Computes a consensus identification from peptide identification engines.
potential predecessor tools | ![]() ![]() | 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:
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 Mon Aug 18 2014 14:41:09 using doxygen 1.8.7 |