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Daniel Raftery, PhD

  • Professor,  Dept. of Anesthesiology and Pain Medicine, University of Washington
  • Adjunct Professor, Department of Chemistry, University of Washington,
  • Member, Fred Hutchinson Cancer Research Center,
  • Director, NORC Metabolomics Sub-Core Facility

Research Interests

My research group focuses on the development of new methods in and applications of metabolite profiling using a combination of mass spectrometry and NMR platforms which provide a broad based approach for biomarker discovery and systems biology research. We have worked closely with a large number of scientific and clinical collaborators and biostatisticians on various metabolomics projects such as the identification of cancer biomarkers for early detection, recurrence monitoring and therapy prediction. We are also involved in studies of diabetes and heart diseases as well as nutrition based disease prevention and aging. Our group has a strong interest in expanding the understanding of disease risk factors using metabolite profiling approaches. We have extensive experience in the quantitative determination of metabolite concentrations in a variety of samples including serum/plasma, urine, cells and tissue extracts. In conjunction with the Northwest Metabolomics Research Center that we established several years ago, we have developed a large number of assays and approaches for metabolite profiling. We utilize a range of platforms including targeted LC-MS/MS for broad based and quantitative profiling and targeted pathway assays, LC-MS for global aqueous profiling and lipidomics, and GC-MS and NMR global profiling methods that provide excellent coverage of the metabolome. We also perform isotope tracer analysis using GC-MS and NMR based approaches. We have significant experience and expertise in the use of a number of multivariate statistical methods as well as metabolic pathway analysis tools. My group has experience running large metabolomics sample sets that incorporate a number of quality control measures to ensure reliability of large datasets.

  • Metabolite profiling, methods development and applications
  • Disease diagnostics development and systems biology research
  • NMR spectroscopy and mass spectrometry


  • A.B.:Harvard College, 1984
  • Visiting Scientist: CERN, Geneva Switzerland, 1985
  • Ph.D.: University of California, Berkeley, 1991
  • Postdoctoral Scientist: University of Pennsylvania 1992-94

Honors and Awards

  • 1982-84 Harvard College Scholarship
  • 1987-88 Chateaubriand International Research Scholarship
  • 1997-99 Research Corporation Cottrell Scholars Award
  • 1999-01 Alfred P. Sloan Research Fellow
  • 2011 Purdue School of Science Engagement Award

Selected Publications Unknown Object

  • Raftery, ed., Mass Spectrometry in Metabolomics: Methods and Protocols, Methods in Molecular Biology, Vol. 1198. Humana Press/Springer Science. (2014). ISBN 978-1-4939-1257-5.
  • J. Zhu, D. Djukovic, L. Deng, H. Gu, F. Himmati, E.G. Chiorean, D. Raftery, “Colorectal Cancer Detection using Targeted Serum Metabolic Profiling,” J. Prot Res. 13, 4120-30 (2014).
  • G.A. Nagana Gowda, Y.N. Gowda, D. Raftery, “Expanding the Limits of Human Blood Metabolite Quantitation using NMR Spectroscopy,” Anal. press.
  • P. Carroll, D. Diolaiti, L. McFerrin, H. Gu, D. Djukovic, D. Du, P.F. Cheng, S. Anderson, M. Ulrich, J.B. Hurley, D. Raftery, D.E. Ayer, R.N. Eisenman, “Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis,” Cancer Cell, in press.
  • D.F. Dai, P.P. Karunadharma, Y.A. Chiao, N. Basisty, D. Crispin E.J. Hsieh, T. Chen, H. Gu, D. Djukovic, D. Raftery, R.P. Beyer, M.J. MacCoss, P.S. Rabinovitch, “Altered Proteome Turnover and Remodeling by Subacute Caloric Restriction and Rapamycin Rejuvenate the Aging Heart,” Aging Cell 13, 529-539 (2014).
  • H. Baniasadi, G. A. Gowda, H. Gu, A. Zeng, S. Zhuang, N. Skill, M. Maluccio, D. Raftery, “Targeted Metabolic Profiling of Hepatocellular Carcinoma and Hepatitis C using LC-MS/MS, Electrophesis 34, 2910-7 (2013).
  • F. Tayyari, G. A. Nagana Gowda, H. Gu, D. Raftery, “15N-Cholamine – A Smart Isotope Tag for Combining NMR- and MS-Based Metabolite Profiling,” Anal. Chem. 85, 8715-8721 (2013).
  • H. Gu, G. A. Nagana Gowda, F. Carnevale Neto, M. R. Opp, D. Raftery, “RAMSY: Ratio Analysis of Mass Spectrometry to Improve Compound Identification,” Anal. Chem. 85, 10771-10779 (2013).
  • J. Zhang, J. Bowers, L. Liu, S. Wei, G.A. Naga Gowda, Z. Hammoud, and D. Raftery, “Esophageal Cancer Metabolite Biomarkers Detected by LC-MS and NMR Methods,” PLoS ONE, e301181 (2012).
  • H. Gu, Z. Pan, B. Xi, V. Asiago, B. Musselman, and D. Raftery, “Principal Component Directed Partial Least Squares Analysis for Combining NMR and MS Data in Metabolomics: Application to the Detection of Breast Cancer,” Anal. Chim. Acta 57-63 (2011).
  • V. Asiago, L. Alvarado, N. Shanaiah, K. Owusu-Sarfo, G. A. Nagana Gowda, R. Ballas, and D. Raftery, “Early Detection of Recurrent Breast Cancer Using Metabolite Profiling,” Cancer Res. 8309-8318 (2010).
  • D. Djukovic, H. R.Baniasadi, R. Kc, Z. Hammoud, and D. Raftery, “Targeted Serum Metabolite Profiling of Nucleosides in Esophageal Adenocarcinoma,” Rapid Comm. Mass Spectrom. 3057-62 (2010).
  • G. A. Nagana Gowda, F. Tayyari, T. Ye, Y. Suryani, S. Wei, N. Shanaiah and D, Raftery, “Quantitative Analysis of Blood Plasma Metabolites Using Isotope Enhanced NMR Methods,” Anal. Chem. 8983-90 (2010).
  • S. Zhang, G. A. N. Gowda, V. Asiago, N. Shanaiah, C. Barbas, and D. Raftery, “Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats,” Anal. Biochem. 383, 76-84 (2008).
  • G. A. N. Gowda, S. Zhang, H. Gu, V. Asiago, N. Shanaiah and D. Raftery, Metabolomics-Based Methods for Early Disease Diagnostics: A Review,”Expert Rev. Mol. Diagnos., 8(5):617-33 (2008).


Contact Information

Mitochondria and Metabolism Center
850 Republican St, Room S148
University of Washington, Box 358057
Seattle, WA 98109-8057
Phone: 206-543-9709
Fax: 206-616-4819