Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Characterizing a protein structure is essential for understanding its function. Mass spectrometry has emerged as a powerful tool for this purpose, especially for protein systems that are difficult to study by traditional methods. To study a protein structure by mass spec, specific chemical reactions are performed in solution that encode a protein structural information into its mass.

One particularly effective approach is to use reagents that covalently modify solving accessible amino acids side chains. These reactions lead to mass increases that can be localized with residue level resolution when combined with proteolytic digestion and tandem mass spectrometry. Here, we described the protocols associated with use of diethyl pyrocarbonate or DEPC as a covalent labeling reagent together with mass spec detection.