Computes a consensus identification from peptide identification engines.
| potential predecessor tools | ConsensusID | potential successor tools |
| MascotAdapter (or other ID engines) | FalseDiscoveryRate | |
| IDPosteriorErrorProbability | ||
| IDMapper |
This implementation (for PEPMatrix and PEPIons) is described in
Nahnsen S, Bertsch A, Rahnenfuehrer J, Nordheim A, Kohlbacher O
Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification
Journal of Proteome Research (2011), DOI: 10.1021/pr2002879
The input file can contain several searches, e.g., from several identification engines. In order to use the PEPMatrix or the PEPIons algorithm, posterior error probabilities (PEPs) need to be calculated using the IDPosteriorErrorProbability tool for all individual search engines. After PEP calculation, the different search engine results have to be combined using IDMerger. Identification runs can be mapped to featureXML and consensusXML with the IDMapper tool. The merged file can now be fed into into the ConsensusID tool. For the statistical assessment of the results it is recommended to use target-decoy databases for peptide identifications. The false discovery rates (FDRs) can be calculated using the FalseDiscoveryRate tool.
The command line parameters of this tool are:
ConsensusID -- Computes a consensus identification from peptide identifications of several identification
engines.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
ConsensusID <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 (valid formats: 'idXML', 'featureXML', 'consensusXML')
-out <file>* Output file (valid formats: 'idXML', 'featureXML', 'consensusXML')
-rt_delta <value> Maximum allowed precursor RT deviation between identifications. (default: '0.1' min:
'0')
-mz_delta <value> Maximum allowed precursor m/z deviation between identifications. (default: '0.1' min:
'0')
-min_length <value> Minimum of length of peptides for final consensus list (default: '6' min: '1')
-use_all_hits If 'true' not only the first hit, but all are used (peptides only)
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 Consensus algorithm 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.
INI file documentation of this tool:
For the parameters of the algorithm section see the algorithms documentation:
Consensus algorithm
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |