Last week I put up a post about a simpler method for reduction alkylation used in some recent studies that I liked. That post is here. I don't think I've ever received (real) comments on a post so quickly and I suggest that you check those out.
One comment will lead you to this great recent paper that takes a deep look at these issues.
These authors take a good hard look at 2-chloroacetamide and find that it comes with it's own special annoyances. Massive increases in methionine oxidation compared to iodoacetamide and both singly and double oxidations of tryptophan (I'm having trouble imagining where that second oxidation goes...I should get more coffee). They also examine how different buffer conditions will lead to increased/decreased off-target alkylation effects.
This is obviously a complex issue that requires a lot more consideration than this blogger is willing to do on a Sunday afternoon, but I'm hoping to get to a single standardized protocol for my experiments soon. When I settle on something I'm just going to do it this way for years. I need to be able to go back to historic data and match it to new stuff and any tweaks in sample prep that lead to improved IDs aren't worth sacrificing my ability to easily align and remine old data.
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