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ConsensusID

Computes a consensus from results of multiple peptide identification engines.

potential predecessor tools $ \longrightarrow $ ConsensusID $ \longrightarrow $ potential successor tools
IDPosteriorErrorProbability PeptideIndexer
IDFilter
IDMapper

Reference:

Nahnsen et al.: Probabilistic consensus scoring improves tandem mass spectrometry peptide identification (J. Proteome Res., 2011, PMID: 21644507).

Algorithms:

ConsensusID offers several algorithms that can aggregate results from multiple peptide identification engines ("search engines") into consensus identifications - typically one per MS2 spectrum. This works especially well for search engines that provide more than one peptide hit per spectrum, i.e. that report not just the best hit, but also a list of runner-up candidates with corresponding scores.

The available algorithms are (see also OpenMS::ConsensusIDAlgorithm and its subclasses):

PEPs for search results can be calculated using the IDPosteriorErrorProbability tool, which supports a variety of search engines.

Note
Important: All protein-level identification results will be lost by applying ConsensusID. (It is unclear how potentially conflicting protein-level results from different search engines should be combined.) If necessary, run the PeptideIndexer tool to add protein references for peptides again.
Peptides with different post-translational modifications (PTMs), or with different site localizations of the same PTMs, are treated as different peptides by all algorithms. However, a qualification applies for the PEPMatrix algorithm: The similarity scoring method used there can only take unmodified peptide sequences into account, so PTMs are ignored during that step. However, the PTMs are not removed from the peptides, and there will be separate results for differently-modified peptides.

File types:

Different input files types are supported:

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

Filtering:

Generally, search results can be filtered according to various criteria using IDFilter before (or after) applying this tool. ConsensusID itself offers only a limited number of filtering options that are especially useful in its context (see the filter parameter section):

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Jan 20 2016 22:50:36 using doxygen 1.8.9.1