Chapter 4. Mass Spectrometry-Based Approaches to Study Biomolecular Higher-Order Structure

  1. Igor A. Kaltashov and
  2. Stephen J. Eyles

Published Online: 27 JAN 2005

DOI: 10.1002/0471705179.ch4

Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules

Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules

How to Cite

Kaltashov, I. A. and Eyles, S. J. (2005) Mass Spectrometry-Based Approaches to Study Biomolecular Higher-Order Structure, in Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules, John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/0471705179.ch4

Author Information

  1. University of Massachusetts at Amherst, USA

Publication History

  1. Published Online: 27 JAN 2005
  2. Published Print: 6 APR 2005

Book Series:

  1. Wiley-Interscience Series in Mass Spectrometry

Book Series Editors:

  1. Dominic M. Desiderio2 and
  2. Nico M. M. Nibbering3

Series Editor Information

  1. 2

    Departments of Neurology and Biochemistry, University of Tennessee Health Science Center, USA

  2. 3

    Vrije Universiteit Amsterdam, The Netherlands

ISBN Information

Print ISBN: 9780471456025

Online ISBN: 9780471705178



  • chemical cross-linking;
  • selective chemical labeling;
  • nonspecific labeling (foot-printing);
  • hydrogen/deuterium exchange;
  • controlled ion fragmentation


Obtaining higher-order structures of biopolymers is usually a first step in analyzing their behavior and understanding function. While X-ray crystallography and high-field NMR undoubtedly provide the highest quality information, limitations of these techniques (as discussed in Chapter 3) often make such high-resolution structures unavailable for a variety of important proteins and their assemblies. This chapter discusses various MS-based approaches to evaluate higher order structure at various levels of spatial resolution when the crystallographic and NMR data are unavailable or insufficient. The chapter begins with a discussion of methods used to probe biomolecular topology and topography. These methods generally utilize chemical cross-linking to characterize tertiary and quaternary contacts by generating “proximity maps.” We then proceed to a discussion of various methods of mapping solvent accessibility of protein segments. In addition to covalent modification of protein surfaces in both specific and nonspecific fashion, we briefly discuss application of hydrogen-deuterium exchange to mapping protein-protein interfaces. The chapter concludes with a brief overview of two emerging low-resolution methods that aim at evaluating the overall geometry of biopolymers and their assemblies. The first one uses controlled fragmentation of protein complex ions in the gas phase to identify neighboring subunits and hierarchical organization of protein quaternary structure. The second emerging method provides an estimate of the solvent-accessible surface area in proteins and protein complexes (based on the number of charges accommodated by the protein).