Joshua J. Coon

Joshua J. Coon Headshot


4422 Genetics Biotechnology Center

425 Henry Mall

Madison, WI 53706 

The Coon Research Group

Phone: (608) 263-1718


• B.S., Central Michigan University
• Ph.D. 2002, University of Florida
• Postdoctoral Fellow at 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
• WARF Romnes Faculty Fellowship, University of Wisconsin-Madison, 2014

Research Interests
My research group has the overarching goal of catalyzing evolution in the rapidly developing field of proteomics and to use these technologies to address fundamental problems in developmental biology. With emphasis on ion chemistry and instrumentation, we seek to develop and apply new enabling mass spectrometry-based (MS) proteomic technologies. These cutting-edge tools allow us to examine, with unprecedented chemical detail and sensitivity, the molecular events that commit human embryonic stem cells (hES cells) to exit the pluripotent state. Here we are focused on both intracellular signaling and the epigenetic regulation of pluripotency. For the former we ask which branches of the FGF signaling pathway are active in hES cells and which proteins/networks are phosphorylated upon differentiation. Epigenetics is believed to play a critical role in the establishment and maintenance of pluripotency; thus, we have also aimed our new technologies at interpreting the epigenetic codes and monitoring how these messages change during hES cell differentiation.

Active Projects
Research projects in the Coon lab include: (1) instrumentation development, (2) data analysis software design, (3) fundamental ion chemistry studies, and (4) biological applications of the technology. Biological applications include global identification of protein post-translational modification (specifically phosphorylation), quantitative analysis of protein phosphorylation (i.e., comparative analysis of two cellular states), and cancer biomarker discovery.


Publications of Note

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• 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.

• Sun LL, Hebert AS, Yan XJ, Zhao YM, Westphall MS, Rush MJP, et al.. Over 10000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry. Angewandte Chemie-International Edition. 2014;53:13931-13933.