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Cell lysis is the breaking down of the cell membrane and the separation of proteins from the non-soluble parts of the cell. Lysate buffers contain different detergents that help to release soluble proteins (Triton-X, Tween, SDS, CHAPS). Dependent on the location of the protein of interest, a different lysate buffer is needed to obtain a high yield and purity of the protein.
However, every protein is different and may react differently with the buffers and detergents. If you don’t get your protein of interest in solution or you are studying a special protein–protein interaction, you can try different buffers and exchange the detergents.
The most commonly used buffers are RIPA and NP-40. RIPA buffer’s harsh properties are best suited for hard to-solubilize proteins.
RIPA is the preferred choice here. However, fractions protocols are often used to increase the concentration of the desired protein.
A Tris-HCl lysis sometimes shows advantages over RIPA buffer. Optimal conditions should be tested for the protein of interest.
Denaturation/proteolysis and dephosphorylationen (in case of phosphoproteins) should always be kept to a minimum and added freshly to the cell lysate (EDTA, sodium orthovanadate, PSMF, Aprotinin).