It definitely depends on the end use of the protein, for an SDS-PAGE gel both can work, but acetone (or better yet TCA) is usually preferred. For retained enzymatic activity, Am sulfate is often better.
It also depends on the reason for choosing precipitation. For example if your goal is a native fold and/or activity, I agree with @Edward that ammonium sulfate is usually much better. If you are attempting to remove detergent (e.g., SDS, Triton) then a variety of acetone precipitation is of course better. Also used for membrane proteins. If you need small scale precipitation, this procedure has worked well in my lab.
Analytical Biochemistry (1984) 138, pp 141–143
Here is a good example of procedural variations for acetone precipitation.
Analytica Chimica Acta, (2013) 796, pp 48–54
Why are you considering acetone precipitation?
Thank you very much for your feedback @Edward & @Kurt.I will definitely let you know the outcome. Basically i am trying to identify my proteins through SDS-PAGE but had doubt it.
One more doubt i have. If i go for SDS-PAGE without dialysing my ammonium sulphate precipitates,will it give me nice resolved bands,in other words it wont cause tailing?
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