The VICC.ORG Directory of Doctors, Healthcare Providers & Researchers
David B. Friedman, Ph.D.
Associate Director, Proteomics Laboratory
Research Associate Professor of Biochemistry
Researcher
Contact Information:
Vanderbilt University Medical Center
9114C MRB III
Nashville, TN 37232
615-343-7333
Research Specialty
Proteomics; differential protein expression and protein/peptide mass spectrometry.
Research Description
Proteomics is the study of the dynamic protein expression of a tissue, cell type or organism. As an Associate Director of the Proteomics Laboratory in the Mass Spectrometry Research Center, I direct research and technology that targets differential protein expression upon various experimental treatments/conditions, and subsequent protein identification using mass spectrometry. In addition, the Proteomics Laboratory offers the ability to identify proteins resolved on SDS-PAGE gels or in biochemical fractions, as well as characterize and map sites of post-translational modification using mass spectrometry.
The Proteomics Laboratory offers two main proteomics technology platforms, and also embarks on specialized research problems that often go beyond these commercially-available technologies. The first is sensitive and rapid protein identification technologies using single- and multi-dimensional HPLC peptide separations coupled directly to tandem mass spectrometry. The second technology utilizes established 2D gel technology with newly-available flourscent protein tags. Termed DIGE, this technology allows for multiple samples to be separated together and to be compared to a common standard sample. This allows for quantitative comparisons across a minimal number of 2D gels without interference from gel-to-gel variation. This is coupled with rapid and sensitive protein identification using mass spectrometry.
Publications
- Loh, JT, Friedman, DB, Piazuelo, MB, Bravo, LE, Wilson, KT, Peek, RM, Correa, P, Cover, TL Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression. Infect Immun, 80(9), 3094-106, 2012.
- Friedman, DB Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments. Methods Mol Biol, 85431-45, 2012.
- Wegrzynowicz, M, Holt, HK, Friedman, DB, Bowman, AB Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant huntingtin and manganese. J Proteome Res, 11(2), 1118-32, 2012.
- Viquez, OM, Caito, SW, McDonald, WH, Friedman, DB, Valentine, WM Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat. Chem Res Toxicol, 25(11), 2310-21, 2012.
- Pruitt, RN, Chumbler, NM, Rutherford, SA, Farrow, MA, Friedman, DB, Spiller, B, Lacy, DB Structural determinants of Clostridium difficile toxin A glucosyltransferase activity. J Biol Chem, 287(11), 8013-20, 2012.
- Venkateswaran, A, Friedman, DB, Walsh, AJ, Skala, MC, Sasi, S, Rachakonda, G, Crooks, PA, Freeman, ML, Sekhar, KR The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Invest New Drugs, 2012.
- Takahashi, K, Mernaugh, RL, Friedman, DB, Weller, R, Tsuboi, N, Yamashita, H, Quaranta, V, Takahashi, T Thrombospondin-1 acts as a ligand for CD148 tyrosine phosphatase. Proc Natl Acad Sci U S A, 109(6), 1985-90, 2012.
- Boutt¿¿, AM, Friedman, DB, Bogyo, M, Min, Y, Yang, L, Lin, PC Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis. FASEB J, 25(8), 2626-37, 2011.
- Smith, AL, Friedman, DB, Yu, H, Carnahan, RH, Reynolds, AB ReCLIP (reversible cross-link immuno-precipitation): an efficient method for interrogation of labile protein complexes. PLoS One, 6(1), e16206, 2011.
- Friedman, DB, Andacht, TM, Bunger, MK, Chien, AS, Hawke, DH, Krijgsveld, J, Lane, WS, Lilley, KS, MacCoss, MJ, Moritz, RL, Settlage, RE, Sherman, NE, Weintraub, ST, Witkowska, HE, Yates, NA, Turck, CW The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics, 11(8), 1371-81, 2011.
- Nam, EA, Zhao, R, Glick, GG, Bansbach, CE, Friedman, DB, Cortez, D Thr-1989 phosphorylation is a marker of active ataxia telangiectasia-mutated and Rad3-related (ATR) kinase. J Biol Chem, 286(33), 28707-14, 2011.
- Loh, JT, Gupta, SS, Friedman, DB, Krezel, AM, Cover, TL Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system. J Bacteriol, 192(8), 2034-43, 2010.
- Dimitrova, YN, Li, J, Lee, YT, Rios-Esteves, J, Friedman, DB, Choi, HJ, Weis, WI, Wang, CY, Chazin, WJ Direct ubiquitination of beta-catenin by Siah-1 and regulation by the exchange factor TBL1. J Biol Chem, 285(18), 13507-16, 2010.
- Sarilla, S, Habib, SY, Tollefsen, DM, Friedman, DB, Arnett, DR, Verhamme, IM Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli. Anal Biochem, 406(2), 166-75, 2010.
- Cates, JM, Friedman, DB, Seeley, EH, Dupont, WD, Schwartz, HS, Holt, GE, Caprioli, RM, Young, PP Proteomic analysis of osteogenic sarcoma: association of tumour necrosis factor with poor prognosis. Int J Exp Pathol, 91(4), 335-49, 2010.
- Torres, VJ, Attia, AS, Mason, WJ, Hood, MI, Corbin, BD, Beasley, FC, Anderson, KL, Stauff, DL, McDonald, WH, Zimmerman, LJ, Friedman, DB, Heinrichs, DE, Dunman, PM, Skaar, EP Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect Immun, 78(4), 1618-28, 2010.
- Franco, AT, Friedman, DB, Nagy, TA, Romero-Gallo, J, Krishna, U, Kendall, A, Israel, DA, Tegtmeyer, N, Washington, MK, Peek, RM Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics, 8(8), 1947-58, 2009.
- Friedman, DB, Hoving, S, Westermeier, R Isoelectric focusing and two-dimensional gel electrophoresis. Methods Enzymol, 463515-40, 2009.
- Wang, Y, Azuma, Y, Friedman, DB, Coffey, RJ, Neufeld, KL Novel association of APC with intermediate filaments identified using a new versatile APC antibody. BMC Cell Biol, 1075, 2009.
- Gibson, F, Anderson, L, Babnigg, G, Baker, M, Berth, M, Binz, PA, Borthwick, A, Cash, P, Day, BW, Friedman, DB, Garland, D, Gutstein, HB, Hoogland, C, Jones, NA, Khan, A, Klose, J, Lamond, AI, Lemkin, PF, Lilley, KS, Minden, J, Morris, NJ, Paton, NW, Pisano, MR, Prime, JE, Rabilloud, T, Stead, DA, Taylor, CF, Voshol, H, Wipat, A, Jones, AR Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol, 26(8), 863-4, 2008.
- Friedman, DB, Lilley, KS Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol, 42893-124, 2008.
- Meyrick, BO, Friedman, DB, Billheimer, DD, Cogan, JD, Prince, MA, Phillips, JA, Loyd, JE Proteomics of transformed lymphocytes from a family with familial pulmonary arterial hypertension. Am J Respir Crit Care Med, 177(1), 99-107, 2008.
- Hamblin, M, Friedman, DB, Hill, S, Caprioli, RM, Smith, HM, Hill, MF Alterations in the diabetic myocardial proteome coupled with increased myocardial oxidative stress underlies diabetic cardiomyopathy. J Mol Cell Cardiol, 42(4), 884-95, 2007.
- Wang, SE, Narasanna, A, Whitell, CW, Wu, FY, Friedman, DB, Arteaga, CL Convergence of p53 and Transforming Growth Factor beta (TGFbeta) Signaling on Activating Expression of the Tumor Suppressor Gene maspin in Mammary Epithelial Cells. J Biol Chem, 282(8), 5661-9, 2007.
- Robertson, PD, Warren, EM, Zhang, H, Friedman, DB, Lary, JW, Cole, JL, Tutter, AV, Walter, JC, Fanning, E, Eichman, BF Domain architecture and biochemical characterization of vertebrate MCM10. J Biol Chem, 2007.
- Khoshnoodi, J, Hill, S, Tryggvason, K, Hudson, B, Friedman, DB Identification of N-linked glycosylation sites in human nephrin using mass spectrometry. J Mass Spectrom, 42(3), 370-379, 2007.
- Friedman, DB, Wang, SE, Whitwell, CW, Caprioli, RM, Arteaga, CL Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling. Mol Cell Proteomics, 6(1), 150-69, 2007.
- Keller, JW, Franklin, JL, Graves-Deal, R, Friedman, DB, Whitwell, CW, Coffey, RJ Oncogenic KRAS provides a uniquely powerful and variable oncogenic contribution among RAS family members in the colonic epithelium. J Cell Physiol, 210(3), 740-9, 2007.
- Viquez, OM, Valentine, HL, Friedman, DB, Olson, SJ, Valentine, WM Peripheral Nerve Protein Expression and Carbonyl Content in N,N-Diethlydithiocarbamate Myelinopathy. Chem Res Toxicol, 2007.
- Pollins, AC, Friedman, DB, Nanney, LB Proteomic Investigation of Human Burn Wounds by 2D-Difference Gel Electrophoresis and Mass Spectrometry. J Surg Res, 2007.
- Friedman, DB Quantitative proteomics for two-dimensional gels using difference gel electrophoresis. Methods Mol Biol, 367219-39, 2007.
- Haas, KF, Miller, SL, Friedman, DB, Broadie, K The ubiquitin-proteasome system postsynaptically regulates glutamatergic synaptic function. Mol Cell Neurosci, 35(1), 64-75, 2007.
- Wang, SE, Shin, I, Wu, FY, Friedman, DB, Arteaga, CL HER2/Neu (ErbB2) signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor beta. Cancer Res, 66(19), 9591-600, 2006.
- Anumanthan, G, Halder, SK, Friedman, DB, Datta, PK Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism. Cancer Res, 66(22), 10824-32, 2006.
- Busler, VJ, Torres, VJ, McClain, MS, Tirado, O, Friedman, DB, Cover, TL Protein-protein interactions among Helicobacter pylori cag proteins. J Bacteriol, 188(13), 4787-800, 2006.
- Friedman, DB, Stauff, DL, Pishchany, G, Whitwell, CW, Torres, VJ, Skaar, EP Staphylococcus aureus redirects central metabolism to increase iron availability. PLoS Pathog, 2(8), e87, 2006.
- Tabb, DL, Friedman, DB, Ham, AJ Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006.
- Vanacore, RM, Friedman, DB, Ham, AJ, Sundaramoorthy, M, Hudson, BG Identification of S-hydroxylysyl211-methionine93 as the covalent crosslink of the noncollagenous (NC1) hexamer of the alpha 1alpha 1alpha 2 collagen IV network: A role for the posttranslational modification of lysine211 to hydroxylysine211 in hexamer assembly. J Biol Chem, 2005.
- Zhang, Yong Q, Friedman, David B, Wang, Zhe, Woodruff, Elvin, Pan, Luyuan, O''donnell, Janis, Broadie, Kendal Protein expression profiling of the drosophila fragile X mutant brain reveals upregulation of monoamine synthesis. Mol Cell Proteomics, 2005.
- Tian, C, Breyer, RM, Kim, HJ, Karra, MD, Friedman, DB, Karpay, A, Sanders, CR Solution NMR spectroscopy of the human vasopressin V2 receptor, a G protein-coupled receptor. J Am Chem Soc, 127(22), 8010-1, 2005.
- Lilley, KS, Friedman, DB All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics, 1(4), 401-9, 2004.
- Chytil, Anna, Waltner-Law, Mary, West, Robert, Friedman, David, Aakre, Mary, Barker, Dana, Law, Brian Construction of a cyclin D1-Cdk2 fusion protein to model the biological functions of cyclin D1-Cdk2 complexes. J Biol Chem, 279(46), 47688-98, 2004.
- Friedman, DB, Hill, S, Keller, JW, Merchant, NB, Levy, SE, Coffey, RJ, Caprioli, RM Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics, 4(3), 793-811, 2004.
- Daikoku, Takiko, Tranguch, Susanne, Friedman, David B, Das, Sanjoy K, Smith, David F, Dey, Sudhansu K Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus. Mol Endocrinol, 2004.
- Zhang, YQ, Matthies, HJ, Mancuso, J, Andrews, HK, Woodruff, E, Friedman, D, Broadie, K The Drosophila fragile X-related gene regulates axoneme differentiation during spermatogenesis. Dev Biol, 270(2), 290-307, 2004.
- Vanacore, Roberto M., Shanmugasundararaj, Sivananthaperumal, Friedman, David B., Bondar, Olga, Hudson, Billy G., Sundaramoorthy, Munirathinam The a1.a2-network of collagen IV: Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys crosslinks. J Biol Chem, 2004.
- Gerbasi, Vincent R, Weaver, Connie M, Hill, Salisha, Friedman, David B, Link, Andrew J Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol Cell Biol, 24(18), 8276-87, 2004.
- Low, RL, Orton, S, Friedman, DB A truncated form of DNA topoisomerase IIbeta associates with the mtDNA genome in mammalian mitochondria. Eur J Biochem, 270(20), 4173-86, 2003.
- Matsuoka, TA, Zhao, L, Artner, I, Jarrett, HW, Friedman, D, Means, A, Stein, R Members of the large Maf transcription family regulate insulin gene transcription in islet beta cells. Mol Cell Biol, 23(17), 6049-62, 2003.
- Sekhar, KR, Crooks, PA, Sonar, VN, Friedman, DB, Chan, JY, Meredith, MJ, Starnes, JH, Kelton, KR, Summar, SR, Sasi, S, Freeman, ML NADPH oxidase activity is essential for Keap1/Nrf2-mediated induction of GCLC in response to 2-indol-3-yl-methylenequinuclidin-3-ols. Cancer Res, 63(17), 5636-45, 2003.
- Friedman, DB, Kern, JW, Huneycutt, BJ, Vinh, DB, Crawford, DK, Steiner, E, Scheiltz, D, Yates, J, Resing, KA, Ahn, NG, Winey, M, Davis, TN Yeast Mps1p phosphorylates the spindle pole component Spc110p in the N-terminal domain. J Biol Chem, 276(21), 17958-67, 2001.
- Kironmai, KM, Muniyappa, K, Friedman, DB, Hollingsworth, NM, Byers, B DNA-binding activities of Hop1 protein, a synaptonemal complex component from Saccharomyces cerevisiae. Mol Cell Biol, 18(3), 1424-35, 1998.
- Friedman, DB, Sundberg, HA, Huang, EY, Davis, TN The 110-kD spindle pole body component of Saccharomyces cerevisiae is a phosphoprotein that is modified in a cell cycle-dependent manner. J Cell Biol, 132(5), 903-14, 1996.
- Friedman, DB, Hollingsworth, NM, Byers, B Insertional mutations in the yeast HOP1 gene: evidence for multimeric assembly in meiosis. Genetics, 136(2), 449-64, 1994.
- Friedman, DB, Johnson, TE A mutation in the age-1 gene in Caenorhabditis elegans lengthens life and reduces hermaphrodite fertility. Genetics, 118(1), 75-86, 1988.
- Friedman, DB, Johnson, TE Three mutants that extend both mean and maximum life span of the nematode, Caenorhabditis elegans, define the age-1 gene. J Gerontol, 43(4), B102-9, 1988.
- Johnson, TE, Friedman, DB, Fitzpatrick, PA, Conley, WL Mutant genes that extend life span. Basic Life Sci, 4291-100, 1987.
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