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/a75b99f29c49ee98/845ace41d79afb83?lnk=gst&q=release#845ace41d79afb83
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.
