An illustration of the effect of using consistency constraint in PSM re-ranking. Here each solid circle represents a hypothetical peptide-spectrum pair, whose position is proportional to the ranking score. The consistency constraint shortens the distance between two related PSMs to increase their mutual affinity, leading to new ranking scores. If we consider the PSMs above the threshold to be correct, the 2nd PSM in case 1 becomes correct and the 1st PSM in case 2 becomes incorrect after the transformation. In case 3 and case 4, the consistency constraint has no effect on the correctness state of PSMs.