When using SEQUEST, what represents a good score? When using Mascot, what is the trade-off of missed identifications to false positives? These are hard questions whose answers depend on the instrument, sample complexity, FASTA database size, and experimental design. The PeptideProphet algorithm gives the answers.
PeptideProphet™ was developed by Keller, Nesvizhskii, et al. at The Institute for Systems Biology as a Bayesian statistical algorithm to convert SEQUEST scores into probabilities