It is important to note that for rescoring, features need to be carefully evaluated to ensure that they are unbiased. Features considered by the classifier should be very similar between decoys and incorrect target PSMs. Else, rather than resulting in a better separation between correct and incorrect PSMs, the classifier would systematically assign higher scores to target PSMs compared to the decoys and produce biased results. For example, a feature included in the initial version of Percolator describing the number of PSMs that match to the same protein (numProt) was identified as a biased feature , probably because it is more likely that proteins from which incorrect target peptides are derived have a higher PSM count compared to decoy proteins.