Evaluation of Metalloendopeptidase Lys-N Protease Performance under Different Sample Handling Conditions

Trypsin, the most widely used enzyme in proteomics, has a few caveats as it does not perform well under certain harsh sample handling conditions and creates relatively short peptides less amenable to, for instance, electron transfer dissociation. There is, thus, room for improvement using alternative proteases. Here, we evaluate the performance of such an alternative protease, the metalloendopeptidase Lys-N, in sample preparation for proteomic analyses under various experimental conditions. The experimental parameters we evaluated were protein-to-protease ratio, incubation time, temperature, and several concentrations of denaturing modifiers often used in proteomics sample handling. Our data reveal that Lys-N is still very efficient under some very harsh (denaturing) conditions (e.g., 8 M urea, 80% acetonitrile) and at temperatures as low as 4 degrees C and up to 80 degrees C but severely hampered by guanidine hydrochloride and methanol. These rather unique features make Lys-N a good candidate for a variety of applications, such as membrane proteomics and possibly HID exchange mass spectrometry. Additionally, we show that Lys-N is capable of, in contrast to trypsin or Lys-C, cleaving adjacent to mono- and dimethylated lysines, making it a good candidate for targeted epigenetic analysis of for instance histones.