Fig. 2.

Separating true matches from false matches. Mixture spectra were simulated by a linear combination of two single-peptide spectra. Correct matches are cases where both peptides in a PPSM are correct, incorrect matches are cases where both peptides are incorrect, and half-correct matches are cases where one peptide is correct and one peptide is incorrect. The distribution of joint probability and conditional probability for correct matches (blue bars), incorrect matches (red bars), and half-correct matches (yellow bars) are shown. As shown in A, the distributions of joint probability are well-separated between correct and incorrect matches. However, there is considerable overlap between the joint probability distribution of correct matches and half-correct matches (see B). On the other hand, conditional probability is a better approach for separating correct matches from half-correct matches as shown in C).