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Automation of H/D Exchange by MS

A fully automated system for performing detailed studies has been developed to improve the reproducibility and throughput (Fig. 12.2) [8]. It consists of two functional components; a sample-deuteration device and a protein processing unit. The preparation operations (shown at the top of Fig. 12.2) are performed by two robotic arms equipped with low volume syringes and two temperature-controlled chambers, one held at 25 ° C and the other held at 1 ° C. To initiate the exchange experiment, a small amount of protein solution is mixed with a deuter-ated buffer and the mixture is then incubated for a programmed period of time in the temperature-controlled chamber. This on-exchanged sample is immediately transferred to the cold chamber where a quench solution is added to the mixture.

Fig. 12.2 Diagram of a fully automated system for acquiring H/D exchange MS data starting with a stock solution of the nondeuterated protein. In this system [8], the liquid handler mixes a small amount of concentrated protein solution with a selected deuterated buffer and the mixture is incubated for a programmed period of time. The exchange reaction is conducted in a temperature-controlled chamber held at 25 °C. The mixture is then transferred to an acidic quench solution held at 1 °C. After quenching the exchange reaction, the entire sample is injected onto an LC-MS system

Fig. 12.2 Diagram of a fully automated system for acquiring H/D exchange MS data starting with a stock solution of the nondeuterated protein. In this system [8], the liquid handler mixes a small amount of concentrated protein solution with a selected deuterated buffer and the mixture is incubated for a programmed period of time. The exchange reaction is conducted in a temperature-controlled chamber held at 25 °C. The mixture is then transferred to an acidic quench solution held at 1 °C. After quenching the exchange reaction, the entire sample is injected onto an LC-MS system which includes injection loops, protease column(s), a trap, an analytical column, and isocratic and gradient pumps. The injector, columns, and electronically controlled valves reside in a low temperature chamber to minimize the loss of deuterium by backexchange. The quenched protein solution is pumped in series over a column containing immobilized protease and a reverse-phase trap to capture the peptide fragments. The gradient pump is activated following the digestion and the peptides captured on the trap are eluted into the mass spectrometer after separation in the analytical column.

The exchange-quenched solution is then injected onto the protein processing system which includes injection loops, protease column(s), a trap column, an analytical column, electronically controlled valves, and isocratic and gradient pumps. The injector, columns and valves reside in a low temperature chamber to minimize the loss of deuterium by back exchange (Fig. 12.2). The quenched protein solution is pumped in series through a column containing an immobilized protease and a trap column to capture the peptide fragments. The gradient pump is activated following digestion and the peptides captured on the trap column are eluted and separated over an analytical reverse-phase HPLC column directly into the mass spectrometer.

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