When you set an FDR target value for a decoy database search, the application determines and applies filter thresholds to identified matches so that the resulting FDR is not greater than the set target value. The application distributes the confidence indicators applied to each peptide match according to these calculated filter thresholds.
You must specify two target values for a decoy database search: a strict target FDR and a more relaxed FDR. See the Peptide confidence indicators topic for an example that shows the decoy search setting with target FDRs of one percent and five percent. After completing a search for two target FDRs, the system automatically determines two sets of filter settings so that the resulting separate FDRs do not exceed their corresponding target value.