Hi Lik, Your output indicates that you were specifying "tandem" as the "scoring, algorithm" for your search. If I were you, I would drop this parameter completely from the X! Tandem search parameters. You only need to specify "scoring, algorithm" when you want something other than X! Tandem native scoring. From your report, it seems as though X! Tandem itself simply ignores this parameter and uses the default, if it does not match a known scoring algorithm. PeptideProphet could certainly be fixed to do the same, but the simpler solution is for you to use X! Tandem parameters that will get you all the way through this pipeline. And, those do exist. Just remove "scoring, algorithm" from your X! Tandem parameters.
Good luck. --Brendan On Sep 6, 4:00 pm, LW <[email protected]> wrote: > Hi, > > I use xtandem with native scoring and also TPP 4.4.1 > The Tandem2XML converted .pep.xml file has: > <parameter name="scoring, algorithm" value="tandem"/> > However, PeptideProphet complains about it: > > Error: The X! Tandem scoring algorithm 'tandem' is not supported. > > It will go through if I change it to read"native" in the .pep.xml > file. I am > wondering why the discrepancy "native" in PeptideProphet and > "tandem" in XTandem. Or did I miss something? > > Thanks, > Lik -- 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.
