After some reading and discussions at ASMS, it seems that it would be really nice to add an FLR calculation to pyAscore. For the user, this would just be another command line argument. Internally, the Ascore agorithm will be run on each PSM with the decoy amino acid tacked on to the possible amino acids for a mod. I.e. if a user specifies phospho on STY and a decoy AA as A, then internally we run Ascore as phospho on STYA and handle the FLR calculations. Right now the idea would be to sort the PSMs based on score and then report the FLR at each score threshold.
After some reading and discussions at ASMS, it seems that it would be really nice to add an FLR calculation to pyAscore. For the user, this would just be another command line argument. Internally, the Ascore agorithm will be run on each PSM with the decoy amino acid tacked on to the possible amino acids for a mod. I.e. if a user specifies phospho on STY and a decoy AA as A, then internally we run Ascore as phospho on STYA and handle the FLR calculations. Right now the idea would be to sort the PSMs based on score and then report the FLR at each score threshold.