I've removed a novel stain (which was the subject of my PhD project) from SDS-PAGE gels using Bio Rad trans-blotter, and some Whatman's filter papers to mop up the dye. I should imagine there was/is some loss of proteins by this method.

Alternatively, I have also successfully removed stains from protein gels by using the destain solution (usually an aqueous mix of methanol and acetic acid). The greater the volume you use, and the more often you change the solution, the fast the stain is displaced.

Finally, you may be able to blot the proteins with the stain in place and either; remove the stain using a suitable solvent after they have been bound to the membrane, or (and this is what I would try first), simple run the test on the stained proteins (you may well find it works in the presence of the dye).

Thanks for your response! I'll try blotting with the stains in place first and see what happens.

I thought I'd post an update (2 years later!) to this question in case anyone is curious and wondering if previously stained protein gels can be transferred to membranes for immunoblots. The short answer is no.

The transfer won't work because the proteins are fixed in the gel before the stain is applied. Fixing works by denaturing protein to immobilize it within the gel, thus preventing diffusion during staining. Once immobilized, the protein will not transfer well. In addition, fixing strips SDS off the protein, which is necessary for transfer.

So, because fixation is part of the staining process, you can't transfer stained gels for immunoblots.

Thank you Kate for the update. The update was useful to me.

Thank you Kate. The update was useful to me as well!