Development of an Online LC‐MS/MS Method for the Investigation of Enzyme Kinetics Using Trypsinization of Apomyoglobin Protein as a Model System

Abstract

The optimization of enzymatic protein cleavage by trypsin is often performed “in the dark” wherein researchers perform the reaction under different conditions on a laboratory bench for a single or a small selection of time points. Upon quenching of the trypsinization reaction with a strong acid, the resulting protein reaction mixture is injected onto a liquid chromatography column for profiling of the peptide mixture. The arbitrary selection of enzyme reaction time presents a major limitation to this experimental approach. Herein, we present a “real time” optimization of the enzymatic reaction enabled by performing the reaction within a vial in an autosampler with regular sampling of the mixture. Using this method, we are able to simultaneously monitor degradation of the intact protein target and the release of its tryptic peptides. Peptides with missed cleavage sites may appear and then disappear with time as fully tryptic peptides dominate the endpoint of the reaction. The method can be multiplexed in that we can sample many parallel mixtures in series. This allows us to directly compare such variables as pH, solvent, ionic strength, protein to enzyme ratio, enzyme concentration and metal salts on digestion efficiency while always including a positive control for reference. Our liquid chromatograph-tandem mass spectrometry analysis platform uses a Dionex Ultimate 3000 interfaced with a hybrid quadrupole-Orbitrap (Q-Exactive) mass spectrometer capable of mass resolution of 140,000 and a mass accuracy better than 10 ppm. We are able to monitor the efficiency and kinetics of tryptic digestion of apomyoglobin with high resolution in the time dimension. At room temperature, the enzymatic reaction can take in excess of 12 hours to reach completion compared with about 3 hours at 38oC. A low percentage of ethanol (~ 0.1%) added to the reaction mixture was shown to double the yield of most peptides while the addition of alkaline earth metals also had beneficial effects, in particular 10 mM barium chloride. Other metals were shown to either inhibit the degradation of apomyoglobin (zinc) or to prevent the detection of the resulting peptides (lead). Overall, the effects of adding barium in the presence of 0.1% ethanol improved peptide yield as much as 11-fold for the LFTGHPETLEK peptide of apomyoglobin while showing no effect on the tryptic release of the YLEFISDAIIHVLHSK peptide. This method offers a promising strategy for the optimization of targeted protein quantitation as well as a means to study the kinetics and characterize the specificity of other proteolytic enzymes.