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<div class="title">IDMassAccuracy </div> </div>
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<div class="textblock"><p>Calculates a distribution of the mass error from given mass spectra and IDs.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
IDMassAccuracy -- Calculates a distribution of the mass error from given mass spectra and IDs.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
IDMassAccuracy <options>
Options (mandatory options marked with '*'):
-in <file list>* Input mzML file list, containing the spectra. (valid formats: 'mzML')
-id_in <file list>* Input idXML file list, containing the identifications. (valid formats
: 'idXML')
-precursor_out <file> Output file which contains the deviations from the precursors (valid
formats: 'csv')
-precursor_columns <columns> Columns which will be written to the output file (default: '[MassDiff
erence]' valid: 'MassDifference')
-precursor_error_ppm If this flag is used, the precursor mass tolerances are estimated in
ppm instead of Da.
-fragment_out <file> Output file which contains the fragment ion m/z deviations (valid
formats: 'csv')
-fragment_columns <columns> Columns which will be written to the output file (default: '[MassDiff
erence]' valid: 'MassDifference')
-fragment_error_ppm If this flag is used, the fragment mass tolerances are estimated in
ppm instead of Da.
-fragment_mass_tolerance <tolerance> Maximal fragment mass tolerance which is allowed for MS/MS spectra,
used for the calculation of matching ions. (default: '0.5')
-separator <character> Character which should be used to separate the columns in the output
files (default: ' ')
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (defau
lt: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</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">+IDMassAccuracy</span><span class="node_description">Calculates a distribution of the mass error from given mass spectra and IDs.</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 'IDMassAccuracy'</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 mzML file list, containing the spectra.</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;">id_in</span><span class="item_value">[]</span>
<span class="item_description">Input idXML file list, containing the identifications.</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_out</span><span class="item_value"></span>
<span class="item_description">Output file which contains the deviations from the precursors</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_columns</span><span class="item_value">[MassDifference]</span>
<span class="item_description">Columns which will be written to the output file</span><span class="item_tags"></span><span class="item_restrictions">MassDifference</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_error_ppm</span><span class="item_value">false</span>
<span class="item_description">If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da.</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;">fragment_out</span><span class="item_value"></span>
<span class="item_description">Output file which contains the fragment ion m/z deviations</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fragment_columns</span><span class="item_value">[MassDifference]</span>
<span class="item_description">Columns which will be written to the output file</span><span class="item_tags"></span><span class="item_restrictions">MassDifference</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fragment_error_ppm</span><span class="item_value">false</span>
<span class="item_description">If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da.</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;">fragment_mass_tolerance</span><span class="item_value">0.5</span>
<span class="item_description">Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">separator</span><span class="item_value"> </span>
<span class="item_description">character which should be used to separate the columns in the output files</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;">number_of_bins</span><span class="item_value">100</span>
<span class="item_description">Number of bins that should be used to calculate the histograms for the fitting.</span><span class="item_tags"></span><span class="item_restrictions">10:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">generate_gnuplot_scripts</span><span class="item_value">false</span>
<span class="item_description">If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots. The options 'precursor_out' and 'fragment_out' must be set to take this effect.</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>
<p>Given a number of peak maps and for each of the maps an idXML file which contains peptide identifications the theoretical masses of the identifications and the peaks of the spectra are compared. This can be done for precursor information stored in the spectra as well as for fragment information.</p>
<p>The result is a distribution of errors of experimental vs. theoretical masses. Having such distributions given the search parameters of the sequence database search can be adjusted to speed-up the identification process and to get a higher performance. </p>
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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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