Reversible Lysine Derivatization Enables High Specificity of Arg-C Digestion Using Trypsin

Bottom-up proteomics approach has become an important strategy in diverse areas of biological research, and the enzymatic digestion is essential for this technology. Endopeptidase Arg-C catalyzing the hydrolytic cleavage of peptide bonds C-terminal to arginine could be an important protease in bottom-up proteomics. However, it has been seldom applied due to its low specificity and high cost. Reversible chemical derivatization of amine allows a real Arg-C digestion using trypsin. In this paper, a reversible amine derivatization method, citraconylation and decitraconylation were optimized and evaluated for large-scale proteomics studies. Combination of the reversible derivatization and trypsin digestion (termed Arg-C* digestion to distinguish from the conventional Arg-C digestion) resulted in 64.2% more peptide identification (11,925 ± 199 vs 7,262 ± 59) and significantly higher cleavage specificity (95.6% vs 73.6%) than the conventional Arg-C digestion. Comparison of Arg-C* digestion with the widely used trypsin and Lys-C digestion revealed that Arg-C* performed equally or slightly better than Lys-C although not comparable to trypsin. Therefore, the well-established Arg-C* digestion method is a promising approach for proteomics studies and could be used as the prior alternative digestion method to trypsin digestion in order to achieve higher proteome coverage.