Matthew Champion

Associate Professor

140B Mccourtney Hall
Notre Dame, IN 46556
+1 574-631-1787


Research Areas

  • Biochemistry
  • Physical/Analytical Chemistry

Research Specialties

  • Life Processes
  • Measurement

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Year Title
2019-present Associate Professor, University of Notre Dame
2015-2019 Research Associate Professor, University of Notre Dame
2009-2015 Research Assistant Professor, University of Notre Dame
2003-2009 Applied Biosystems (AB Sciex), Mass-Spectrometry-Proteomics Group
2005 Ph.D. in Biochemistry, Texas A&M University
1997 B.S. in Microbiology, University of Iowa

Research Interests

The Champion group is 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.

Selected Publications

  • Hu, D. D.; Weaver, S. D.; Collars, O. A.; Champion, P. A. and Champion, M. M. "N-Terminal Proteomics of Mycobacterium Marinum using Bottom-Up Label-Free Quantitative Analysis in Data-Dependent Acquisition Mode on a timsTOF Pro Mass Spectrometer" 2024 Microbiology Resource Announcements, 13 (4), e01263-23. DOI: 10.1128/mra.01263-23.
  • Lundgren, T. J.; Clark, P. L. and Champion, M. M. "Fit for Purpose Approach to Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics" 2024 Journal of Proteome Research, 23 (4), pp.1263-1271. DOI: 10.1021/acs.jproteome.3c00730.
  • Nicholson, K. R.; Cronin, R. M.; Prest, R. J.; Menon, A. R.; Yang, Y. W.; Jennisch, M. K.; Champion, M. M.; Tobin, D. M. and Champion, P. A. "The Antagonistic Transcription Factors, EspM and EspN, Regulate the ESX-1 Secretion System in M. Marinum" 2024 Mbio, 15 (4), e03357-23. DOI: 10.1128/mbio.03357-23.
  • Huge, B. J.; Kerr, C. M.; Wanigasinghe, S.; Champion, M. M. and Dovichi, N. J. "Optimized Sample Buffer for Dispersed, High-Resolution Capillary Zone Electrophoretic Separation of Escherichia Coli B" 2023 Scientific Reports, 13 (1), 22269. DOI: 10.1038/s41598-023-49669-y.
  • Nandana, V.; Rathnayaka-Mudiyanselage, I. W.; Muthunayake, N. S.; Hatami, A.; Mousseau, C. B.; Ortiz-Rodríguez, L. A.; Vaishnav, J.; Collins, M.; Gega, A.; Mallikaarachchi, K. S.; Yassine, H.; Ghosh, A.; Biteen, J. S.; Zhu, Y. X.; Champion, M. M.; Childers, W. S. and Schrader, J. M. "The BR-Body Proteome Contains a Complex Network of Protein-Protein and Protein-RNA Interactions" 2023 Cell Reports, 42 (10), 113229. DOI: 10.1016/j.celrep.2023.113229.
  • Avila-Cobian, L. F.; Hoshino, H.; Horsman, M. E.; Nguyen, V. T.; Qian, Y. Y.; Feltzer, R.; Kim, C.; Hu, D. D.; Champion, M. M.; Fisher, J. F. and Mobashery, S. "Amber-Codon Suppression for Spatial Localization and in Vivo Photoaffinity Capture of the Interactome of the Pseudomonas Aeruginosa Rare Lipoprotein A Lytic Transglycosylase" 2023 Protein Science, 32 (10), e4781. DOI: 10.1002/pro.4781.

>> See full list of publications at PubMed >>