Lys-C/Arg-C, a New Enzyme Combination for Next-Generation Proteomics

Today, the most widely used bottom-up proteomics studies necessitate a proteolysis step prior to MS analysis. Trypsin is often the best protease in choice due to its high specificity and MS-favored proteolytic products. Trypsin has been challenged for its low cleavage efficiency at Lys-X bonds, and tandem Lys-C/trypsin digestion approach has been developed to alleviate the problem. However, the identification capacity of the two digestions often disagrees among different research groups. Herein, we report a new tandem digestion using Lys-C and Arg-C (Lys-C/Arg-C), which we have proven to be more efficient and specific than trypsin and Lys-C/trypsin approaches. Analysis of our previous data (Anal. Chem. 2018, 90, 1554-1559) revealed that both Lys-C and Arg-C perform better in trypsin-mode digestion. In particular for Arg-C, the identification capacity is increased to 2.6 times and even comparable with trypsin. The good complementarity, high digestion efficiency and high specificity of Lys-C and Arg-C prompt a tandem Lys-C/Arg-C digestion. We systematically evaluated the Lys-C/Arg-C digestion using qualitative and quantitative proteomics approaches and confirmed its superior performance in digestion efficiency, specificity and identification capacity to the currently widely used trypsin and Lys-C/trypsin digestions. As a result, we concluded that Lys-C/Arg-C digestion approach would be the choice of next-generation digestion approach for better results in both qualitative and quantitative proteomics studies.