Dear all, I wonder why PeptideProphet (PeP) is still selecting decoy hits as valid ones. Why is PeP not using the decoy hits for building the vector machine but when discriminating not applying it on the decoy hits instead taking the first non-decoy hit. Consider the case where the best hit of a spectra is a decoy peptide and the second best is a non-decoy. If both have good scores (xcorr, ...) it makes sense to still consider the decoy peptide for the machine learning, as it holds information about the distribution of random hits which have good scores. But for my end results I would like to have only non-decoy peptide. What do I miss here? And If my assumptions are right how can PeP build the vector machine on one data set (only best hits) but applying it onto another (only best non-decoy hits).
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