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=0BxCqzqYo07lLNjQ5ZjIwMTMtODc3ZC00YzY2LTkzYzAtNjU0NTk4NzFkNzc2&hl=en&authkey=CKWfjc4N Link 2: https://docs.google.com/leaf?id=0BxCqzqYo07lLZjhkYTgxZTctZDRjMS00NjM0LTk2YWUtZTQ3ZjE5M2I1YjE3&hl=en&authkey=CIG57PsO Link 3: https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0BxCqzqYo07lLNWI1YmQ0ZGUtMjllNS00ZDJmLWE5MTEtMGYzZWNlNDAyOGY4&hl=en&authkey=CNXIkdMI -- 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.
