Trichloroacetic acid (TCA) precipitates proteins. The proteins are then collected as a pellet by centrifugation. Molecules that do not precipitate are in the supernatant. The best method for desalting them depends on their size. If they are small peptides, the best method is probably reverse-phase HPLC. The salts elute at the beginning and the peptides are eluted later. Larger peptides can be desalted by gel filtration chromatography, dialysis, or ultrafiltration using suitable resin or molecular weight cutoff dialysis or ultrafiltration membranes.
The answer will depend very much on what effect you are trying to asses - anti-microbial? anti-cancer? anti-oxydants? ______? There is no one answer fit them all