Precipitating macromolecules with organic solventsGeneral principles
Acetone and alcohols (EtOH, MeOH) precipitate proteins and nucleic acids. Avoid inorganic salts which coprecipitate. Precipitate small amounts so that precipitate washes and dissolves easily. Use a carrier; Ficoll is convenient. It's not viscous, doesn't migrate on gels and doesn't stain by common procedures. Precipitation is normally virtually instantaneous at room temperature (include enough carrier to see ppt). Wash pellet with MeOH which is especially volatile. Acetone is generally a better precipitant, but keep in mind that it precipitates phospholipids.
Precipitating proteins from acids
Formic acid is a common solvent for partial acid hydrolysis and CNBr digestions. Trifluoromethanesulfonic acid is a common deglycosylation reagent. Although proteins won't precipitate directly from acids, neutralizing organic acids with an organic base (I use N-ethylmorpholine) permits straightforward precipitation (these salts are soluble in acetone and alcohols!). Be sure to use an ice bath and small volumes because neutralization is exothermic. For specific formic acid and peptide CNBr mapping protocols see - Skopp, R.N. and Lane, L.C. 1989. Fingerprinting of proteins cleaved in solution by cyanogen bromide. Appl. and Theoret. Electrophoresis 1, 61-64. Precipitation with TCA following neutralization with a weak base is yet more efficient.
Ammonium acetate
The pKa of acetic acid is 4.75 and that of ammonia is 9.25. (Roger J. Williams, Carl M. Lyman, JACS 54, 1911-12 (1932) A neutral buffered standard for hydrogen ion work and accurate titrations which can be prepared in one minute.) The resulting salt is a pH 7 buffer with moderate buffering capacity and good solubility in organic solvents. It's simpler and easier to prepare than tris buffers!
Lithium chloride
Lithium chloride is moderately soluble in alcohols and acetone (much more so than potassium or sodium salts) and is the salt of choice for precipitating macromolecules with organic solvents.