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Protein Characterization / Modification

Liebler, D.C. (2003) Analysis of protein modifications with LC-MS and the SALSA algorithm: New tools for toxicology. Exp. Lung Res. 29 (Suppl. 1): 88-92.

Manza, L.L., Stamer, S.L., Ham, A.L.L., Codreanu, S.G. and Liebler, D.C. (2005) Sample preparation and digestion for proteomic analyses using spin filters. Proteomics, 2005 May;5(7):1742-5.

Hansen, B. T., Davey, S.W., Ham, A.J.L. & Liebler, D.C. (2005) P-MOD: Algorithm and software to map modifications to peptide sequences using tandem MS data. J. Proteome Res., 2005 4(2):358-368

Zimmerman LJ, Wernke GR, Caprioli RM, Liebler DC, 2005 ”Identification of protein fragments as pattern features in MALDI-MS analyses of serum.” J. Proteome Res. Sep-Oct;4(5):1672-80.

Luka Z, Ham AJ, Norris JL, Yeo EJ, Yermalitsky V, Glenn B, Caprioli RM, Liebler DC, Wagner C., 2006 “Identification of phosphorylation sites in glycine N-methyltransferase from rat liver.” Protein Sci. Apr;15(4):785-94.

Ducharme NA, Hales CM, Lapierre LA, Ham AJ, Oztan A, Apodaca G, Goldenring JR., 2006 “MARK2/EMK1/Par-1Balpha phosphorylation of Rab11-family interacting protein 2 is necessary for the timely establishment of polarity in Madin-Darby canine kidney cells.” Mol Biol Cell. Aug;17(8):3625-37.

Grueter CE, Abiria SA, Dzhura I, Wu Y, Ham AJ, Mohler PJ, Anderson ME, Colbran RJ., 2006 “L-type Ca2+ channel facilitation mediated by phosphorylation of the beta subunit by CaMKII.” Mol Cell. Sep 1;23(5):641-50.

Popescu DC, Ham AJ, Shieh BH., 2006 “Scaffolding protein INAD regulates deactivation of vision by promoting phosphorylation of transient receptor potential by eye protein kinase C in Drosophila.” J Neurosci. Aug 16;26(33):8570-7.

Khoshnoodi J, Hill S, Tryggvason K, Hudsun B and Friedman DB, 2007 “Identification of N-linked Glycosylation sites in Human Nephrin using Mass Spectrometry”. Journal of Mass Spectrometry 42(3):370-379.

2D-DIGE/MS

Friedman, David B., Salisha Hill, Jeffery W. Keller, Nipun B. Merchant, Shawn E. Levy, Robert J. Coffey and Richard M. Caprioli, 2004 "Proteome Analysis of Human Colon Cancer by 2 Dimensional Difference Gel Electrophoresis and Mass Spectrometry", Proteomics 4(3), 793-811.

Zhang, Yong Q., Heinrich J.G. Matthies, Joel Mancuso, Hillary K. Andrews, Elvin Woodruff III, David Friedman and Kendal Broadie, 2004 The Drosophila Fragile X Related Gene Regulates Axoneme Differentiation during Spermatogenesis. Developmental Biology, Jun 15;270(2):290-307.

Vincent R. Gerbasi, Connie M. Weaver, Salisha Hill, David B. Friedman, Andrew J. Link, 2004 Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that negatively regulate gene expression. Mol. Cell. Biol., 24(18):8276-8287.

Daikoku T, Tranguch S, Friedman DB, Das SK, Smith DF and Dey SK, 2005 "Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus." Molecular Endocrinology, 19(3):683-97.

Zhang YQ, Friedman DB, Wang Z, Woodruff E 3rd, Pan L, O'donnell J, Broadie K., 2005 "Protein expression profiling of the drosophila fragile X mutant brain reveals upregulation of monoamine synthesis." Mol. Cell. Proteomics, 4(3):278-290.

Friedman DB, Stauff DL, Pishchany G, Whitwell CW, Torres VJ, Skaar EP, 2006 “Staphylococcus aureus redirects central metabolism to increase iron availability". PLoS Pathog 2(8): e87. DOI: 10.1371/journal.ppat.0020087.

Friedman DB, Wang SE, Whitwell CW, Caprioli RM, Arteaga CL, 2006 “Multi-variable Difference Gel Electrophoresis and Mass Spectrometry: A Case Study on TGF-beta and ErbB2 signaling” Mol Cell Proteomics. 6(1):150-169

Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE. 2005 "Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor." J Mol Endocrinol. 2005 Aug;35(1):73-88.

Busler VJ.., Torres VJ, McClain MS, Tirado O, Friedman DB, and Cover TL, 2006 “Protein-protein interactions among products of the Helicobacter pylori cag pathogenicity island” J. Bacteriology, 188(13): 4787-4800.

Hamblin M, Friedman DB, Hill S, Caprioli RM, Smith HM, and Hill MF, 2007 “Proteomic Identification of Cardiac-Specific Protein Changes Associated With Increased Myocardial Oxidative Stress and Concomitant Left Ventricular Dysfunction in Diabetic Cardiomyopathy”. J Mol Cell Cardiology 42(4):884-895.

Viquez OM, Valentine HL, Friedman DB, Olson SJ, Valentine WM, 2007 ”Peripheral Nerve Protein Expression and Carbonyl Content in N,N-Diethlydithiocarbamate Myelinopathy.” Chem Res Toxicol. 20(3):370-379.

Methods

Mason, D.E. and Liebler, D.C. (2003) Quantitative analysis of modified proteins by LC-MS-MS of peptides labeled with phenyl isocyanate. J. Proteome Res. 2: 265-272.

Manza, L.L., Stamer, S.L., Ham, A.L.L., Codreanu, S.G. and Liebler, D.C. (2004) Sample preparation and digestion for proteomic analyses using spin filters. Proteomics, in press.

Reviews and Book Chapters

Daniel C Liebler, 2004 "Shotgun Mass Spec Goes Independent". Nature Methods 1:16-17 Kathryn S. Lilley and David B. Friedman, 2004 "All About DIGE: Quantification Technology For Differential-Display 2D-Gel Proteomics". Expert Rev. Proteomics, 1(4): 401-409

Liebler, D.C., Hansen, B.T., Jones, J.A., Badghisi, H. & Mason, D.E. (2003) Mapping protein modifications with liquid chromatography-mass spectrometry and the SALSA algorithm. In Proteome Characterization and Proteomics. Advances in Protein Chemistry, Vol. 65 (Smith,R.D. & Veenstra, T.D., eds.) Academic Press, San Diego, pp. 195-216.

David B. Friedman, 2005 "Identification of Proteins from Two-Dimensional Gels" In: The Encyclopedia of Mass Spectrometry: Biological Proteins and Peptides (M.L. Gross and R.M. Caprioli, eds.). Elsevier Science, Inc., pp. 47-54.

Amy-Joan L. Ham, 2005 "Proteolytic Digestion Protocols" In: The Encyclopedia of Mass Spectrometry: Biological Proteins and Peptides (M.L. Gross and R.M. Caprioli, eds.). Elsevier Science, Inc., pp. 10-17.

Kathryn S. Lilley and David B. Friedman, 2004 "All About DIGE: Quantification Technology For Differential-Display 2D-Gel Proteomics". Expert Rev. Proteomics, 1(4): 401-409.

Friedman, DB 2006 “Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis (DIGE).” In: Mass Spectrometry Data Analysis in Proteomics (R. Matthiesen, ed), part of the Methods in Molecular Biology series, The Humana Press, Inc. 367:219-240.

Lilley, KS and Friedman, DB, 2006 “Difference Gel Electrophoresis DIGE” Drug Discovery Today: Technologies (Editors-in-Chief: K. Lam and H. Timmerman) Elsevier Science, 3(3):347-353.

Tabb DL, Friedman DB and Ham AJ, 2006 “Verification of automated peptide indentifications from proteomic tandem mass spectra” Nat Protoc. 1(5):2213-2222.

Representative User Publications

Vanacore RM, Shanmugasundararaj S, Friedman DB, Bondar O, Hudson BG, Sundaramoorthy M., 2004 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, 279(43):44723.

Kundranda MN, Ray S, Saria M, Friedman D, Matrisian LM, Lukyanov P, Ochieng J., 2004 "Annexins expressed on the cell surface serve as receptors for adhesion to immobilized fetuin-A." Biochim Biophys Acta. 2004 Aug 23;1693(2):111-23.

Chytil A, Waltner-Law M, West R, Friedman D, Aakre M, Barker D, Law B., 2004 "Construction of a cyclin D1-Cdk2 fusion protein to model the biological functions of cyclin D1/Cdk2 complexes." J Biol Chem 279(46):47688-47698.

Taka-aki Matsuoka, Li Zhao, Harry W. Jarrett, David Friedman, Anna Means, and Roland Stein, 2003 "Members of the Large Maf Transcription Family Regulate Insulin Gene Transcription in Islet b-Cells." Mol. Cell. Biol. 23(17): 6049-6062.

Konjeti R. Sekhar, Peter A. Crooks, Vijaykumar N. Sonar, David B. Friedman, J.Y. Chan, Joseph H. Starnes, Kathy Kelton, Samantha R. Summar, Soumya Sasi, and Michael L. Freeman, 2003 "NADPH Oxidase Activity is Essential for Keap1-Nrf2-Mediated Induction of GCLC in Response to Highly Functionalized Indoles." Cancer Res 63(17):5636-5645.

Vanacore RM, Friedman DB, Ham AJ, Sundaramoorthy M, Hudson BG, 2005 "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. Aug 12;280(32):29300-29310.

Wang SE, Wu FY, Friedman DB, Arteaga CL., 2006. “ErbB2/HER2 signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor ß.” Cancer Research, 66(19), 66(19):9591-9600.

Tian C, Breyer RM, Kim HJ, Karra MD, Friedman DB, Karpay A, Sanders CR, 2005 “Solution NMR spectroscopy of the human vasopressin v2 receptor, a g protein-coupled receptor” 2005 Jun 8;127(22):8010-1. (Erratum in: J Am Chem Soc. 2006 Apr 19;128(15):5300.)

Anumanthan G, Halder SK, Friedman DB, Datta PK, 2006 ”Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism”. Cancer Res. 66(22):10824-32.

Keller JW, Franklin JL, Graves-Deal R, Friedman DB, Whitwell CW, Coffey RJ. 2007 “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.

Wang SE, Narasanna A, Whitell CW, Wu FY, Friedman DB, Arteaga CL, 2007 “Convergence of p53 and TGF-ß signaling on activating the expression of tumor suppressor gene maspin” J Biol. Chem. 282(8):5661-5669.