James Dowell

Position title: Associate Scientist

Email: jadowell@wisc.edu


  • B.S., Chemistry, University of Kansas-Lawrence
  • Ph.D.. Pharmaceutical Sciences, University of Wisconsin-Madison

Research Interests

James Dowell’s research is focused on the application of mass spectrometry-based proteomics to the identification of novel mechanisms of chromatin remodeling. Specifically, Dowell is developing novel proteomics methodologies to identify histone post-translational modifications and decipher their role in chromatin remodeling.


Society for Neuroscience (SFN)

American Society for Mass Spectrometry (ASMS)


  • American Foundation for Pharmaceutical Education Fellow, University of Wisconsin-Madison, 2006-2008
  • Mern Kier Fellowship in Pharmacy, University of Wisconsin-Madison, 2002-2003                       
  • Honors Program, University of Kansas, 1992-1998

Selected Publications

  • Baeza J., Dowell J.A., Smallegan M.J., Fan J., Amador-Noguez D., Khan Z., Denu J.M. (2014) Stoichiometry of site-specific lysine acetylation in an entire proteome. J. Biol. Chem. 289(31), 21326-21338 [Featured as a JBC Paper of the Week.]
  • Dowell, JA. Gitcho, MA. Johnson, DA. Johnson, JA.  (2011) Identification of TDP-43 interaction partners by co-immunoprecipitation and mass spectrometry in a mouse model of Alzheimer’s disease. (In preparation)
  • Dowell, JA. Johnson, DA. Johnson, JA.  (2011) Quantitative proteomics reveals novel mechanisms of Nrf2-mediated protection against oxidative stress in astrocytes. (In preparation)
  • Sturm, RM. Dowell, JA. Li L. (2010) Rat brain neuropeptidomics: tissue collection, protease inhibition, neuropeptide extraction, and mass spectrometric analysis.  Methods Mol Biol. 2010;615:217-26. 
  • Dowell, JA. Johnson, JA. and Li, L. (2009) Identification of astrocyte secreted proteins with a combination of shotgun proteomics and bioinformatics.  J Proteome Res, 2009 Aug;8(8):4135-43.
  • DeKeyser, S. Dowell, JA. and Li, L. (2009) Mass spectrometric characterization of neuropeptides.  Methods Mol Biol, 2009;492:381-93
  • Calkins, MJ. Johnson, DA. Townsend, JA. Vargas, MR.  Dowell, JA. Williamson, TP. Kraft, AD. Lee, JM. Li, J. Johnson, JA. (2009) The Nrf2/ARE pathway as a potential therapeutic target in neurodegenerative disease.  Antioxidants & Redox Signal, 2009 Mar;11(3): 497-508
  • Dowell, JA. Frost, D. Zhang, J. and Li, L. (2008) Comparison of two-dimensional fractionation techniques for Shotgun Proteomics.  Analytical Chemistry, 2008 Sep 1;80(17):6715-23. [Featured in Journal of Proteome Research on-line news, September 23, 2008]
  • Dowell, JA. Vander Hayden, W. and Li, L. (2006) Rat neuropeptidomics by LC/MS/MS and MALDI-FTMS: enhanced dissection and extraction techniques coupled with 2D RP-RP HPLC. Journal of Proteome Research, 2006 Dec, 5(12):3368-75.  [Featured in the Research Profile Section of Journal of Proteome Research and Bio Sphere News Section in Analytical Chemistry.]