There are many ways to calculate FDR. Proline implements few of them :

• Default Estimator. The FDR is calculated using following rule
  • if Search have been done on a concatenated Target/Decoy bank, FDR = 2 * nbr DecoyPSM / (nbr TargetPSM + bnr DecoyPSM ). PeptideMatches that matches a Target Protein and a Decoy Protein will be count in both case.
  • if Search have been done on a separated Target/Decoy bank, FDR = nbr DecoyPSM / nbr TargetPSM.
• Competition Based FDR Estimator : Uses FDR described in Navarro et al. (JPR, 2009)
  • TO BE DESCRIBED