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 can calculate the false discovery rate (FDR) given a forward and backward search. Most useful is this on protein level, however, it also can be applied to peptides.
The false discovery rate is defined as the number of false discoveries (the hits in the reversed search) over the number of false and correct discoveries (the hits in both databases) given a score.
Prerequisites:
- When using a combined database of forward and reverse hits (thus only using one search run per ID engine), then use PeptideIndexer to index an idXML file generated by a search engine adapter, e.g. MascotAdapter This will allow us to discern which peptides are from the target vs decoy database.
The command line parameters of this tool are: