I love global protein abundance experiments. With today's technology, it is now relatively easy. I like phosphoproteomics a little less because it is much tougher to do. And I probably have to say that I like glycoproteomics the least. I don't like the fact that I have to use ETD and CID/HCD to sequence by sugars and my peptides. That is a lot of work and a long cycle time.
But glycoproteomics continues to climb in importance. I saw a lecture some time this year where the speaker said that every single disease state in man is known to be linked to glycosylation in some form. Sorry, but I forget who said that. It was probably at ASMS, since I haven't been to all that many lectures this year.
What if a very major characteristic of cancer was changes in the glycoproteome? Well then, I guess I'd probably suck it up and fire up the ETD. This paper in PNAS says that its time to heat up that fluoranthene vial . In extremely thorough detail this globally spread team looked at the length of the glyco chains on proteins in various cancer types and found a very strong relationship between short chains and cancer progression. Specifically, the truncation of O-glycans appears to directly induce oncogenesis.
The glycoproteomics was performed with my favorite old workhorse, an Orbi XL + ETD. The level of validation is mind-boggling.
I recommend this paper for anybody doing anything with cancer. It really puts into perspective how little we know, but points us in a direction that we maybe should be looking.
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