As the sample depth of proteomic analysis continues to improve thanks to better/fast mass specs, better sample prep and more sophisticated separation, detecting protein variants is becoming a lot easier. "-er" is an important addition to this word -- cause is sure hasn't got to the "easy" point.
This is a really good "How to" guide that talks about strategies and common pitfalls!
They do a lot of meta-analysis of one of my favorite datasets -- the NCI-60 deep proteomes (Orbitrap Elite, high/high dataset with 24 SCX fractions for each cell line), though they apply these protocols ot the "shallow" proteomes as well (Orbi XL high/low with 12 fractions) that provides a great perspective for mining repositories!
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