While messing around with FDR for LFQ/peak integration, I discovered that there is currently a bug in the implementation of picked-peptide. We need to recalculate FDR/q-values based on the maximum score of the picked-pair, not the hit score. Should also re-visit how much benefit there is to picked-approaches
Note that this only affects peptide FDR, not spectrum or protein.
lazear
commented
1 year ago 
While messing around with FDR for LFQ/peak integration, I discovered that there is currently a bug in the implementation of picked-peptide. We need to recalculate FDR/q-values based on the maximum score of the picked-pair, not the hit score. Should also re-visit how much benefit there is to picked-approaches
Note that this only affects peptide FDR, not spectrum or protein.