Joshua J. Coon

Position title: Professor of Biomolecular Chemistry and Chemistry


Phone: 608.263.1718

Room 4426, Biotechnology Building
425 Henry Mall
Madison, WI 53706

Research Website
Coon Group
Joshua Coon


  • Director, NIGMS National Center for Quantitative Biology of Complex Systems


  • B.S., Central Michigan University
  • 2002 – Ph.D., University of Florida
  • Postdoctoral Fellow at University of Virginia



Research Emphasis: Bioanalytical Chemistry, Mass Spectrometry & Proteomics

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.

Coon Research

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.