I also encounter this problem. The PeptideProphet won't get any hit when uncheck the "Use Gamma distribution to model the negatives ". After tick that, it worked.
On Monday, July 21, 2008 10:38:49 PM UTC+8, [email protected] wrote: > > Hi all, > > Problem solved! The X!Tandem search should of course be done with > mzXML and MGF (or .dta) files in the TPP data tree accessible by the > web server. The "Use Gamma distribution to model the negatives (Tandem > only)" or -G option is strongly recommended - maybe it should be > ticked by default in the Petunia X!Tandem pipeline? > > Does anyone know if there is any critical difference between mzXML 2.0 > and 2.1 (the version generated by compassXport 1.3)? > > Cheers, > > Magnus > > > On Jul 20, 6:34 pm, "[email protected]" > <[email protected]> wrote: > > Dear all, > > > > I'm struggling with the link to the raw data in the pepXML file > > generated by X!Tandem. The MGF file used in the X!Tandem search has > > the spectral numbers in the right format and everything else seem to > > work. Is this a known bug, or am I doing something wrong? I am doing > > the X!Tandem search on the command line from an MGF file generated by > > mzXML2Search as the searching the mzXML file directly doesn't work > > with our mzXML files (X!Tandem complains they are not in the correct > > format). > > > > Any suggestions? > > > > Cheers, > > > > Magnus -- 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/-/MF9rhoSEttwJ. 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.
