Protein Fragmentation by Proteolysis

To localize the rate of deuterium buildup to specific amides, the analyte protein is fragmented into a collection of peptides using combinations of endo- and exo-proteases. Due to the low pH of the quench conditions in which the protein and peptide samples are maintained after deuterium labeling, acid-reactive proteases such as pepsin must be employed. Studies with combinations of acid-reactive en-doproteinases and carboxypeptidases have been employed to achieve greater sequence coverage and higher amide resolution [42, 45].

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