- Trypsin - preferentially cleaves proteins at the carboxyl group of basic residues, Arg and Lys, except where these residues are directly followed by a Pro residue.
- Chymotrypsin - preferentially cleaves at the carboxyl group of aromatic residues, Phe, Tyr and Trp. It almost never cleaves at Asp, Glu, Gly or Pro.
- Pepsin - relatively nonspecific, preferentially cleaves at the carboxyl group of aromatic residues (Phe, Tyr, Trp) and Leu. It does not cleave at Val, Ala or Gly.
- Endoproteinase Lys-C - cleaves at the carboxyl group of Lys residues and is very effective in gel digests.
- Endoproteinase Glu-C - prefers cleavage at Glu residues over Asp residues at 100-fold greater rate in all buffers. It cleaves Glu-Pro and Asp-Pro bonds very slowly.
- Cyanogen bromide - cleaves at the carboxyl group of Met residues. Since this amino acid is relatively infrequent in proteins, this cleavage tends to produce relatively large and few peptides. Met-X amino acid bonds are cleaved specifically and almost quantitatively, with the exception of Met-Ser and Met-Thr bonds, where the hydroxyl group of the neighboring side chain may interfere with ring opening of the iminolactone intermediate.