Distribution of (a) InsPecT MQScore and (b) X!Tandem E-Value, for the peptides identified in Shewanella-1784 dataset against Shewanella and decoy databases. X-axes show the database search scores, and Y-axes show the fraction of identifications with that score. The Kolmogorov-Smirnov (KS) distance between the two distributions is 0.28 for InsPecT scores and 0.58 for X!Tandem scores. (c) Distribution of Energy(P, S) for the same dataset (the KS distance is 0.77). (d) Distribution of −log10(SpectralP robability) (the KS distance is 0.78). Spectral P robability of the pair (P, S) is defined as the sum of probabilities of all peptides whose score is larger or equal to the score Score(P, S) of the match between peptide P and spectrum S.