This is a thorough analysis of HLA peptide enrichment and purification strategies that finds -- wait for it -- that how you prep these awful terrible poorly fragmenting (highly deamidated?) and often modified peptides changes the ones you're able to see.
I think they did a great job for this work, so the following should not -- in any way -- be considered a reflection of what I think of the work this team did.
From the abstract --
Again -- our biggest weakness in any head to head with any moron with a Hi-SeQ (or who has $1k to spend on a NanoPore -- which -- is coming fast) is that proteomics, as a field, can not ever once follow the same sample prep procedure, is completely and utterly, in every way, our fault. The moron with the Hi-SeQ just has to follow the directions that came in the box.
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