Where do the peptide probabilities come from?
The peptide probabilities are generated using the algorithm “Peptide Prophet”. Peptide Prophet changes the output from a standard search engine (SEQUEST, Mascot etc.) into a discriminant score. The data from the previous search is mapped on a histogram demarcated by discriminant scores, and Bayesian statistics are used to determine the probability that a match is correct at each discriminant score. If you wish to know more about Scaffold’s peptide prediction software, the Peptide Prophet publication can be found here: Peptide Prophet Reference: Keller A, Nesvizhiskii AI, Kolker E, Aebersold R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem.
