Sure you could...I'd say that a majority of people would be more likely to snap freeze and then store at -80C.  Empirically, who knows what you'd find and how repeatable the results may be. 

Thanks aaron :), I'd want to optimize the extraction condition. It will be perform on ingested yeast by macrophages. In my last experience I noticed that it was very long to infect macrophages by yeast, collect these yeast and extract their whole proteome in the same day. It's for that I want to carry out in two steps. I hope that it will be repeatable.

you'd want to carry out a pilot test on a few of your samples :) That would answer your first question, and should be reliable enough to convince you whether or not to proceed with the rest. Try using conventional off the shelf reagents and methods, plus commercial kits. Its amazing what differences there might be.