CRG - Joshua Coon

Joshua Coon
Principal Investigator
425 Henry Mall
Room #4426
jcoon@chem.wisc.edu

Background

Professor Joshua Coon received his Ph.D. in chemistry from the University of Florida in 2002 during which time he developed an ambient ionization technique for peptide analyses that combined laser desorption and atmospheric pressure chemical ionization. He then conducted his postdoctoral studies in the laboratory of Professor Don Hunt at the University of Virginia where he and John Syka carried out pioneering work on the development of electron transfer dissociation (ETD). This activation technique is now commonly used for the identification of labile post-translational modifications and for large-scale protein sequencing. Coon is an Associate Professor in the Departments of Chemistry and Biomolecular Chemistry at the University of Wisconsin.

His research group is primarily focused on instrumental developments in mass spectrometry and in proteomics to address fundamental questions in cell biology. With emphasis on ion chemistry and instrumentation, his group develops and applies new enabling mass spectrometry-based (MS) proteomic technologies. These cutting-edge tools allow them to examine the molecular events leading to cell differentiation of human embryonic stem cells and the combinatorial combination of histone post-translational modifications in pluripotent stem cells. His research interest also focuses on the development of ETD for intact protein sequencing, and on the use and application of algorithms enabling protein identification from product ion spectra. He holds several patents on ETD and its application to peptide sequencing.


Awards

  • 2012: Biemann Medal (ASMS)
  • 2011: Arthur Findeis Award for Young Analytical Scientists (ACS)
  • 2010: Philip R. Certain Dean's Distinguished Faculty Award
  • 2010: Pittsburgh Conference Achievement Award
  • 2009: Ken Standing Award (University of Manitoba)
  • 2008: NSF CAREER Award
  • 2007: American Society of Mass Spectrometry Research Award
  • 2007: Beckman Young Investigator
  • 2006: Named one of ''Tomorrow's PI's'' by Genome Technology magazine
  • 2003: Ruth L. Kirchstein Individual National Research Service Award (NIH-NRSA)



Publications

  1. Q. W. Xia, M. V. Lee, C. M. Rose, A. J. Marsh, S. L. Hubler, C. D. Wenger, J. J. Coon. Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation, Journal of the American Society for Mass Spectrometry, 2011; 22: 255-264.

  2. C. D. Wenger, D. H. Phanstiel, M. V. Lee, D. J. Bailey, J. J. Coon. COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA, Proteomics, 2011; 11: 1064-74.

  3. Q. W. Xia, D. M. Good, C. D. Wenger, J. J. Coon. Intellinsity: a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events, Rapid Communications in Mass Spectrometry, 2010; 24: 3217-3218.

  4. C. D. Wenger, G. C. McAlister, Q. W. Xia, J. J. Coon. Sub-part-per-million Precursor and Product Mass Accuracy for High-throughput Proteomics on an Electron Transfer Dissociation-enabled Orbitrap Mass Spectrometer, Molecular & Cellular Proteomics, 2010; 9: 754-763.

  5. D. L. Swaney, C. D. Wenger, J. J. Coon. Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics, Journal of Proteome Research, 2010; 9: 1323-1329.

  6. A. C. Peterson, G. C. McAlister, S. T. Quarmby, J. Griep-Raming, J. J. Coon. Development and Characterization of a GC-Enabled QLT-Orbitrap for High-Resolution and High-Mass Accuracy GC/MS, Analytical Chemistry, 2010; 82: 8618-8628.

  7. G. C. McAlister, D. Phanstiel, C. D. Wenger, M. V. Lee, J. J. Coon. Analysis of Tandem Mass Spectra by FTMS for Improved Large-Scale Proteomics with Superior Protein Quantification, Analytical Chemistry, 2010; 82: 316-322.

  8. A. R. Ledvina, N. A. Beauchene, G. C. McAlister, J. E. Syka, J. C. Schwartz, J. Griep-Raming, M. S. Westphall, J. J. Coon. Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture, Anal Chem, 2010; 82: 10068-74.

  9. P. A. Grimsrud, D. L. Swaney, C. D. Wenger, N. A. Beauchene, J. J. Coon. Phosphoproteomics for the Masses, ACS Chemical Biology, 2010; 5: 105-119.

  10. P. A. Grimsrud, D. den Os, C. D. Wenger, D. L. Swaney, D. Schwartz, M. R. Sussman, J. M. Ane, J. J. Coon. Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes, Plant Physiology, 2010; 152: 19-28.

  11. D. M. Good, C. D. Wenger, J. J. Coon. The effect of interfering ions on search algorithm performance for electron-transfer dissociation data, Proteomics, 2010; 10: 164-167.

  12. P. Zurbig, S. Decramer, M. Dakna, J. Jantos, D. M. Good, J. J. Coon, F. Bandin, H. Mischak, J. L. Bascands, J. P. Schanstra. The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease, Proteomics, 2009; 9: 2108-2117.

  13. D. L. Swaney, C. D. Wenger, J. A. Thomson, J. J. Coon. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry, Proceedings of the National Academy of Sciences of the United States of America, 2009; 106: 995-1000.

  14. T. P. Second, J. D. Blethrow, J. C. Schwartz, G. E. Merrihew, M. J. MacCoss, D. L. Swaney, J. D. Russell, J. J. Coon, V. Zabrouskov. Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures, Analytical Chemistry, 2009; 81: 7757-7765.

  15. R. G. Sadygov, D. M. Good, D. L. Swaney, J. J. Coon. A New Probabilistic Database Search Algorithm for ETD Spectra, Journal of Proteome Research, 2009; 8: 3198-3205.

  16. D. Phanstiel, R. Unwin, G. C. McAlister, J. J. Coon. Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry, Analytical Chemistry, 2009; 81: 1693-1698.

  17. H. Mischak, J. J. Coon, J. Novak, E. M. Weissinger, J. P. Schanstra, A. F. Dominiczak. Capillary Electrophoresis-Mass Spectrometry as a Powerful Tool in Biomarker Discovery and Clinical Diagnosis: An Update of Recent Developments, Mass Spectrometry Reviews, 2009; 28: 703-724.

  18. J. V. McGivern, D. L. Swaney, J. J. Coon, M. D. Sheets. Toward Defining the Phosphoproteome of Xenopus laevis Embryos, Developmental Dynamics, 2009; 238: 1433-1443.

  19. J. A. Madsen, M. W. Gardner, S. I. Smith, A. R. Ledvina, J. J. Coon, J. C. Schwartz, G. C. Stafford, J. S. Brodbelt. Top-Down Protein Fragmentation by Infrared Multiphoton Dissociation in a Dual Pressure Linear Ion Trap, Analytical Chemistry, 2009; 81: 8677-8686.

  20. A. R. Ledvina, G. C. McAlister, M. W. Gardner, S. I. Smith, J. A. Madsen, J. C. Schwartz, G. C. Stafford, J. E. P. Syka, J. S. Brodbelt, J. J. Coon. Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry, Angewandte Chemie-International Edition, 2009; 48: 8526-8528.

  21. M. Haubitz, D. M. Good, A. Woywodt, H. Haller, H. Rupprecht, D. Theodorescu, M. Dakna, J. J. Coon, H. Mischak. Identification and Validation of Urinary Biomarkers for Differential Diagnosis and Evaluation of Therapeutic Intervention in Anti-neutrophil Cytoplasmic Antibody-associated Vasculitis, Molecular & Cellular Proteomics, 2009; 8: 2296-2307.

  22. D. M. Good, C. D. Wenger, G. C. McAlister, D. L. Bai, D. F. Hunt, J. J. Coon. Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications, Journal of the American Society for Mass Spectrometry, 2009; 20: 1435-1440.

  23. D. M. Good, J. J. Coon. Mass spectrometric analysis of body fluids for biomarker discovery, Methods Mol Biol, 2009; 566: 277-91.

  24. M. W. Gardner, S. I. Smith, A. R. Ledvina, J. A. Madsen, J. J. Coon, J. C. Schwartz, G. C. Stafford, J. S. Brodbelt. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer, Analytical Chemistry, 2009; 81: 8109-8118.

  25. S. J. Duellman, K. L. Thompson, J. J. Coon, R. R. Burgess. Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function, Journal of General Virology, 2009; 90: 2251-2259.

  26. J. J. Coon. Collisions or Electrons? Protein Sequence Analysis in the 21st Century, Analytical Chemistry, 2009; 81: 3208-3215.

  27. L. U. Zimmerli, E. Schiffer, P. Zurbig, D. M. Good, M. Kellmann, L. Mouls, A. R. Pitt, J. J. Coon, R. E. Schmieder, K. H. Peter, H. Mischak, W. Kolch, C. Delles, A. F. Dominiczak. Urinary proteomic biomarkers on coronary artery disease, Molecular & Cellular Proteomics, 2008; 7: 290-298.

  28. D. Theodorescu, E. Schiffer, H. W. Bauer, F. Douwes, F. Eichhorn, R. Polley, T. Schmidt, W. Schofer, P. Zurbig, D. M. Good, J. J. Coon, H. Mischak. Discovery and validation of urinary biomarkers for propstate cancer, Proteomics Clinical Applications, 2008; 2: 556-570.

  29. D. L. Swaney, G. C. McAlister, J. J. Coon. Decision tree-driven tandem mass spectrometry for shotgun proteomics, Nature Methods, 2008; 5: 959-964.

  30. K. Rossing, H. Mischak, M. Dakna, P. Zurbig, J. Novak, B. A. Julian, D. M. Good, J. J. Coon, L. Tarnow, P. Rossing, P. Network. Urinary proteomics in diabetes and CKD, Journal of the American Society of Nephrology, 2008; 19: 1283-1290.

  31. D. Phanstiel, Y. Zhang, J. A. Marto, J. J. Coon. Peptide and protein quantification using iTRAQ with electron transfer dissociation, Journal of the American Society for Mass Spectrometry, 2008; 19: 1255-1262.

  32. D. Phanstiel, J. Brumbaugh, W. T. Berggren, K. Conard, X. Feng, M. E. Levenstein, G. C. McAlister, J. A. Thomson, J. J. Coon. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells, Proceedings of the National Academy of Sciences of the United States of America, 2008; 105: 4093-4098.

  33. G. C. McAlister, S. E. B. Kiessel, J. J. Coon. In vacuo formation of peptide-metal coordination complexes, International Journal of Mass Spectrometry, 2008; 276: 149-152.

  34. G. C. McAlister, W. T. Berggren, J. Griep-Raming, S. Horning, A. Makarov, D. Phanstiel, G. Stafford, D. L. Swaney, J. E. P. Syka, V. Zabrouskov, J. J. Coon. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer, Journal of Proteome Research, 2008; 7: 3127-3136.

  35. S. L. Hubler, A. Jue, J. Keith, G. C. McAlister, G. Craciun, J. J. Coon. Valence parity renders z(center dot)-type ions chemically distinct, Journal of the American Chemical Society, 2008; 130: 6388-6394.

  36. B. L. Frey, C. J. Krusemark, A. R. Ledvina, J. J. Coon, P. J. Belshaw, L. M. Smith. Ion-ion reactions with fixed-charge modified proteins to produce ions in a single, very high charge state, International Journal of Mass Spectrometry, 2008; 276: 136-143.

  37. J. J. Coon, P. Zurbig, M. Dakna, A. F. Dominicza, S. Decramer, D. Fliser, M. Frommberger, I. Golovko, D. M. Good, S. Herget-Rosenthal, J. Jankowski, B. A. Julian, M. Kellmann, W. Kolch, Z. Massy, J. Novak, K. Rossing, J. P. Schanstra, E. Schiffer, D. Theodorescu, R. Vanholder, E. M. Weissinger, H. Mischak, P. Schmitt-Kopplin. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics, Proteomics Clinical Applications, 2008; 2: 964-973.

  38. J. Brumbaugh, D. Phanstiel, J. J. Coon. Unraveling the histone's potential A proteomics perspective, Epigenetics, 2008; 3: 254-257.

  39. L. Zimmerli, E. Schiffer, P. Zurbig, M. Kellmann, L. Mouls, A. R. Pitt, J. J. Coon, R. E. Schmieder, W. Kolch, H. Mischak, C. Delles, A. F. Dominiczak. Biomarkers for coronary artery disease, Journal of Hypertension, 2007; 25: S10-S10.

  40. D. K. Williams, G. C. McAlister, D. M. Good, J. J. Coon, D. C. Muddiman. Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer, Analytical Chemistry, 2007; 79: 7916-7919.

  41. D. L. Swaney, G. C. McAlister, M. Wirtala, J. C. Schwartz, J. E. P. Syka, J. J. Coon. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors, Analytical Chemistry, 2007; 79: 477-485.

  42. D. L. Swaney, G. C. McAlister, D. Phanstiel, J. Brumbaugh, J. Keith, S. B. Ficarro, X. Feng, V. Ruotti, R. Stewart, J. A. Thomson, T. Berggren, J. J. Coon. New technology to detect and monitor the post-translational modification events that commit human embryonic stem cells to exit the pluripotent state, Molecular & Cellular Proteomics, 2007; 6: 36-36.

  43. D. L. Swaney, J. J. Coon. Laser desorption-atmospheric pressure chemical ionization mass spectrometry., 2007; 6: 635-642.

  44. G. C. McAlister, D. Phanstiel, D. M. Good, W. T. Berggren, J. J. Coon. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer, Analytical Chemistry, 2007; 79: 3525-3534.

  45. S. Lecchi, C. J. Nelson, K. E. Allen, D. L. Swaney, K. L. Thompson, J. J. Coon, M. R. Sussman, C. W. Slayman. Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation, Journal of Biological Chemistry, 2007; 282: 35471-35481.

  46. N. Khidekel, S. B. Ficarro, P. M. Clark, M. C. Bryan, D. L. Swaney, J. E. Rexach, Y. E. Sun, J. J. Coon, E. C. Peters, L. C. Hsieh-Wilson. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics, Nature Chemical Biology, 2007; 3: 339-348.

  47. B. A. Julian, S. Wittke, J. Novak, D. M. Good, J. J. Coon, M. Kellmann, P. Zurbig, E. Schiffer, M. Haubitz, Z. Moldoveanu, S. M. Calcatera, R. J. Wyatt, J. Sykora, E. Sladkova, O. Hes, H. Mischak, B. M. McGuire. Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases, Electrophoresis, 2007; 28: 4469-4483.

  48. D. M. Good, M. Wirtala, G. C. McAlister, J. J. Coon. Performance characteristics of electron transfer dissociation mass spectrometry, Molecular & Cellular Proteomics, 2007; 6: 1942-1951.

  49. D. M. Good, V. Thongboonkerd, J. Novak, J. L. Bascands, J. P. Schanstra, J. J. Coon, A. Dominiczak, H. Mischak. Body fluid proteomics for biomarker discovery: Lessons from the past hold the key to success in the future, Journal of Proteome Research, 2007; 6: 4549-4555.

  50. A. Chi, C. Huttenhower, L. Y. Geer, J. J. Coon, J. E. P. Syka, D. L. Bai, J. Shabanowitz, D. J. Burke, O. G. Troyanskaya, D. F. Hunt. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry, Proceedings of the National Academy of Sciences of the United States of America, 2007; 104: 2193-2198.

  51. G. E. Yue, M. G. Roper, C. Balchunas, A. Pulsipher, J. J. Coon, J. Shabanowitz, D. F. Hunt, J. P. Landers, J. P. Ferrance. Protein digestion and phosphopeptide enrichment on a glass microchip, Analytica Chimica Acta, 2006; 564: 116-122.

  52. L. M. Mikesh, B. Ueberheide, A. Chi, J. J. Coon, J. E. P. Syka, J. Shabanowitz, D. F. Hunt. The utility of ETD mass spectrometry in proteomic analysis, Biochimica Et Biophysica Acta-Proteins and Proteomics, 2006; 1764: 1811-1822.

  53. D. M. Good, J. J. Coon. Advancing proteomics with ion/ion chemistry, Biotechniques, 2006; 40: 783-789.

  54. J. J. Coon, B. Ueberheide, J. E. P. Syka, D. D. Dryhurst, J. Ausio, J. Shabanowitz, D. F. Hunt. Protein identification using sequential ion/ion reactions and tandem mass spectrometry, Proceedings of the National Academy of Sciences of the United States of America, 2005; 102: 9463-9468.

  55. J. J. Coon, J. E. P. Syka, J. Shabanowitz, D. F. Hunt. Tandem mass spectrometry for peptide and protein sequence analysis, Biotechniques, 2005; 38: 519-+.

  56. J. J. Coon, J. Shabanowitz, D. F. Hunt, J. E. P. Syka. Electron transfer dissociation of peptide anions, Journal of the American Society for Mass Spectrometry, 2005; 16: 880-882.

  57. J. E. P. Syka, J. J. Coon, M. J. Schroeder, J. Shabanowitz, D. F. Hunt. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry, Proceedings of the National Academy of Sciences of the United States of America, 2004; 101: 9528-9533.

  58. M. J. Schroeder, J. Shabanowitz, J. C. Schwartz, D. F. Hunt, J. J. Coon. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry, Analytical Chemistry, 2004; 76: 3590-3598.

  59. J. J. Coon, J. E. P. Syka, J. C. Schwartz, J. Shabanowitz, D. F. Hunt. Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions, International Journal of Mass Spectrometry, 2004; 236: 33-42.

  60. J. J. Coon, H. A. Steele, P. J. Laipis, W. W. Harrison. Direct atmospheric pressure coupling of polyacrylamide gel electrophoresis to mass spectrometry for rapid protein sequence analysis, Journal of Proteome Research, 2003; 2: 610-617.

  61. J. J. Coon, H. A. Steele, P. J. Laipis, W. W. Harrison. Laser desorption-atmospheric pressure chemical ionization: a novel ion source for the direct coupling of polyacrylamide gel electrophoresis to mass spectrometry, Journal of Mass Spectrometry, 2002; 37: 1163-1167.

  62. J. J. Coon, K. J. McHale, W. W. Harrison. Atmospheric pressure laser desorption/chemical ionization mass spectrometry: a new ionization method based on existing themes, Rapid Communications in Mass Spectrometry, 2002; 16: 681-685.

  63. J. J. Coon, W. W. Harrison. Laser desorption-atmospheric pressure chemical ionization mass spectrometry for the analysis of peptides from aqueous solutions, Analytical Chemistry, 2002; 74: 5600-5605.