Matthew Champion

Matthew Champion

Research Associate Professor


Dr. Champion has been Associate Professor of Research in the Department of Chemistry and Biochemistry at the University of Notre Dame since May, 2015 and was Assistant Professor of Research from September, 2009. In addition to being an investigator, he also works as a faculty in proteomics within the Mass Spectrometry and Proteomics facility. Prior to Notre Dame, he worked from 2003-2009 in the mass-spectrometry-proteomics group within Applied Biosystems (Now AB Sciex). Dr. Champion earned his B.S. in Microbiology from the University of Iowa in 1997 and his Ph.D. in Biochemistry from Texas A&M University.

Research Interests

We are primarily interested in developing and exploiting novel approaches to identify and characterize the components of secreted proteins from virulent microorganisms. We heavily utilize the 'awesome power of genetics' coupled with state-of-the art quantitative proteomics to enrich, identify and quantify the proteins responsible for biological phenotypes. We have ongoing projects in pathogenic mycobacteria, protein translation in E. coli through the PTRN, and quantitative protein secretion measured using capillary electrophoresis. One example is described below.

Mycobacteria, the causative agent of tuberculosis, like most organisms secretes proteins for biochemical functions. Secreted proteins are a proteome of 'target'-enriched material which contains virulence-factors, antigenic-determinants, and targets for treatment/detection. EsxA and EsxB (ESAT-6 and CFP10) are essential virulence factors exported by mycobacteria and other Gram positive pathogens. Identification of proteins that are required for effective synthesis and secretion of these crucial virulence determinants has been hindered by a lack of saturating genetic screens; high-throughput biochemical detection, and accurate quantification of disease phenotypes. We designed orthogonal antibody-free assays using a slew of proteogenetic approaches to comprehensively dissect the individual contribution of gene products towards a functioning disease secretion system (ESX-1) in pathogenic mycobacterium. This framework is highly extensible to the analysis of other pathogen and protein secretion systems, and has uncovered novel genes, pathways, and crosstalk among secretion systems.

Recent Papers

  • Wojcik, R.; Zhu, G.; Zhang, Z.; Yan, X.; Zhao, Y.; Sun, L.; Champion, M.M.; Dovichi, N.J. "Capillary zone electrophoresis as a tool for bottom-up protein analysis." Bioanalysis 2016, 8(2), 89-92.
  • Sun, L.; Zhu, G.; Yan, X.; Zhang, Z.; Wojcik, R.; Champion, M.M.; Dovichi, N.J. "Capillary zone electrophoresis for bottom-up analysis of complex proteomes." Proteomics 2016, 16(2), 188-196.
  • Sun, L.; Champion, M.M.; Huber, P.W.; Dovichi, N.J. "Proteomics of Xenopus development." Mol. Hum. Reprod. 2016, 22(3), 193-199.
  • Zhao, Y.; Riley, N.M.; Sun, L.; Hebert, A.S.; Yan, X.; Westphall, M.S.: Rush, M.J.; Zhu, G.; Champion, M.M.; Medie, F.; Champion, P.A.; Coon, J.J.; Dovichi, N.J. "Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics. "Anal. Chem. 2015, 87(10), 5422-5429.
  • Sun, L.; Hebert, A.S.; Yan, X.; Zhao, Y.; Westphall, M.S.; Rush, M.J.; Zhu, G.; Champion, M.M.; Coon, J.J.; Dovichi, N.J. "Over 10,000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry." Angew. Chem. Int. Ed. 2014, 53(50), 13931-13933.
  • Ren, G.; Champion, M.M.; Huntley, J.F. "Identification of disulfide bond isomerase substrates reveals bacterial virulence factors." Mol. Microbiol. 2014, 94(4), 926-944.


>> See full list of publications at PubMed >>

Contact Information

  • Research Associate Professor
  • Office: B40B McCourtney Hall
  • Phone: 574-631-1787

Primary Research Areas

Research Specialties