OpenMS
Loading...
Searching...
No Matches
FalseDiscoveryRate

Tool to estimate the false discovery rate on peptide and protein level.

pot. predecessor tools → FalseDiscoveryRate → pot. successor tools
MascotAdapter (or other ID engines) IDFilter
PeptideIndexer

This TOPP tool calculates the false discovery rate (FDR) for results of target-decoy searches. The FDR calculation can be performed for proteins and/or for peptides (more exactly, peptide spectrum matches).

The false discovery rate is defined as the number of false discoveries (decoy hits) divided by the number of false and correct discoveries (both target and decoy hits) with a score better than a given threshold.

PeptideIndexer must be applied to the search results (idXML file) to index the data and to annotate peptide and protein hits with their target/decoy status.

Note
When no decoy hits were found you will get a warning like this:
"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!"
This should be a serious concern, since it indicates a possible problem with the target/decoy annotation step (PeptideIndexer), e.g. due to a misconfigured database.
FalseDiscoveryRate only annotates peptides and proteins with their FDR. By setting FDR:PSM or FDR:protein the maximum q-value (e.g., 0.05 corresponds to an FDR of 5%) can be controlled on the PSM and protein level. Alternatively, FDR filtering can be performed in the IDFilter tool by setting score:pep and score:prot to the maximum q-value. After potential filtering, associations are automatically updated and unreferenced proteins/peptides removed based on the advanced cleanup parameters.
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: