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<div class="title">InspectAdapter </div> </div>
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<div class="textblock"><p>Identifies peptides in MS/MS spectra via Inspect.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> InspectAdapter <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">any signal-/preprocessing tool <br/>
(in mzML format) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> or <br/>
any protein/peptide processing tool </td></tr>
</table>
</center><dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000012">Experimental classes:</a></b></dt><dd>This tool has not been tested thoroughly and might behave not as expected!</dd></dl>
<p>This wrapper application serves for getting peptide peptide_identifications for MS/MS spectra. The wrapper can be executed in three different modes: </p>
<ol>
<li>
<p class="startli">The whole process of ProteinIdentification via Inspect is executed. Inputfile is an mz file containing the MS/MS spectra (Supported spectrum file formats are .mzXML, .mzData) for which the identifications are to be found and one ore more databases in either trie, FASTA or Swissprot format containing the possible proteins. The given databases are converted and merged into one trie database. This is done because Inspect does the conversion anyway (though with a bug) and may actually not use more than two databases (one of them in trie format). Additionally you thus can reuse the database without having Inspect done the conversion every time. The drawback is, of course, that you need the same amount of space for the trie database as well, which can, in case of large and/or many databases, be a problem. The results are written as a idXML output file. This mode is selected by default. </p>
<p class="endli"></p>
</li>
<li>
<p class="startli">Only the first part of the ProteinIdentification process is performed. This means that an Inspect input file is generated and the given databases are converted and merged into one trie database. This file can be used directly with Inspect whereas the created database and the spectrum file(s) have to remain at the given positions. Calling an Inspect process should look like the following:</p>
<div class="fragment"><div class="line">./inspect -i inputfilename -o outputfilename </div>
</div><!-- fragment --><p>Consult your Inspect reference manual for further details.</p>
<p>This mode is selected by the <b>-inspect_in</b> option in the command line. </p>
<p class="endli"></p>
</li>
<li>
<p class="startli">Only the second part of the ProteinIdentification process is performed. This means that the output of an Inspect run is analyzed and the result written to an idXML file.</p>
<p class="endli">This mode is selected by the <b>-inspect_out</b> option in the command line. </p>
</li>
</ol>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
InspectAdapter -- Annotates MS/MS spectra using Inspect.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
InspectAdapter <options>
Options (mandatory options marked with '*'):
-in <file>* Input file in mzXML or mzData format.
Note: In mode 'inspect_out' an Inspect results file is read. (valid forma
ts: 'mzXML', 'mzData')
-out <file>* Output file in idXML format.
Note: In mode 'inspect_in' an Inspect input file is written. (valid forma
ts: 'idXML')
-inspect_in If this flag is set the InspectAdapter will read in mzXML,
write an Inspect input file and generate a trie database
-inspect_out If this flag is set the InspectAdapter will read in a Inspect results file
and write idXML
-inspect_directory <dir> The directory in which Inspect is located
-temp_data_directory <dir> A directory in which some temporary files can be stored
-dbs <file> Name(s) of database(s) to search in (FASTA and SwissProt supported)
-trie_dbs <file> Name(s) of databases(s) to search in (trie-format)
-new_db <file> Name of the merged trie database
-instrument <i> The instrument that was used to measure the spectra
(If set to QTOF, uses a QTOF-derived fragmentation model,
and does not attempt to correct the parent mass.) (valid: 'ESI-ION-TRAP',
'QTOF', 'FT-Hybrid')
-precursor_mass_tolerance <tol> The precursor mass tolerance (default: '2')
-peak_mass_tolerance <tol> The peak mass tolerance (default: '1')
-list_modifications Show a list of the available modifications
-modifications <mods> The colon-separated modifications; may be
<name>,<type>, e.g.: Deamidation,opt or
<composition>,<residues>,<type>,<name>, e.g.: H2C2O,KCS,opt,Acetyl or
<mass>,<residues>,<type>,<name>, e.g.: 42.0367,KCS,opt,Acetyl or
Valid values for type are "fix" and "opt" (default)
If you want terminal PTMs, write "cterm" or "nterm" instead of residues
-use_monoisotopic_mod_mass Use monoisotopic masses for the modifications
-modifications_xml_file <file> Name of an XML file with the modifications
-cleavage <enz> The enzyme used for digestion (default: 'Trypsin')
-inspect_output <file> Name for the output file of Inspect (may only be used in a full run)
-inspect_input <file> Name for the input file of Inspect (may only be used in a full run)
-multicharge Attempt to guess the precursor charge and mass,
and consider multiple charge states if feasible
-max_modifications_pp <num> Number of PTMs permitted in a single peptide. (default: '-1')
-tag_count <num> Number of tags to generate (default: '-1')
-no_tmp_dbs No temporary databases are used
-p_value <prob> Annotations with inferior p-value are ignored (default: '1')
Options for blind search:
-blind:blind Perform a blind search (allowing arbitrary modification masses),
is preceeded by a normal search to gain a smaller database.
(in full mode only)
-blind:blind_only Like blind but no prior search is performed to reduce the database size
-blind:p_value_blind <prob> Used for generating the minimized database (default: '1')
-blind:snd_db <file> Name of the minimized trie database generated when using blind mode.
-blind:max_ptm_size <num> Maximum modification size (in Da) to consider (default: '250')
-contact_name <name> Name of the contact (default: 'unknown')
-contact_institution <name> Name of the contact institution (default: 'unknown')
-contact_info <info> Some information about the contact (default: 'unknown')
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>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">+InspectAdapter</span><span class="node_description">Annotates MS/MS spectra using Inspect.</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 'InspectAdapter'</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 in mzXML or mzData format.<br>Note: In mode 'inspect_out' an Inspect results file is read.</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzXML,*.mzData</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 in idXML format.<br>Note: In mode 'inspect_in' an Inspect input file is written.</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">inspect_in</span><span class="item_value">false</span>
<span class="item_description">if this flag is set the InspectAdapter will read in mzXML,<br>write an Inspect input file and generate a trie database</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;">inspect_out</span><span class="item_value">false</span>
<span class="item_description">if this flag is set the InspectAdapter will read in a Inspect results file<br>and write idXML</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;">inspect_directory</span><span class="item_value"></span>
<span class="item_description">the directory in which Inspect is located</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">temp_data_directory</span><span class="item_value"></span>
<span class="item_description">a directory in which some temporary files can be stored</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">dbs</span><span class="item_value"></span>
<span class="item_description">name(s) of database(s) to search in (FASTA and SwissProt supported)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">trie_dbs</span><span class="item_value"></span>
<span class="item_description">name(s) of databases(s) to search in (trie-format)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">new_db</span><span class="item_value"></span>
<span class="item_description">name of the merged trie database</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">instrument</span><span class="item_value"></span>
<span class="item_description">the instrument that was used to measure the spectra<br>(If set to QTOF, uses a QTOF-derived fragmentation model,<br>and does not attempt to correct the parent mass.)</span><span class="item_tags"></span><span class="item_restrictions">ESI-ION-TRAP,QTOF,FT-Hybrid</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_mass_tolerance</span><span class="item_value">2</span>
<span class="item_description">the precursor mass tolerance</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">peak_mass_tolerance</span><span class="item_value">1</span>
<span class="item_description">the peak mass tolerance</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">list_modifications</span><span class="item_value">false</span>
<span class="item_description">show a list of the available modifications</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;">modifications</span><span class="item_value"></span>
<span class="item_description">the colon-separated modifications; may be<br><name>,<type>, e.g.: Deamidation,opt or<br><composition>,<residues>,<type>,<name>, e.g.: H2C2O,KCS,opt,Acetyl or<br><mass>,<residues>,<type>,<name>, e.g.: 42.0367,KCS,opt,Acetyl or<br>Valid values for type are "fix" and "opt" (default)<br>If you want terminal PTMs, write "cterm" or "nterm" instead of residues</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">use_monoisotopic_mod_mass</span><span class="item_value">false</span>
<span class="item_description">use monoisotopic masses for the modifications</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;">modifications_xml_file</span><span class="item_value"></span>
<span class="item_description">name of an XML file with the modifications</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">cleavage</span><span class="item_value">Trypsin</span>
<span class="item_description">the enzyme used for digestion</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">inspect_output</span><span class="item_value"></span>
<span class="item_description">name for the output file of Inspect (may only be used in a full run)</span><span class="item_tags">output file</span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">inspect_input</span><span class="item_value"></span>
<span class="item_description">name for the input file of Inspect (may only be used in a full run)</span><span class="item_tags">input file</span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">multicharge</span><span class="item_value">false</span>
<span class="item_description">attempt to guess the precursor charge and mass,<br>and consider multiple charge states if feasible</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;">max_modifications_pp</span><span class="item_value">-1</span>
<span class="item_description">number of PTMs permitted in a single peptide.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">tag_count</span><span class="item_value">-1</span>
<span class="item_description">number of tags to generate</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">no_tmp_dbs</span><span class="item_value">false</span>
<span class="item_description">no temporary databases are used</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;">p_value</span><span class="item_value">1</span>
<span class="item_description">annotations with inferior p-value are ignored</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">contact_name</span><span class="item_value">unknown</span>
<span class="item_description">Name of the contact</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">contact_institution</span><span class="item_value">unknown</span>
<span class="item_description">Name of the contact institution</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">contact_info</span><span class="item_value">unknown</span>
<span class="item_description">Some information about the contact</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">+++blind</span><span class="node_description">Options for blind search</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">blind</span><span class="item_value">false</span>
<span class="item_description">perform a blind search (allowing arbitrary modification masses),<br>is preceeded by a normal search to gain a smaller database.<br>(in full mode only)</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;">blind_only</span><span class="item_value">false</span>
<span class="item_description">like blind but no prior search is performed to reduce the database size</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;">p_value_blind</span><span class="item_value">1</span>
<span class="item_description">used for generating the minimized database</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">snd_db</span><span class="item_value"></span>
<span class="item_description">name of the minimized trie database generated when using blind mode.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">max_ptm_size</span><span class="item_value">250</span>
<span class="item_description">maximum modification size (in Da) to consider</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000032">Todo:</a></b></dt><dd>rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ...</dd></dl>
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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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