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University of Washington
Thursday May 23 , 2013
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David Goodlett

Professor David Goodlett
Professor, Medicinal Chemistry
 PH: 206 616 4586
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Lab Website

ACADEMIC BIO

  • B.S., 1982, Auburn University, Alabama
  • M.S., 1988, Auburn University, Alabama
  • Ph.D., 1991, North Carolina State University


RESEARCH OVERVIEW

We are a bioanalytical laboratory that develops separation science and mass spectrometric methods to solve structure-function problems in biology and medicine. In general we seek to use mass spectrometry to extract the maximum amount of information with a minimum of effort prior to MS analysis, which we facetiously refer to as Indolent Driven Science. Our primary tool is mass spectrometry and specifically Fourier transform Ion Cyclotron Resonance Mass Spectrometry (FTICRMS). We have upgraded a Bruker APEX III 4.7 Tesla instrument to allow electron capture dissociation (ECD) with infrared multi-photon dissociation (IRMPD) as well as collision induced dissociation of ions in quadrupoles located prior to the ICR cell. Additionally, we have implemented a simple version of Dynamic Range Enhancement Applied to Mass Spectrometry (DREAMS) on this instrument (see Below et al. Anal Chem 2001). We have also modified our Thermo Fisher LTQFT to allow ECD and IRMPD and replaced the standard source with an ion funnel (see Kelly et al. Mass Spectrom Rev 2009). We are currently pursuing data-independent analysis of complex mixtures using a protocol we refer to as Precursor Acquisition Independent from Ion Count (PAcIFIC; see Panchaud et al. Anal Chem 2009 and Anal Chem 2011) that is related to a type of data produced by a novel tandem mass spectrometer (see Wang RCMS 2007). Other workhorse instruments in the laboratory include a Waters SYNAPT, a Thermo LTQ-Velos and a Thermo LTQ-Orbitrap all fitted with Waters NanoAcquity HPLCs. In support of these instruments and data types we have published informatic solutions to protein chemical crosslinking (see Singh et al. Anal Chem 2008 and Panchaud et al. JPR 2010), lipid A structure assignment (Ting et al. JASMS 2011) and top-down proteomics (Tsai et al. JASMS 2009). We are applying these and other technologies with our collaborators who are in the fields of microbiology, prostate cancer, urinary tract disorders, HIV and fatigue, acute respiratory distress syndrome, and pediatric medulloblastomas. Finally, we are part of the University of Washington's Proteomics Resource (UWPR) consortium developed to aid proteomics research on campus (see http://proteomicsresource.washington.edu/index.php).


RECENT SELECTED PUBLICATIONS

  • Chu LJ, Yang H, Shih P, Kao Y, Tsai YS, Chen J, Huang G, Weng RR, Ting YS, Fang X, von Haller PD, Goodlett DR, Ng WV. "Metabolic Capabilities and Systems Fluctuations in Haloarcula marismortui Revealed by Integrative Genomics and Proteomics Analyses." J Proteome Res, 10(7), 3261-73, 2011.
  • Thatcher JE, Buttrick B, Shaffer SA, Shimshoni JA, Goodlett DR, Nelson WL, Isoherranen N. "Substrate specificity and ligand interactions of CYP26A1, the human liver retinoic acid hydroxylase." Mol Pharmacol, online, 2011.
  • Ting YS, Shaffer SA, Jones JW, Ng WV, Ernst RK, Goodlett DR. "Automated lipid a structure assignment from hierarchical tandem mass spectrometry data." J Am Soc Mass Spectrom, 22(5), 856-66, 2011.
  • Yu L, Tan Y, Tsai Y, Goodlett DR, Polfer NC. "On the relevance of peptide sequence permutations in shotgun proteomics studies." J Proteome Res, 10(5), 2409-16, 2011.
  • Devic I, Hwang H, Edgar JS, Izutsu K, Presland R, Pan C, Goodlett DR, Wang Y, Armaly J, Tumas V, Zabetian CP, Leverenz JB, Shi Mu, Zhang J. "Salivary {alpha}-synuclein and DJ-1: potential biomarkers for Parkinson's disease." Brain, 134 (pt 7), e178, 2011.
  • Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR. "Faster, quantitative, and accurate precursor acquisition independent from ion count." Anal Chem, 83(6), 2250-7, 2011.
  • Mealman TD, Bagai I, Singh P, Goodlett DR, Rensing C, Zhou H, Wysocki VH, McEvoy MM. "Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry." Biochemistry, 50(13), 2559-66, 2011.
  • Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. "Landscape of the SOX2 protein-protein interactome." Proteomics, 11(5), 921-34, 2011.
  • Fang X, Yoon JG, Li L, Yu W, Shao J, Hua D, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. "The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis." BMC Genomics, 12, 11, 2011.
  • Chu LJ, Chen MC, Setter J, Tsai YS, Yang H, Fang X, Ting YS, Shaffer SA, Taylor GK, von Haller PD, Goodlett DR, Ng WV. "New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis." J Proteome Res, 10(3), 1170-8, 2011.
  • Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, Rocap G. "Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction." ISME J. 2010 Feb 18 [Epub ahead of print].
  • Reiner CL, McCullar JS, Kow RL, Le JH, Goodlett DR, Nathanson NM. "RACK1 associates with muscarinic receptors and regulates M(2) receptor trafficking." PLoS One, 5(10), e13517, 2010.
  • Wilderman PR, Shah MB, Liu T, Li S, Hsu S, Roberts AG, Goodlett DR, Zhang Q, Woods VL Jr, Stout CD, Halpert JR. "Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography." J Biol Chem, 285(49), 38602-11, 2010.
  • Malmstrom L, Goodlett DR. "Protein structure modeling." Methods Mol Biol, 673, 63-72, 2010.
  • Sanowar S, Singh P, Pfuetzner RA, Andre I, Zheng H, Spreter T, Strynadka NC, Gonen T, Baker D, Goodlett DR, Miller SI. "Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system." MBio, 1(3), 2010.
  • Goo YA, Tsai YS, Liu AY, Goodlett DR, Yang CC. "Urinary proteomics evaluation in interstitial cystitis/painful bladder syndrome: a pilot study." Int Braz J Urol, 36(4), 464-78; discussion 478-9, 479, 2010.


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