I've been doing this stuff for a long time now. And I'm starting to feel like I'm pretty good at it. Once in a while, however, I read a paper that makes me feel like I'm still a bit of an amateur.
There is one in press right now at MCP. This comes from Alejandro et. al., out of Boris Macek's lab and you can find it (currently open access!) here.
Strategy? Let's start with a complex multiplex SILAC labeling scheme with an internal control (woo!) and do quantitative proteomics on it. Then let's follow that up with phosphoproteomics of the same sample And lets take the relative quan data from the SILAC, standardize it with our internal control and then compare the whole quan to the phospho at multiple stages across the yeast life cycle.
Whole proteomics was done with an Orbi Velos and Elite. The phospho was performed with an Orbi XL running CID neutral loss MS3. Yes, I know, its another yeast study. But take this one as a proof of concept paper. We know a lot of these phospho events that we are seeing and when these observations line up it shows that we can get this amazing degree of quantitative certainty using only mass spectrometry.
Awesome study and great post acquisition analysis. Strongly recommended, phospho people!
Back to serious business:
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