John Klassen

B.Sc., Queen's University
Ph.D., University of Alberta

Office: CCIS 4-084
Phone: (780) 492-3501

Group Web Page:


Our research program focuses on the development and application of mass spectrometry-based techniques, implemented with a 4.7 tesla Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) equipped with a nanoflow electrospray (nanoES) source, to study the composition, topology and physicochemical properties of protein complexes in the gas and condensed phases. One component of our research program involves the use of time-resolved ion-molecule and ion-dissociation reactions to study the structure and reactivity of gaseous protein assemblies and protein-ligand complexes. These studies are of considerable fundamental importance, providing insight into the intrinsic properties of proteins and protein complexes in the absence of solvent, and are critical to the evolution of mass spectrometry as a powerful tool for proteomics. A second area of research deals with the development of novel strategies to map protein interaction sites and quantify association free energies in the aqueous phase. Some of the specific research projects in our laboratory are described below.

  1. Structural Characterization of Protein Assemblies

    We are using time-resolved dissociation experiments to dissect gaseous protein assemblies to obtain information on composition, quaternary structure and binding energetics. While the concept is straightforward, implementation is hindered by the limited fragmentation observed for the assemblies and an incomplete understanding of the dissociation mechanisms. Using the blackbody infrared radiative dissociation (BIRD) technique, we are investigating the dissociation pathways, kinetics and energetics of assemblies in the gas phase. These studies provide new insight into the dissociation mechanism and the influence of charge and higher order structure thereon and suggest new strategies to increase the structural information available from MS.

  2. Mapping Intrinsic Protein-Ligand Interactions

    Our laboratory is mapping the intermolecular interactions present in gaseous protein-ligand complexes. Using a functional group replacement strategy and a thermal activation technique, the nature and strength of the dominant intermolecular interactions in gaseous protein-oligosaccharide complexes are being determined. Comparison of the gas phase data with solution thermochemistry and crystal structures provides new insights into the structural and energetic role of solvent in association. The protein-ligand interaction energies determined in this work are also important for the development of accurate force fields for improved molecular modeling of biomolecules and their complexes.

  3. Binding Affinity and Stoichiometry of Protein-Ligand Complexes

    Another component of our research program deals with the application of nanoES-FT-ICR MS to evaluate the affinity and stoichiometry of weakly-binding protein-ligand complexes in solution. Quantification of the solution composition based on the gas-phase ion abundance is often hindered by spectral artifacts originating from the nanoES process (e.g. non-specific binding) and gas-phase processes (e.g.decomposition). We are exploring aspects of the nanoES process as well as the relative stability of specific and non-specific protein-ligand complexes to establish experimental conditions that minimize such artifacts.

Selected Publications

J. Sun, W. Wang, E.N. Kitova and J.S. Klassen “A Method for Distinguishing Specific and Nonspecific Protein-Ligand Complexes in Nanoelectrospray Ionization Mass Spectrometry” Anal. Chem. 2006, in press.

E.N. Kitova, R. Daneshfar, P. Marcaoto, G. Mulvey, G.D. Armstrong and J.S. Klassen “Stability of the Homopentameric B Subunits of Shiga Toxins 1 and 2 in Solution and the Gas Phase as Revealed by NanoES-FT-ICR/MS” J. Am. Soc. Mass Spectrom. 2005, 16, 1957-1968.

W. Wang, E.N. Kitova and J.S. Klassen “Nonspecific Protein-Carbohydrate Complexes Produced by Nanoelectrospray Ionization. Factors Influencing their Formation and Stability” Anal. Chem. 2005, 77, 3060-3071.

E.N. Kitova, D.R. Bundle and J.S. Klassen “Partitioning of Solvent Effects and Intrinsic Interactions in Biological Recognition” Angew. Chemie Int. Ed. 2004, 43, 4183-4186.

R. Daneshfar, E.N. Kitova and J.S. Klassen “Determination of Protein-Ligand Association Thermochemistry Using Variable-Temperature Nanoelectrospray Mass Spectrometry” J. Am. Chem. Soc. 2004, 126, 4786-4787.