I'm obviously on a big automation kick recently. But maybe the whole field is. Last week I was at an incredible lab I don't think I can tell you about, but they had a GIANT robot that did all of their digestion and sample cleanup. For those of us that can't afford that kind of thing, small time optimization with stuff that is already available may be the best option.
In this paper at JPR, the Jensen lab demonstrates such a process using disposable StageTips and something that looks like an EasyNLC 1000. Using tons of E.coli preps they demonstrate they can achieve CVs <10% with their technique. While I'd rather have the giant secret robot (and maybe you would too) this might be a great paper to check out for automated proteomics processing in a more affordable format.
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