Trypsin has a wide range of applications including amino acid analysis and protein sequencing, mapping and structural studies. Enzymes such as trypsin and chymotrypsin have become important tools in sequencing studies since they are highly selective in their cleavage of peptide bonds. Trypsin cleaves only those peptide bonds in which the carboxyl group is contributed by a lysine or an arginine residue, regardless of the length or amino acid sequence of the chain.

Immobilized trypsin can be substituted for free trypsin in any application, and is advantageous because it virtually eliminates autolysis, eliminates contamination of a sample with the protease and allows control of the digestion by removing the trypsin. Immobilized trypsin is also more stable against heat-induced denaturation, resulting in longer maintenance of activity.