I discovered a trick at ASMS that allows us to compute q-value using the accepted (decoy + 1) / target. This wasn't previously possible b/c the highest scoring peptide would have qvalue = 0.5. What we do is compute q-value from bottom to top, low scoring to high scoring. And, we keep the minimum q-value between previous and current. That way the the q-value doesn't creep in the backward direction ever, having achieved a certain value.
This results in the highest scoring PSM to have an above zero q-value always (which is cosmetically bad). However, there is an expected increase in PSM count and peptide count (according to the Noble group).
I discovered a trick at ASMS that allows us to compute q-value using the accepted (decoy + 1) / target. This wasn't previously possible b/c the highest scoring peptide would have qvalue = 0.5. What we do is compute q-value from bottom to top, low scoring to high scoring. And, we keep the minimum q-value between previous and current. That way the the q-value doesn't creep in the backward direction ever, having achieved a certain value.
This results in the highest scoring PSM to have an above zero q-value always (which is cosmetically bad). However, there is an expected increase in PSM count and peptide count (according to the Noble group).