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
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