Protocol

Fragmentation of Protein Using Trypsin

This protocol was adapted from "Peptide Mapping and Sequence Analysis of Gel-Resolved Proteins," Chapter 7 in Proteins and Proteomics (ed. Simpson). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2003.

INTRODUCTION

In this protocol, the highly specific protease trypsin is used to hydrolyze a protein completely. Proteolysis is carried out with high levels of trypsin to ensure total proteolysis. (Trypsin is a robust enzyme; hence, proteolysis can also be carried out under denaturing conditions such as 2 M guanidine-HCl, 0.1% SDS, and >10% acetonitrile to ensure complete digestion.) Trypsin cleaves the peptide bond between the carboxyl group of arginine or the carboxyl group of lysine and the amino group of the adjacent amino acid. The rate of cleavage occurs more slowly when the lysine and arginine residues are adjacent to acidic amino acids in the sequence or cystine. Cleavage does not occur when lysine or arginine is followed by proline. The sites of trypsin cleavage can be limited to arginine peptide bonds by succinylation. or citraconylation prior to trypsin digestion.