OpenMS
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IDFilter

Filters peptide/protein identification results by different criteria.

potential predecessor tools → IDFilter → potential successor tools
MascotAdapterOnline (or other ID engines) PeptideIndexer
IDFileConverter ProteinInference
FalseDiscoveryRate IDMapper
ConsensusID ProteinQuantifier (for spectral counting)

This tool is used to filter the identifications found by a peptide/protein identification engine like Mascot. Different filters can be applied. To enable any of them, just change their default value. All active filters are applied in order.

Most filtering options should be straight-forward - see the documentation of the different parameters. For some filters that warrent further discussion, see below.

Score filters (score:pep, score:prot):

Peptide or protein hits with scores at least as good as the given cut-off are retained by the filter; hits with worse scores are removed. Whether scores should be higher or lower than the cut-off depends on the type/orientation of the score.

The score that was most recently set by a processing step is considered for filtering. For example, it could be a Mascot score (if MascotAdapterOnline was applied) or an FDR (if FalseDiscoveryRate was applied), etc. IDScoreSwitcher is useful to switch to a particular score before filtering.

Protein accession filters (whitelist:proteins, whitelist:protein_accessions, blacklist:proteins, blacklist:protein_accessions):

These filters retain only peptide and protein hits that do (whitelist) or do not (blacklist) match any of the proteins from a given set. This set of proteins can be given through a FASTA file (...:proteins) or as a list of accessions (...:protein_accessions).

Note that even in the case of a FASTA file, matching is only done by protein accession, not by sequence. If necessary, use PeptideIndexer to generate protein references for peptide hits via sequence look-up.

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.

The command line parameters of this tool are:

INI file documentation of this tool: