There are several ways to calculate FDR depending on the database search type. In Proline the FDR is calculated at peptide and protein levels using the following rules:

• if the Search has been done on a concatenated Target/Decoy bank, FDR = 2 * nbr DecoyPSM / (nbr TargetPSM + bnr DecoyPSM ). Note: when computing PSM FDR, peptide sequences matching a Target Protein and a Decoy Protein is taken into account in both cases.
• if the Search has been done on a separated Target/Decoy bank, FDR = nbr DecoyPSM / nbr TargetPSM.