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I've done O- and N- linked enzymatic deglycosylation of purified and lyophilized proteins. Following some modifications to the manufacture's protocol, I had great results.

I now want a student to deglycosylate some total cell lysates (TCL) of infected cells. Can he just Vacufuge/vac-spin Triton-X TCL's and then proceed with the deglycosylation? The first step is often resuspend in water. I'm wondering if ether the salts would need be removed by dialysis, or if it doesn't matter, if he can start just from the lysate.

The antibodies we have for western detection are excellent, so that is unlikely to be a limiting factor.

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I can tell you anecdotally that, at least when I did it, all was fine just using the raw lysates. You have to use the total protein content which means, of course, your favorite protein will be in lower concentration, but c'est la vie. –  Amory Oct 30 '13 at 21:28
    
@Amory Did you dehydrate at all, or did you just go with fresh lysates? –  Atl LED Oct 30 '13 at 21:53
    
"Fresh" as in not dehydrated, yes, just straight lysates. –  Amory Oct 30 '13 at 22:16

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So we went ahead and did this. The efficiency was much lower, which you might expect, and dehydration did aid the process. We found that taking raw lysates and running them through the linked protocol, had about ~20% the efficiency of conducting it on purified protein. I assume the majority of the loss was due to reagents being expended on proteins that were not of interest.

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