Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein-DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.

Faculty of Sciences Charles University Prague Czech Republic

Heinrich Pette Institute Leibniz Institute for Experimental Virology Hamburg Germany

Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic

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Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry