A method for identifying peptides using tandem mass spectrometry takes the spectrum for a peptide to be analyzed and uses a scoring function to score a match between the spectrum and each candidate peptide in a peptide database. The scoring function has a value corresponding to a number of fragment peaks in the spectrum that match fragment peaks in a spectrum of the candidate peptide. Using the match scores, a generating function of the spectrum is computed to determine the number of peptide reconstructions at each value of the scoring function. The generating function is then used to determine the number of candidate peptides for each match score and the probability of a peptide having a given match score to the spectrum. A spectral probability can be determined by calculating the total probability of all peptides with scores equal to or larger than the given match score.