Luis, we have deployed on our Linux cluster TPP version 4.3.2, but with that I see identical result to the one I described before. Is there issue with the Linux version?
Tomas On Dec 17, 5:34 pm, Luis Mendoza <[email protected]> wrote: > Hello Tomas, > The behavior you describe is the default (or typical) for the original > ProteinProphet tool. As of TPP version 4.2.0. (released February 2009), > subsumed proteins are "grouped" with their parent ones and displayed under a > single entry. Please upgrade your TPP to take advantage of this and other > features, including the MININDEP option in ProteinProphet. The release > notes when this change was made can be found > here:http://groups.google.com/group/spctools-discuss/browse_thread/thread/... > > Hope this helps, > --Luis > > On Thu, Dec 17, 2009 at 2:46 PM, Tomas <[email protected]> wrote: > > 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]<spctools-discuss%[email protected]> > > . > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. -- 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.
