Unfortunately your "good" spectra scores overlap significantly with you bad spectrum scores. So PeptideProphet has trouble classifying this dataset. Can you tell us more about your dataset and the search parameters used? Does your database contain any decoys?
Thanks, David On Sep 16, 2012 7:57 PM, "Claire" <[email protected]> wrote: > Hi Bjorn, > > Did you ever get a solution to this problem? > > I keep encountering the same issue. > > Thanks, > > Claire > > On Friday, August 27, 2010 1:23:54 AM UTC+9:30, Bjorn wrote: >> >> Hi, >> >> I can do a tandem database search that results in a .tandem file. >> I successfully convert it into a .tandem.pep.xml where I clearly see >> that I have 2+ and 3+ spectra with hyperscores of +700. >> When I run peptideprophet on that file, the result is a .pep.xml file >> with only the 1+ left (no 2+ or 3+) >> Where have all the good spectra I had before Xinteract gone?? >> I would expect those to be still there and have high probability >> scores... >> >> Any suggestion is welcome. >> >> I'm using TPP 4.4.0 on Mac OS X 10.6.4. >> >> Bjorn > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/WFHXaitAt_4J. > 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. > -- 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.
