LSL S503


Biological mass spectrometry, protein folding and dynamics

Background and Training

PhD: Department of Chemistry, University of Oxford, UK

Postdoctoral training: University of Massachusetts Amherst

Research Summary

Mass spectrometry has become a major analytical technique in the life sciences arena over the past several years. Most commonly used in the field of proteomics for investigating how proteins populations change within cells in response to external stimuli, there is also a great deal of interest in understanding how mass spectrometry (MS) can help in our understanding of protein folding, protein dynamics and protein assembly. With the advent of softer ionization techniques such as MALDI (matrix-assisted laser desorption/ionization) and ESI (electrospray ionization) and in particular nanospray (nanoESI), MS has proven itself a valuable tool in the biophysical arena. It is now possible to spray intact macromolecular complexes from solution into the mass spectrometer and determine the molecular weight of the intact complex. Coupled with mild excitation techniques, one can also induce dissociation of the complex, either partially or completely, in order to get an idea of the interacting partners.

Another field of intense interest is the application of hydrogen/deuterium exchange coupled with MS to study protein dynamics. Briefly, backbone amide hydrogens involved in protein structure by hydrogen bonding or otherwise sequestered from solvent will be protected against exchange with bulk solvent. If the bulk solvent is heavy water (2H2O) then unprotected amides will exchange hydrogen for deuterium, leading to a 1 Da mass increase, which can be measured by mass spectrometry.  In this way the response of proteins to changes in solvent conditions or the presence of cofactors or other binding partners can be measured by MS.

As Director of the University Mass Spectrometry Center, my goal is to make our state-of-the-art MS instrumentation available to researchers across campus in order to address their analytical needs. We work closely with members of many of the departments on campus, including Chemistry, to develop new analytical methods that can be applied to biochemical questions. The Mass Spectrometry Center is available to all members of the campus community and the Five College Consortium. A variety of instruments and ionization sources are available. Please see the website for details.


  • Guerra, D., Truebridge, I., Eyles, S.J., Treffon, P., Vierling, E. (2018) “Direct measurement of S-nitrosothiols with an Orbitrap Fusion mass spectrometer: S-nitrosoglutathione reductase as a model protein” Methods Molec. Biol.1747, 143-160.
  • He, T., Gershenson, A., Eyles, S.J., Lee, Y.J., Liu, W.R., Wang, J., Roberts, M.F. (2015) “Fluorinated aromatic amino acids distinguish cation- interactions from membrane insertion” J. Biol. Chem. 290, 19334-19442.
  • Koshy, S.S., Li, X., Eyles. S.J., Weis, R.M., Thompson, L.K. (2014) “Hydrogen exchange differences between chemoreceptor signaling complexes localize to functionally important subdomains” Biochemistry 53, 7755-7764.
  • Kaltashov, I.A., Eyles, S.J. Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics and Interaction of Biomolecules, 2nd edition, John Wiley & Sons. 2012. 325 pp.
  • Al-Amier, H., Eyles, S.J., Craker, L.E. Evaluation of extraction methods for isolation and detection of formononetin in black cohosh (Actaea racemosa L.). J. Medicinally Active Plants (2012) 1, 6-12.
  • Eyles, S.J., Gierasch, L.M. Nature's molecular sponges: Small heat shock proteins grow into their chaperone roles. Proc. Natl. Acad. Sci. (2010) 107, 2727-2728.
  • Kaltashov, I.A., Eyles, S.J., Mohimen, A., Hoerner, J.K., Abzalimov, R.R., Griffith, W.P. Analysis of partially folded proteins by electrospray ionization mass spectrometry In: Methods in Protein Structure and Stability Analysis: NMR and EPR Spectroscopies, Mass-Spectrometry and Protein Imaging. V. Uversky, ed. Hauppauge, New York: Nova Science Publishers, Inc., 2008. pp. 175-196.
  • Kaltashov, I.A., Abzalimov, R.R., Eyles, S.J., Frimpong, A.K. (2008) “Studies of intact proteins and protein complexes: ESI MS approaches” In: Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics. M. Chance, ed. Boston: Wiley-Blackwell, 2008. pp. 215-240.
  • Chen, Y.-H., Comeaux, L.M., Eyles, S.J., Knapp, M.J. Auto-hydroxylation of FIH-1: an Fe(II), alpha-ketoglutarate-dependent human hypoxia sensor. Chem. Commun. 2008. 4768-4770. [PubMed]