Hello Magnus, Do you see any errors or other messages when you generate the Pep3D image? For probabilities to show up, you will need to use the post-PeptideProphet pep.xml file as the input (mzXML files won't work), make sure you select "All" or "Peptide" under Display Peptides in the entry form, and "PeptideProphet probability" as the Score Type (with an appropriate range).
Note that you can also directly call up Pep3D from the PepXML Viewer; there is a button under the "Other Actions" tab. Hope this helps, --Luis On Tue, Jan 19, 2010 at 3:48 AM, [email protected] < [email protected]> wrote: > Dear all, > > I am trying to plot an LC-MS/MS dataset with the CID events and > peptide identifications (probabilities). It has worked for me in the > past, using Mascot and mzXML files made by Bruker's compassXport. > However, I do not seem to be able to get the peptide probabilities in > the Pep3D plot anymore, only the CID events. I have tried both putting > the interact.pep.xml file as well as a file with the same name as the > mzXML file, but with the .pep.xml extension, but neither method work. > Any hints on how it is supposed to work? > > All the best, > > Magnus Palmblad > Leiden University Medical Center > > -- > 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. > > > >--
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