Dear all, I still didn't get an answer. Am I asking something obvious, or already discussed in this group? In that case, can someone address me to another thread, as I couldn't find a similar discussion.
Thanks again, Salvo On Jan 14, 4:57 pm, Skdona <[email protected]> wrote: > Dear all, > when we run PeptideProphet on pepXML Mascot DAT files, we always > notice an 'odd' peak on the f-values charts (see link 1). > It is a sharp peak positioned at negative f-values, somewhere in > between the positions where one would expect the Gamma and Normal > distributions of the negative and positive models. > It is always present in the charts for charge +2 and often visible in > the charts for charge +3. > I have never seen such a peak in the distributions presented in > Peptide Prophet papers or presentations. > And I dont' see it if I repeat the search with xTandem (see link 2). > > I have checked the f-values in Excel and I have noticed that almost 5% > of the PSM are assigned exactly the same f-value (corresponding to > this peak), even if they have different ion scores (see link 3). > > In particular, the attached distribution was obtained from a search > with a concatenated decoy database containing reversed hits. > In this case I could decide whether to use the semi-supervised > approach or the non-parametric approach. > As you can see, with the non parametric approach, the odd peak is > fully associated with the positive model and I can get a higher number > of identified peptides. > > I have no idea about the nature of this sharp peak, but it scares me a > bit, because I do not know whether I can trust my results. > Is it an artifact of the algorithm to obtain discriminant scores from > Mascot scores? > > Would you trust these results? > > (Nested Question: How shall I decide between semi-supervised and non- > parametric approach?) > > We have been facing this issue for a while now, so I hope that someone > can help me. > > Best regards, > Salvo > > Link > 1:https://docs.google.com/leaf?id=0BxCqzqYo07lLNjQ5ZjIwMTMtODc3ZC00YzY2... > > Link > 2:https://docs.google.com/leaf?id=0BxCqzqYo07lLZjhkYTgxZTctZDRjMS00NjM0... > > Link > 3:https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0Bx... -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
