I have a peculiar problem - two highly homologous proteins where I identified bunch of peptides for one of them (including peptides unique for it) and for the other I "identified" only peptides which are shared by both proteins. The TPP (ProteinProphet) gives the first one protein probability 1.0 and the second probability 0.0 (as expected), but it separates them in the output, e.g. does not generate a "protein group" where the first would be the main protein and the other an "indistinguishable" group member. Instead what TPP did is that it indicated the second one as a "subsumed entry" of the first one as well as listing it separately as a protein with 0.0 protein probability (giving it unique protein number). Would anybody have explanation why not a group but subsumed entry and what is the distinction between these two?
I use TPP v3.4 SQUALL rev.2, Build 200906181759. Thanks, Tomas -- 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.
