I've gotta move fast today, so I'm going to just leave this here. If you're looking at MHC/HLA petpidomics stuff -- this new study is an understated gold mine.
This phenomenal amount of work was done on a Q Exactive Plus using 150 minute gradients. If you are doing this stuff, I'd suggest paying particular attention to the LC separation and the MaxQuant data processing parameters. I'm not 100% sold on the 95% confidence logic, but they make a solid argument.
This is still in press at MCP, so PRIDE/ProteomeXchange hasn't released the data yet. I did bug the corresponding author, extremely out of normal working hours on a weekend to see if they could release it early so I stare at all of it. He said it will go live next week! (Thank you!) When it does it can be found here!
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