This is a really nice analysis. It stems from the fact that we're a field of rebels and no one will use the exact same techniques as anyone else. The paper in question is this one from Evgeny Kanshin et. al., and it investigates the effects of different harvesting techniques on phosphoproteomics output.
The good news? Phosphoproteomics seems pretty tough. Using different buffers and methods doesn't seem to change things all that much. I'd bet $10 though if we did a a PCA analysis of the observations from different methods we'd see some level of batch effects, but the fact they didn't see completely different things is super encouraging!
An interesting (unexpected!) observation is that the use of some phosphate buffers appears to bias the results by causing some new activations.
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