Luckily, PSM rescoring using predicted fragment ion intensities (with tools such as #Prosit, #MS2Rescore, etc.) can significantly improve the immunopeptidomics results over standard sequence database searching. 💪

Unfortunately, existing fragment ion intensity prediction models have been developed for #Orbitrap instruments. In contrast, #timsTOF instruments are increasingly popular for immunopeptidomics due to their increased sensitivity.

@translational_proteomics Oh, interesting! Yes, I'd definitely defer to someone who has experience in #timsTOF and TMT. When I learned mass analyzers, it was an article of faith that TOF shouldn't be considered high-resolution, but the technology has clearly come a long way.