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Mass spectrometry has become a powerful tool for determining the composition, stoichiometry, subunit interactions, and architectural organization of non-covalent protein complexes. The vast majority of assemblies studied so far by this approach are those that contain a sufficient amount of electrostatic interactions and hydrogen bonds that can survive the transition from solution to the gas-phase and maintain the structural features of the vaporized ions. An intriguing question that naturally arises is whether mass spectrometry can also be harnessed for the study of molecular systems dominated by non-polar interactions. Here we address this issue and discuss the fate of hydrophobic complexes in the absence of bulk water molecules. We emphasize the progress that has been accomplished in this field that is moving towards the analysis of larger and more complex hydrophobic systems. We attribute this advance to recent developments of mass spectrometry and its application to non-covalent complexes in general, and to the understanding of experimental and biochemical conditions for the preservation of hydrophobic interactions in particular. Furthermore, we discuss the ability of mass spectrometry to serve as a quantitative tool for assessing the strength, binding energies, and stoichiometries of hydrophobic interactions. Overall, we aim to stimulate research in this area and to establish mass spectrometry as a tool for analyzing hydrophobic interactions within complex biological systems. ©2011 Bentham Science Publishers Ltd.

Original publication




Journal article


Current Proteomics

Publication Date





47 - 58