I'm studying on the epidermal fish mucus to identify and isolate the possible antibacterial peptides. What do you think is the best protein precipitation method for the early study of protein profile using SDS-PAGE and the subsequent ion exchange and reverse phase chromatography? In the studies on fish mucus, none of the conventional methods for example acetone, TCA-acetone precipitation, ...have been applied. why?
Anti-bacterial peptides are usually quite short (around 20 aa),so they can penetrate Gram-negative bacteria. The methods you suggested are used for larger proteins. I would consider reverse-phase HPLC for a project like this, after sample clean-up to remove slime-forming substances. Tricine-SDS-PAGE may also work, but you'd be at the lower end of molecular mass range.
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