 section for peak picking</span></div>
<div class="node"><span class="node_name">++++PeakPicker</span><span class="node_description"></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">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:40px;">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:40px;">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:40px;">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:40px;">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:40px;">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:40px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:56px;">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:56px;">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:56px;">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:56px;">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:56px;">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:56px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:56px;">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:56px;">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:56px;">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:56px;">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:64px;">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:64px;">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:64px;">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:64px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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:48px;">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>
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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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