Research Overview


Most proteins, particularly those that accomplish complicated tasks, form assemblies with other proteins and molecules that are critical to their function. Established structural biology tools are most effective for highly purified samples that have limited conformational variability, which makes it challenging to apply those methods to capture a systems-wide understanding of the structures, interactions, and dynamics that are present under different cellular conditions. The Bush Lab develops and applies mass spectrometry based techniques that are fast, sensitive, and tolerant of heterogeneity for characterizing the native structures of biological assemblies.

Modelling biomolecular assemblies using constraints from mass spectrometry (MS) and ion mobility (IM) experiments. The masses and identities of individual proteins (subunits) are determined using proteomics (a). The stoichiometry of the intact assembly is determined using MS from a native-like buffer (b). Subassemblies are generated by disrupting the assembly in solution and characterized by MS (c). Collision cross sections (Ω) of the intact assembly and subassemblies provide conformational information (d). The masses of subunits and subassemblies from MS are used to generate 2D interaction maps (e). 3D models are constructed using these maps, Ω values, and any complementary structural information (f). Atomic structures and models can then be docked into these models (g).

Native Mass Spectrometry

Gas-phase ions of biological assemblies can retain significant memories of their native structures in solution. Many measurements of stoichiometry, connectivity, and shape have shown that these aspects of assembly structure can be strongly correlated in both environments. Gas-phase techniques, including mass spectrometry, ion mobility, and ion chemistry are used to probe the native structures of biological assemblies. Accurate models of protein assemblies, including those that are heterogeneous, dynamic, and/or membrane-bound, are built based on results from both gas-phase experiments and complementary techniques.

  • Lab Contacts: Seoyeon (Cece) Hong, Daniele Canzani
  • Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry Strategy. Daniele Canzani, Domnita̧ -Valeria Rusnac, Ning Zheng, and Matthew F. Bush. Anal. Chem. 201991, 12775–12783. (Link)
  • Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity Connie Lu, Stewart Turley, Samuel T. Marionni, Young-Jun Park, Kelly K. Lee, Marcella Patrick, Ripal Shah, Maria Sandkvist, Matthew F. Bush, Wim G.J. Hol. Structure 2013, 21, 1707–1717. (Link|PUBMED)
  • SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket Weiman Xing, Luca Busino, Thomas R. Hinds, Samuel T. Marionni, Nabiha H. Saifee, Matthew F. Bush, Michele Pagano, Ning Zheng. Nature 2013496, 64–68. (Link|PUBMED)

Innovations in Instrumentation

The Bush Lab is focused on pushing the frontiers of chemical measurements, including maximizing the value of measurements using existing commercial instruments and developing next-generation instruments with unique functionality. We’re particularly interested in standardizing ion mobility measurements and increasing the orthogonality between ion mobility and mass spectrometry. Towards that end, we’ve developed radio-frequency confining drift cells, which we use for determining absolute collision cross section values, and extended the Structures for Lossless Ion Manipulations (SLIM) architecture to native-like ions, which we use for multidimensional ion mobility. Members of the Bush Lab benefit from the resources of the Student Innovation Center.

Our latest platform for tandem ion mobility, mass spectrometry.
  • Lab Contact: AnneClaireWageman, Ben Zercher
  • Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c.Samuel J. Allen, Rachel M. Eaton, Matthew F. Bush. Anal. Chem. 2017, DOI: 10.1021/acs.analchem.7b01234. (Link)
  • Analysis of Native-Like Ions using Structures for Lossless Ion Manipulations. Samuel J. Allen, Rachel M. Eaton, Matthew F. Bush. Anal. Chem. 2016, 88, 9118–9126. (Link)
  • Radio-Frequency (RF) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures. Samuel J. Allen, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2016, DOI: 10.1007/s13361-016-1479-9. (Link)

Relationship between Structure, Charge State, and Collision Cross Section

Ion mobility mass spectrometry probes the structures of protein ions in the gas phase, but electrospray ionization yields ions with a range of charge state and ions of different charge state usually exhibit different collision cross section values. No consensus has emerged regarding how results for different charge states should be integrated into the structural elucidation process. The Bush Lab uses experimental and computational methods to probe the relationship between these properties with the objective of understanding the relationship between the structures of proteins in solution and the observables of structural MS experiments.

  • Lab Contact: Meagan Gadzuk-Shea
  • Effects of Solution Structure on the Folding of Lysozyme Ions in the Gas-Phase. Kenneth J. Laszlo, Eleanor B. Munger, Matthew F. Bush. J. Phys. Chem. B 2017121, 2759–2766. (Link)
  • Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions (CAPTR). Kenneth J. Laszlo, Eleanor B. Munger, and Matthew F. Bush. J. Am. Chem. Soc. 2016, 138, 9581–9588. (Link|PUBMED)
  • Effects of Polarity on the Structures and Charge States of Native-like Proteins and Protein Complexes in the Gas Phase Samuel J. Allen, Alicia M. Schwartz, Matthew F. Bush. Anal. Chem. 2013, 85, 12055–12061. (Link|PUBMED)

Ion Mobility Theory

The Bush Lab develops theory to predict the collision cross sections of ions based on atomic models and the information content of ion mobility separations based on the design of the experiment. The outcomes of these projects increase the value of current ion mobility measurements and guide our efforts to develop higher-performance implementations of ion mobility.

  • Lab Contacts: Theresa Gozzo
  • Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. Daniele Canzani, Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A 2018122, 5625−5634. (Link)
  • Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids. Kimberly L. Davidson and Matthew F. Bush. Anal. Chem. 201789, 2017–2023. (Link)