Our Research: Faculty/Research Laboratories

Andy Hoofnagle MD, PhD

Assistant Professor, Department of Laboratory Medicine

Email Address: ahoof@u.washington.edu
Departmental Website: http://depts.washington.edu/labweb/

Andy Hoofnagle MD, PhD

Background:

Andy Hoofnagle received his undergraduate education at Cornell University. He obtained his medical degree from the University of Colorado Health Sciences and his PhD from the University of Colorado, Boulder as part of the Medical Scientist Training Program. His PhD advisor was Natalie Ahn. During his residency and chief residency in Clinical Pathology in the Department of Laboratory Medicine at the University of Washington, he did his post-doctoral work in the laboratory of Jay Heinecke, Department of Medicine. Upon completion of his residency, he was promoted to Assistant Professor of Laboratory Medicine and now serves as the Director of Clinical Mass Spectrometry.

Focus:

Dr. Hoofnagle’s laboratory focuses on using proteomic and metabolomic approaches to investigate the intersection of inflammation and lipid metabolism. His laboratory has built robust assays for the quantification of proteins in lipoproteins using targeted proteomic approaches to investigate the changes in the HDL proteome due to diabetes and obesity. They are pioneering the use of immunoaffinity peptide enrichment strategies of analyte-specific peptides from tryptic digests in the clinical analysis of low-abundance serum proteins. The laboratory has developed assays for small molecule analytes, including arginine, arginine metabolites, and vitamin D, which are being used in basic science and large-scale clinical studies. Several mouse models are being used to assess the importance of complement regulatory proteins in insulin sensitivity and lipid metabolism. All of these studies are in collaboration with outstanding investigators from the University of Washington and elsewhere.

Representative Publications:

Hoofnagle AN, Becker JO, Wener MH, and Heinecke JW. (2008) Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry. Clin Chem. 54:1796-804.

Marney LC, Laha TJ, Baird, GS, Rainey PM, and Hoofnagle AN. (2008) Isopropanol
Protein Precipitation for the Analysis of Plasma Free Metanephrines by Liquid Chromatography-Tandem Mass Spectrometry. Clin Chem. 54:1729-32.

Hoofnagle AN, Peterson GN, Kelly JL, Sayre CA, Chou D, and Hirsch IB. (2008) Utilization of Serum and Plasma Glucose Measurements as a Benchmark for Improved Hospital-wide Glycemic Control. Endocr Pract. 14:556-63.

Hoofnagle AN and Heinecke JW. (2009) Lipoproteomics: Using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins. J Lipid Res. 50:1967-75.

Hoofnagle AN and Wener MH. (2009) The Fundamental Flaws of Immunoassays and
Potential Solutions Using Tandem Mass Spectrometry. J Immunol Methods. 347:3-11.

Hoofnagle AN, Laha TJ, Donaldson TF. (2010) A rubber transfer gasket to improve the throughput of liquid-liquid extraction in 96-well plates: application to vitamin D testing. J Chromatogr B Analyt Technol Biomed Life Sci. 878:1639-42.

  • Amukele TK, Hoofnagle AN, and Astion ML. (2009) Use of a Resident On-call Database to Characterize Failures in Communication of Critical Laboratory Results. Clin Chem. 55:1590-1.

    Hoofnagle AN, Becker JO, Wener MH, and Heinecke JW. (2008) Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry. Clin Chem. 54:1796-804.

    Marney LC, Laha TJ, Baird, GS, Rainey PM, and Hoofnagle AN. (2008) Isopropanol Protein Precipitation for the Analysis of Plasma Free Metanephrines by Liquid Chromatography-Tandem Mass Spectrometry. Clin Chem. 54:1729-32.

    Hoofnagle AN, Peterson GN, Kelly JL, Sayre CA, Chou D, and Hirsch IB. (2008) Utilization of Serum and Plasma Glucose Measurements as a Benchmark for Improved Hospital-wide Glycemic Control. Endocr Pract. 14:556-63.

    Sours KM, Kwok SC, Rachidi T, Lee T, Ring A, Hoofnagle AN, Resing KA, and Ahn NG. (2008) Hydrogen-Exchange Mass Spectrometry Reveals Activation-Induced Changes in the Conformational Mobility of p38alpha MAP Kinase. J Mol Biol. 379:1075-93.

    Vaisar T, Pennathur S, Green PS, Gharib SA, Hoofnagle AN, Cheung MC, Byun J, Vuletic S, Kassim S, Singh P, Chea H, Knopp RH, Brunzell J, Geary R, Chait A, Zhao1 X, Elkon K, Marcovina S, Ridker P, Oram JF, and Heinecke JW. (2007) Shotgun Proteomics Implicates Protease Inhibition and Complement Activation in the Anti-inflammatory Properties of HDL.J Clin Invest. 117:746-56.

    Hoofnagle AN, Chou D, and Astion ML. (2007) Online Database for Documenting Clinical Pathology Resident Education. Clin Chem. 53:134-7.

    Hoofnagle AN, Laha TJ, Rainey PM, and Sadrzadeh SMH. (2006) Specific detection of anabasine, nicotine and nicotine metabolites in urine by liquid chromatography-tandem mass spectrometry. Am J Clin Path. 126:880-7.

    Pierce KM, Hoggard JC, Hope JL, Rainey PM, Hoofnagle AN, Jack RM, Wright BW, and Synovec RE. (2006) Fisher Ratio Method Applied to Third-Order Separation Data To Identify Significant Chemical Components of Metabolite Extracts. Anal Chem. 78:5068-75.

    Lee T, Hoofnagle AN, Resing KA, Ahn NG. (2005) Hydrogen exchange solvent protection by an ATP analogue reveals conformational changes in ERK2 upon activation.  J Mol Biol. 353:600-12.

    Lee T, Hoofnagle AN, Kabuyama Y, Stroud J, Min X, Goldsmith EJ, Chen L, Resing KA, and Ahn NG. (2004) Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry. Mol Cell. 14:43-55.

    Hoofnagle AN, Stoner JW, Lee T, Eaton SS, and Ahn, NG. (2004)  Phosphorylation-dependent changes in structure and dynamics in ERK2 detected by SDSL and EPR. Biophys J. 86:395-403.

    Emrick MA, Hoofnagle AN, Miller AS, Ten Eyck LF, and Ahn NG. (2001) Constitutive activation of extracellular signal-regulated kinase 2 by synergistic point mutations. J Biol Chem. 276:46469-79.

    Hoofnagle AN, Resing KA, Goldsmith EJ, and Ahn NG. (2001) Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange.  Proc Natl Acad Sci U S A. 98:956-61.

    de Beer T, Hoofnagle AN, Enmon JL, Bowers RC, Yamabhai M, Kay BK, and Overduin M. (2000) Molecular mechanism of NPF recognition by EH domains.  Nat Struct Biol. 7:1018-22.

    Resing KA, Hoofnagle AN, and Ahn NG. (1999) Modeling deuterium exchange behavior of ERK2 using pepsin mapping to probe secondary structure.  J Am Soc Mass Spectrom. 10:685-702.

    Hoofnagle AN and Heinecke JW. (2009) Lipoproteomics: Using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins. J Lipid Res.50:1967-75.

    Hoofnagle AN and Wener MH. (2009) The Fundamental Flaws of Immunoassays and Potential Solutions Using Tandem Mass Spectrometry. J Immunol Methods. 347:3-11.

    Paulovich AG, Whiteaker JR, Hoofnagle AN, and Wang P. (2008) The Interface between Biomarker Discovery and Clinical Validation: The Tar Pit of the Protein Biomarker Pipeline. Proteomics: Clin Appl. 2:1386-1402.

    Hoofnagle AN and Wener MH. (2006) Serum thyroglobulin: A model of immunoassay imperfection. Clin Lab Int. 12:12-4.

    Hoofnagle AN, Resing KA, and Ahn NG. (2004) Practical Methods for Deuterium Exchange/Mass Spectrometry. Methods Mol Biol. 250:283-98.

    Hoofnagle AN, Resing KA, and Ahn NG. (2003) Protein Analysis by Hydrogen Exchange Mass Spectrometry.  Annu Rev Biophys Biomol Struct. 32:1-25.

    Hoofnagle AN, Laha TJ, Donaldson TF. (2010) A rubber transfer gasket to improve the throughput of liquid-liquid extraction in 96-well plates: application to vitamin D testing. J Chromatogr B Analyt Technol Biomed Life Sci. 878:1639-42.

Current Collaborations:

Within the Diabetes and Obesity Center of Excellence and its Affiliated Members
Jay Heinecke
Tomas Vaisar
Alan Chait
Renee LeBoeuf
Outside the Diabetes & Obesity Center of Excellence
John Brunzell, University of Washington
Steven Kahn, Seattle VA Puget Sound Health Care System
Ian de Boer, University of Washington
Bryan Kestenbaum, University of Washington
Phyllis Wise, University of Washington
Larry Kessler, University of Washington
Tim Lyons, University of Oklahoma Health Sciences Center
Joshua Bornhorst, University of Arkansas
Leigh Anderson, Plasma Proteome Institute, Washington, DC
Terry Pearson, University of Victoria, BC

Lab Members:

Fred Strathmann, PhD
Jessica Becker, MT (ASCP)
Tom Laha, MT (ASCP)