Peptide identification results of Mix 2. This figure illustrates the peptide identification results of Mix 2. They have the same trend as the results of Mix 1. Both peptide identification results indicate that IM can identify more true positive and less false positive peptides than PeptideProphet. This can be attributed to the feedback framework, which recomputes the probability of true peptides with low PeptideProphet probability, and eliminates negative peptides of unidentified proteins.