Hi, I have a question about how ProteinProphet makes calls within a group if there are both proteins having non-degenerate peptides (Class 1 proteins) and those categorized as indistinguishable and not subsumed (Class 2 proteins).
For these examples, let's assume all peptides have initial probability > 0.9. In a simple case, for a group containing only Class 2 proteins, ProteinProphet will select a "representative" and assign a score of, e.g. 1. This is appropriate and as expected. In a more complex case, let's say there are both Class 1 and Class 2 proteins in a group. Class 1 are assigned a protein probability = 1 while the Class 2 proteins = 0. In the extreme case I'm seeing, a Class 1 protein (x) has 2 peptides, one degenerate, one not. The Class 2 protein (y) has 25 peptides, one of which is shared with the Class 1 and all are shared with 2 other proteins. ProteinProphet assigns x=1 and y=0. I feel y should also get a score of 1 since all of the peptides in the group are not accounted for by x. Note that I only did a deep dive into this one group...I haven't yet checked to see if this behavior is consistent, but I assume it is. What I'm trying to figure out is if ProteinProphet neglects to pick representatives from Class 2 once it finds a Class 1 within a group. Thanks, John -- 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.
