Joshua J. Coon

Position title: Professor


Phone: (608) 263-1718

4422 Genetics Biotechnology Center
425 Henry Mall, Madison, WI 53706

Joshua Coon

The Coon Lab Website


• B.S. 1998, Central Michigan University
• Ph.D. 2002, University of Florida
• Postdoctoral Fellow, 2003-2005, University of Virginia

Honors & Awards

• Ruth L. Kirchstein Individual National Research Service Award, 2003
• Named as one of Tomorrow’s PIs by Genome Technology magazine, 2006
• American Society of Mass Spectrometry Research Award, 2007
• Beckman Young Investigator Award, 2007
• Eli Lilly and Company Young Investigator, 2007
• National Science Foundation Career Award, 2008
• Ken Standing Award, University of Manitoba, 2009
• Philip  R. Certain Dean’s Distinguished Faculty Award, 2010
• Pittsburg Conference Achievement Award, 2010
• Arthur F. Findeis Award for Achievements by a Young Analytical Scientist, American Chemical Society, 2011
• Biemann Medal (ASMS), 2012
• WARF Romnes Faculty Fellowship, University of Wisconsin-Madison, 2014
• Thomas and Margaret Pyle Chair at the Morgridge Institute for Research, 2018

Research Interests

The sequencing of the human genome marked the beginning of a collective scientific expedition to understand complex organisms. Genes, of course, merely contain the instructions for which proteins will populate the cell. Untangling the multi-faceted networks that regulate complex organisms and their diseases will require innovative technologies to globally monitor many classes of biomolecules, including nucleic acids, proteins, and metabolites. High-throughput technologies for gene and transcript measurement are well-developed and broadly accessible, and, as such, have had a fantastic and transformative impact on modern biology and medicine. For numerous reasons, methods for global analysis of proteins and metabolites – crucial biological effector molecules – are less evolved and markedly less accessible.

The overarching mission of my program is to (1) facilitate expedient, comprehensive analysis of proteins and metabolites by innovating new mass spectrometric technologies and (2) apply these techniques to advance biomedical research.

Publications of Note

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•Lee JH, Mand MR, Kao CH, Zhou Y, Ryu SW, Richards, AL  et al.. ATM Directs DNA Damage Responses and Proteostasis via Genetically Separable Pathways. Science Signaling. 2018;11.

• Riley NM, Coon JJ. The Role of Electron Transfer Dissociation in Modern Proteomics. Analytical Chemistry. 2018;90:40-64.

• Overmyer KA, Tyanova S, Hebert AS, Westphall MS, Cox J, Coon JJ. Multiplexed Proteome Analysis with Neutron-Encoded Stable Isotope Labeling in Cells and Mice. Nature Protocols. 2018;13:293-306.

• Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, et al.. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Molecular Cell. 2015;57:83-94.

• Ulbrich A, Merrill AE, Hebert AS, Westphall MS, Keller MP, Attie AD, et al.. Neutron-Encoded Protein Quantification by Peptide Carbamylation. Journal of the American Society for Mass Spectrometry. 2014;25:6-9.

• Ulbrich A, Bailey DJ, Westphall MS, Coon JJ. Organic Acid Quantitation by NeuCode Methylamidation. Analytical Chemistry. 2014;86:4402-4408.

• Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, et al.. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 2014;86:2314-2319.

• Lemke RAS, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellstrom H, Coon JJ, et al.. Synthesis and scavenging role of furan fatty acids. Proceedings of the National Academy of Sciences of the United States of America. 2014;111:E3450-E3457.

• Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, et al.. NeuCode Labels for Relative Protein Quantification. Molecular & Cellular Proteomics. 2014;13:2503-2512.

• Parreiras LS, Breuer RJ, Narasimhan RA, Higbee AJ, La Reau A, Tremaine M, et al.. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover. Plos One. 2014;9.

• Keating DH, Zhang YP, Ong IM, McIlwain S, Morales EH, Grass JA, et al.. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification. Frontiers in Microbiology. 2014;5

• Bhatnagar S, Soni MS, Wrighton LS, Hebert AS, Zhou AS, Paul PK, et al.. Phosphorylation and Degradation of Tomosyn-2 De-represses Insulin Secretion. Journal of Biological Chemistry. 2014;289:25276-25286.

• Peterson AC, Hauschild JP, Quarmby ST, Krumwiede D, Lange O, Lemke RAS, et al.. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part I: Design and Characterization. Analytical Chemistry. 2014;86:10036-10043.

• Peterson AC, Balloon AJ, Westphall MS, Coon JJ. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part II: New Approaches for Discovery Metabolomics. Analytical Chemistry. 2014;86:10044-10051.

• Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, et al.. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2014;111:E4697-E4705.