This is a nice walkthrough on using transcriptomics to guide the discovery of new neo-antigens, including the use of synthetic peptides and MHC binding tools to help support your results.
You might get to the flow chart on how they did the informatics and think about pursuing a different field of study, because....ouch....there are 40+ steps here. It sure seems simpler to not do the transcriptomics at all. I wonder when we'll hit that tipping point? Some journals don't require that you validate your mass spec data with western blots or other rabbit blood based techniques now. How far are we from just using the mass spectra and not needing the noisy crazy looking next gen sequencing data?
In terms of the details, the samples were a leukemia monocyte cell line and the data was generated on an Orbitrap Fusion in high/high mode (orbi-orbi) with HCD. Most of the data analysis on the proteomics side was done in PEAKs.