Ammonium sulphate precipitation assay pH dependence
I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a lot of base to adjust the pH.  

When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned.  I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification.