Bradford Gibson, PhD
Professor Emeritus
Pharmaceutical Chemistry
School of Pharmacy

Education & Training

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• Postdoctoral Chemistry Cambridge 1985
• Ph.D. Chemistry M.I.T. 1983
• Chemistry Stanford 1979
• B.A. Biochemistry University of California, Santa Barbara 1975

Websites

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• Profile at bts.ucsf.edu (pspg.ucsf.edu)

Grants and Projects

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• Lysine Acetylation in N. gonorrhoeae Quorum Sensing and Biofilm Formation, NIH, 2014-2020
• Innate immune response to microbial infection, NIH, 1999-2015
• Bio-Organic Biomedical Mass Spectrometry Resource, NIH, 1982-2015
• TripleTOF 5600 High Resolution Mass Spectrometer, NIH, 2013-2014
• Mass spectrometry and imaging technologies in Geroscience, NIH, 2007-2013
• Mitochondrial Dysfunction in Aging and Disease, NIH, 2005-2013
• Resource for Biocomputing, Visualization, and Informatics, NIH/NCRR, 1976-2012
• AB SCIEX QTRAP 5500 LC MS/MS system, NIH, 2010-2011
• Basic Mechanisms in Aging and Age Related Disease, NIH, 2005-2011
• QSTAR Elite Quadrupole-o-TOF LC/MS/MS System, NIH, 2007-2008
• Structure and Function of Haemophilus ducreyi LOS, NIH, 1994-2008
• 4000 Q TRAP triple quadrupole/linear ion trap LC/MS/MS, NIH, 2005-2006
• Proteomics of Complex 1 Inhibition in GSH-Depleted Cells, NIH, 2003-2006
• LCQ-DECA ION-TRAP HPLC/MS SYSTEM, NIH, 2000-2001

Publications (137)

Top publication keywords:
Bacterial ProteinsHaemophilus influenzaeProteomeTandem Mass SpectrometryHaemophilus ducreyiLipopolysaccharidesFrancisella tularensisProteomicsProtein Processing, Post-TranslationalMass SpectrometryLysineMitochondria, LiverLipid AChromatography, LiquidSpectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

• Promises and Challenges of populational Proteomics in Health and Disease.
  Molecular & cellular proteomics : MCP 2024 Sun BB, Suhre K, Gibson BW
• Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics.
  Journal of proteome research 2024 Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW
• Plasma proteomic associations with genetics and health in the UK Biobank.
  Nature 2023 Sun BB, Chiou J, Traylor M, Benner C, Hsu YH, Richardson TG, Surendran P, Mahajan A, Robins C, Vasquez-Grinnell SG, Hou L, Kvikstad EM, Burren OS, Davitte J, Ferber KL, Gillies CE, Hedman ÅK, Hu S, …
• Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs.
  The Journal of biological chemistry 2022 Bai N, Riching KM, Makaju A, Wu H, Acker TM, Ou SC, Zhang Y, Shen X, Bulloch DN, Rui H, Gibson BW, Daniels DL, Urh M, Rock BM, Humphreys SC
• Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation.
  Journal of the American Society for Mass Spectrometry 2021 Bagal D, Gibson BW

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• Proteome and Secretome Dynamics of Human Retinal Pigment Epithelium in Response to Reactive Oxygen Species.
  Scientific reports 2019 Meyer JG, Garcia TY, Schilling B, Gibson BW, Lamba DA
• Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.
  Cell metabolism 2019 Softic S, Meyer JG, Wang GX, Gupta MK, Batista TM, Lauritzen HPMM, Fujisaka S, Serra D, Herrero L, Willoughby J, Fitzgerald K, Ilkayeva O, Newgard CB, Gibson BW, Schilling B, Cohen DE, Kahn CR
• SILAC Analysis Reveals Increased Secretion of Hemostasis-Related Factors by Senescent Cells.
  Cell reports 2019 Wiley CD, Liu S, Limbad C, Zawadzka AM, Beck J, Demaria M, Artwood R, Alimirah F, Lopez-Dominguez JA, Kuehnemann C, Danielson SR, Basisty N, Kasler HG, Oron TR, Desprez PY, Mooney SD, Gibson BW, …
• JNK modifies neuronal metabolism to promote proteostasis and longevity.
  Aging cell 2019 Wang L, Davis SS, Borch Jensen M, Rodriguez-Fernandez IA, Apaydin C, Juhasz G, Gibson BW, Schilling B, Ramanathan A, Ghaemmaghami S, Jasper H
• Temporal dynamics of liver mitochondrial protein acetylation and succinylation and metabolites due to high fat diet and/or excess glucose or fructose.
  PloS one 2018 Meyer JG, Softic S, Basisty N, Rardin MJ, Verdin E, Gibson BW, Ilkayeva O, Newgard CB, Kahn CR, Schilling B
• Simultaneous Quantification of the Acetylome and Succinylome by 'One-Pot' Affinity Enrichment.
  Proteomics 2018 Basisty N, Meyer JG, Wei L, Gibson BW, Schilling B
• The Mitochondrial Acylome Emerges: Proteomics, Regulation by Sirtuins, and Metabolic and Disease Implications.
  Cell metabolism 2018 Carrico C, Meyer JG, He W, Gibson BW, Verdin E
• An acetylatable lysine controls CRP function in E. coli.
  Molecular microbiology 2017 Davis R, Écija-Conesa A, Gallego-Jara J, de Diego T, Filippova EV, Kuffel G, Anderson WF, Gibson BW, Schilling B, Canovas M, Wolfe AJ
• Characterization of Inner and Outer Membrane Proteins from Francisella tularensis Strains LVS and Schu S4 and Identification of Potential Subunit Vaccine Candidates.
  mBio 2017 Post DMB, Slütter B, Schilling B, Chande AT, Rasmussen JA, Jones BD, D'Souza AK, Reinders LM, Harty JT, Gibson BW, Apicella MA
• Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.
  Nature communications 2017 Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S,…
• PIQED: automated identification and quantification of protein modifications from DIA-MS data.
  Nature methods 2017 Meyer JG, Mukkamalla S, Steen H, Nesvizhskii AI, Gibson BW, Schilling B
• Identification and characterization of AckA-dependent protein acetylation in Neisseria gonorrhoeae.
  PloS one 2017 Post DMB, Schilling B, Reinders LM, D'Souza AK, Ketterer MR, Kiel SJ, Chande AT, Apicella MA, Gibson BW
• Lysine desuccinylase SIRT5 binds to cardiolipin and regulates the electron transport chain.
  The Journal of biological chemistry 2017 Zhang Y, Bharathi SS, Rardin MJ, Lu J, Maringer KV, Sims-Lucas S, Prochownik EV, Gibson BW, Goetzman ES
• Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers.
  Methods in molecular biology (Clifton, N.J.) 2017 Schilling B, Gibson BW, Hunter CL
• Vitamin D Promotes Protein Homeostasis and Longevity via the Stress Response Pathway Genes skn-1, ire-1, and xbp-1.
  Cell reports 2016 Mark KA, Dumas KJ, Bhaumik D, Schilling B, Davis S, Oron TR, Sorensen DJ, Lucanic M, Brem RB, Melov S, Ramanathan A, Gibson BW, Lithgow GJ
• Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH).
  Journal of the American Society for Mass Spectrometry 2016 Meyer JG, D'Souza AK, Sorensen DJ, Rardin MJ, Wolfe AJ, Gibson BW, Schilling B
• Gadd45a Protein Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4.
  The Journal of biological chemistry 2016 Bullard SA, Seo S, Schilling B, Dyle MC, Dierdorff JM, Ebert SM, DeLau AD, Gibson BW, Adams CM
• Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications.
  Infection and immunity 2016 Post DM, Ketterer MR, Coffin JE, Reinders LM, Munson RS, Bair T, Murphy TF, Foster ED, Gibson BW, Apicella MA
• Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows.
  Analytical chemistry 2015 Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW
• Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits.
  Nature medicine 2015 Min SW, Chen X, Tracy TE, Li Y, Zhou Y, Wang C, Shirakawa K, Minami SS, Defensor E, Mok SA, Sohn PD, Schilling B, Cong X, Ellerby L, Gibson BW, Johnson J, Krogan N, Shamloo M, Gestwicki J, Masliah E, …
• Protein acetylation dynamics in response to carbon overflow in Escherichia coli.
  Molecular microbiology 2015 Schilling B, Christensen D, Davis R, Sahu AK, Hu LI, Walker-Peddakotla A, Sorensen DJ, Zemaitaitis B, Gibson BW, Wolfe AJ
• SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target.
  Molecular cell 2015 Nishida Y, Rardin MJ, Carrico C, He W, Sahu AK, Gut P, Najjar R, Fitch M, Hellerstein M, Gibson BW, Verdin E
• Integration-independent Transgenic Huntington Disease Fragment Mouse Models Reveal Distinct Phenotypes and Life Span in Vivo.
  The Journal of biological chemistry 2015 O'Brien R, DeGiacomo F, Holcomb J, Bonner A, Ring KL, Zhang N, Zafar K, Weiss A, Lager B, Schilling B, Gibson BW, Chen S, Kwak S, Ellerby LM
• SIRT1 deacetylates RORγt and enhances Th17 cell generation.
  The Journal of experimental medicine 2015 Lim HW, Kang SG, Ryu JK, Schilling B, Fei M, Lee IS, Kehasse A, Shirakawa K, Yokoyama M, Schnölzer M, Kasler HG, Kwon HS, Gibson BW, Sato H, Akassoglou K, Xiao C, Littman DR, Ott M, Verdin E
• MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.
  Molecular & cellular proteomics : MCP 2015 Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW
• SIRT1 deacetylates RORγt and enhances Th17 cell generation.
  The Journal of experimental medicine 2015 Lim HW, Kang SG, Ryu JK, Schilling B, Fei M, Lee IS, Kehasse A, Shirakawa K, Yokoyama M, Schnölzer M, Kasler HG, Kwon HS, Gibson BW, Sato H, Akassoglou K, Xiao C, Littman DR, Ott M, Verdin E
• SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase.
  PloS one 2015 Zhang Y, Bharathi SS, Rardin MJ, Uppala R, Verdin E, Gibson BW, Goetzman ES
• Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.
  Molecular & cellular proteomics : MCP 2015 Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, …
• Comparative analyses of proteins from Haemophilus influenzae biofilm and planktonic populations using metabolic labeling and mass spectrometry.
  BMC microbiology 2014 Post DM, Held JM, Ketterer MR, Phillips NJ, Sahu A, Apicella MA, Gibson BW
• Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.
  Journal of proteome research 2014 French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, Townsend RR, Sherrod SD, Goodwin CR, McLean JA, Tabb DL
• The E. coli sirtuin CobB shows no preference for enzymatic and nonenzymatic lysine acetylation substrate sites.
  MicrobiologyOpen 2014 AbouElfetouh A, Kuhn ML, Hu LI, Scholle MD, Sorensen DJ, Sahu AK, Becher D, Antelmann H, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ
• Iron promotes protein insolubility and aging in C. elegans.
  Aging 2014 Klang IM, Schilling B, Sorensen DJ, Sahu AK, Kapahi P, Andersen JK, Swoboda P, Killilea DW, Gibson BW, Lithgow GJ
• Panorama: a targeted proteomics knowledge base.
  Journal of proteome research 2014 Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B
• RPL24: a potential therapeutic target whose depletion or acetylation inhibits polysome assembly and cancer cell growth.
  Oncotarget 2014 Wilson-Edell KA, Kehasse A, Scott GK, Yau C, Rothschild DE, Schilling B, Gabriel BS, Yevtushenko MA, Hanson IM, Held JM, Gibson BW, Benz CC
• Variation and quantification among a target set of phosphopeptides in human plasma by multiple reaction monitoring and SWATH-MS2 data-independent acquisition.
  Electrophoresis 2014 Zawadzka AM, Schilling B, Held JM, Sahu AK, Cusack MP, Drake PM, Fisher SJ, Gibson BW
• A framework for installable external tools in Skyline.
  Bioinformatics (Oxford, England) 2014 Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B
• Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.
  PloS one 2014 Kuhn ML, Zemaitaitis B, Hu LI, Sahu A, Sorensen D, Minasov G, Lima BP, Scholle M, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ
• Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma.
  Molecular & cellular proteomics : MCP 2014 Zawadzka AM, Schilling B, Cusack MP, Sahu AK, Drake P, Fisher SJ, Benz CC, Gibson BW
• Francisella tularensis Schu S4 lipopolysaccharide core sugar and O-antigen mutants are attenuated in a mouse model of tularemia.
  Infection and immunity 2014 Rasmussen JA, Post DM, Gibson BW, Lindemann SR, Apicella MA, Meyerholz DK, Jones BD
• SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks.
  Cell metabolism 2013 Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, …
• Sirtuin 3 (SIRT3) protein regulates long-chain acyl-CoA dehydrogenase by deacetylating conserved lysines near the active site.
  The Journal of biological chemistry 2013 Bharathi SS, Zhang Y, Mohsen AW, Uppala R, Balasubramani M, Schreiber E, Uechi G, Beck ME, Rardin MJ, Vockley J, Verdin E, Gibson BW, Hirschey MD, Goetzman ES
• Sirt3 regulates metabolic flexibility of skeletal muscle through reversible enzymatic deacetylation.
  Diabetes 2013 Jing E, O'Neill BT, Rardin MJ, Kleinridders A, Ilkeyeva OR, Ussar S, Bain JR, Lee KY, Verdin EM, Newgard CB, Gibson BW, Kahn CR
• Site-specific acylation changes in the lipid A of Escherichia coli lpxL mutants grown at high temperatures.
  Innate immunity 2013 Schilling B, Hunt J, Gibson BW, Apicella MA
• Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).
  Molecular & cellular proteomics : MCP 2013 Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, …
• Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions.
  International journal of proteomics 2013 Held JM, Schilling B, D'Souza AK, Srinivasan T, Behring JB, Sorensen DJ, Benz CC, Gibson BW
• Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW
• Elucidation of N-glycosites within human plasma glycoproteins for cancer biomarker discovery.
  Methods in molecular biology (Clifton, N.J.) 2013 Drake P, Schilling B, Gibson B, Fisher S
• Targeted quantitation of acetylated lysine peptides by selected reaction monitoring mass spectrometry.
  Methods in molecular biology (Clifton, N.J.) 2013 Rardin MJ, Held JM, Gibson BW
• No consistent bioenergetic defects in presynaptic nerve terminals isolated from mouse models of Alzheimer's disease.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2012 Choi SW, Gerencser AA, Ng R, Flynn JM, Melov S, Danielson SR, Gibson BW, Nicholls DG, Bredesen DE, Brand MD
• Adipose-specific deletion of TFAM increases mitochondrial oxidation and protects mice against obesity and insulin resistance.
  Cell metabolism 2012 Vernochet C, Mourier A, Bezy O, Macotela Y, Boucher J, Rardin MJ, An D, Lee KY, Ilkayeva OR, Zingaretti CM, Emanuelli B, Smyth G, Cinti S, Newgard CB, Gibson BW, Larsson NG, Kahn CR
• Tor1 regulates protein solubility in Saccharomyces cerevisiae.
  Molecular biology of the cell 2012 Peters TW, Rardin MJ, Czerwieniec G, Evani US, Reis-Rodrigues P, Lithgow GJ, Mooney SD, Gibson BW, Hughes RE
• Proteogenomics of synaptosomal mitochondrial oxidative stress.
  Free radical biology & medicine 2012 Flynn JM, Czerwieniec GA, Choi SW, Day NU, Gibson BW, Hubbard A, Melov S
• QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation.
  Analytical chemistry 2012 Ma ZQ, Polzin KO, Dasari S, Chambers MC, Schilling B, Gibson BW, Tran BQ, Vega-Montoto L, Liebler DC, Tabb DL
• Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins.
  PloS one 2012 Phillips NJ, Steichen CT, Schilling B, Post DM, Niles RK, Bair TB, Falsetta ML, Apicella MA, Gibson BW
• Ligand binding promotes CDK-dependent phosphorylation of ER-alpha on hinge serine 294 but inhibits ligand-independent phosphorylation of serine 305.
  Molecular cancer research : MCR 2012 Held JM, Britton DJ, Scott GK, Lee EL, Schilling B, Baldwin MA, Gibson BW, Benz CC
• Ubiquitin-specific peptidase 9, X-linked (USP9X) modulates activity of mammalian target of rapamycin (mTOR).
  The Journal of biological chemistry 2012 Agrawal P, Chen YT, Schilling B, Gibson BW, Hughes RE
• Inhibition of lipid signaling enzyme diacylglycerol kinase epsilon attenuates mutant huntingtin toxicity.
  The Journal of biological chemistry 2012 Zhang N, Li B, Al-Ramahi I, Cong X, Held JM, Kim E, Botas J, Gibson BW, Ellerby LM
• Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.
  Molecular & cellular proteomics : MCP 2012 Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW
• Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.
  Journal of proteome research 2012 Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP…
• O-antigen and core carbohydrate of Vibrio fischeri lipopolysaccharide: composition and analysis of their role in Euprymna scolopes light organ colonization.
  The Journal of biological chemistry 2012 Post DM, Yu L, Krasity BC, Choudhury B, Mandel MJ, Brennan CA, Ruby EG, McFall-Ngai MJ, Gibson BW, Apicella MA
• Proteomic analysis of age-dependent changes in protein solubility identifies genes that modulate lifespan.
  Aging cell 2011 Reis-Rodrigues P, Czerwieniec G, Peters TW, Evani US, Alavez S, Gaman EA, Vantipalli M, Mooney SD, Gibson BW, Lithgow GJ, Hughes RE
• Regulatory control or oxidative damage? Proteomic approaches to interrogate the role of cysteine oxidation status in biological processes.
  Molecular & cellular proteomics : MCP 2011 Held JM, Gibson BW
• Life span extension via eIF4G inhibition is mediated by posttranscriptional remodeling of stress response gene expression in C. elegans.
  Cell metabolism 2011 Rogers AN, Chen D, McColl G, Czerwieniec G, Felkey K, Gibson BW, Hubbard A, Melov S, Lithgow GJ, Kapahi P
• Mass spectrometric identification of novel lysine acetylation sites in huntingtin.
  Molecular & cellular proteomics : MCP 2011 Cong X, Held JM, DeGiacomo F, Bonner A, Chen JM, Schilling B, Czerwieniec GA, Gibson BW, Ellerby LM
• N-acylethanolamine signalling mediates the effect of diet on lifespan in Caenorhabditis elegans.
  Nature 2011 Lucanic M, Held JM, Vantipalli MC, Klang IM, Graham JB, Gibson BW, Lithgow GJ, Gill MS
• Confident identification of 3-nitrotyrosine modifications in mass spectral data across multiple mass spectrometry platforms.
  Journal of proteomics 2011 Li B, Held JM, Schilling B, Danielson SR, Gibson BW
• The lipid A from Vibrio fischeri lipopolysaccharide: a unique structure bearing a phosphoglycerol moiety.
  The Journal of biological chemistry 2011 Phillips NJ, Adin DM, Stabb EV, McFall-Ngai MJ, Apicella MA, Gibson BW
• Quantitative mapping of reversible mitochondrial Complex I cysteine oxidation in a Parkinson disease mouse model.
  The Journal of biological chemistry 2011 Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK
• Identification of new modulators and protein alterations in non-apoptotic programmed cell death.
  Journal of cellular biochemistry 2010 Sperandio S, Poksay KS, Schilling B, Crippen D, Gibson BW, Bredesen DE
• A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma.
  Analytical biochemistry 2010 Drake PM, Schilling B, Niles RK, Braten M, Johansen E, Liu H, Lerch M, Sorensen DJ, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ
• Identification, characterization and immunogenicity of an O-antigen capsular polysaccharide of Francisella tularensis.
  PloS one 2010 Apicella MA, Post DM, Fowler AC, Jones BD, Rasmussen JA, Hunt JR, Imagawa S, Choudhury B, Inzana TJ, Maier TM, Frank DW, Zahrt TC, Chaloner K, Jennings MP, McLendon MK, Gibson BW
• ErbB2 trafficking and degradation associated with K48 and K63 polyubiquitination.
  Cancer research 2010 Marx C, Held JM, Gibson BW, Benz CC
• Targeted quantitation of site-specific cysteine oxidation in endogenous proteins using a differential alkylation and multiple reaction monitoring mass spectrometry approach.
  Molecular & cellular proteomics : MCP 2010 Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW
• Utilizing the O-antigen lipopolysaccharide biosynthesis pathway in Escherichia coli to interrogate the substrate specificities of exogenous glycosyltransferase genes in a combinatorial approach.
  Glycobiology 2010 Johansen EB, Szoka FC, Zaleski A, Apicella MA, Gibson BW
• Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.
  Journal of proteome research 2010 Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling…
• Sweetening the pot: adding glycosylation to the biomarker discovery equation.
  Clinical chemistry 2009 Drake PM, Cho W, Li B, Prakobphol A, Johansen E, Anderson NL, Regnier FE, Gibson BW, Fisher SJ
• Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
  Molecular & cellular proteomics : MCP 2009 Paulovich AG, Billheimer D, Ham AJ, Vega-Montoto L, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR…
• Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
  Molecular & cellular proteomics : MCP 2009 Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, …
• The Mycobacterium bovis bacille Calmette-Guerin phagosome proteome.
  Molecular & cellular proteomics : MCP 2009 Lee BY, Jethwaney D, Schilling B, Clemens DL, Gibson BW, Horwitz MA
• A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.
  Journal of visualized experiments : JoVE 2009 Johansen E, Schilling B, Lerch M, Niles RK, Liu H, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ, Drake PM
• Preferentially increased nitration of alpha-synuclein at tyrosine-39 in a cellular oxidative model of Parkinson's disease.
  Analytical chemistry 2009 Danielson SR, Held JM, Schilling B, Oo M, Gibson BW, Andersen JK
• IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
  Journal of proteome research 2009 Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL
• Calpain-1 cleaves and activates caspase-7.
  The Journal of biological chemistry 2009 Gafni J, Cong X, Chen SF, Gibson BW, Ellerby LM
• Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.
  Nature biotechnology 2009 Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, …
• Systematic mapping of posttranslational modifications in human estrogen receptor-alpha with emphasis on novel phosphorylation sites.
  Molecular & cellular proteomics : MCP 2008 Atsriku C, Britton DJ, Held JM, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA
• A novel serine phosphorylation site detected in the N-terminal domain of estrogen receptor isolated from human breast cancer cells.
  Journal of the American Society for Mass Spectrometry 2008 Britton DJ, Scott GK, Schilling B, Atsriku C, Held JM, Gibson BW, Benz CC, Baldwin MA
• Partial acetylation of lysine residues improves intraprotein cross-linking.
  Analytical chemistry 2008 Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy RK, Kuntz ID, Gibson BW
• Characterization of htrB and msbB mutants of the light organ symbiont Vibrio fischeri.
  Applied and environmental microbiology 2007 Adin DM, Phillips NJ, Gibson BW, Apicella MA, Ruby EG, McFall-Ngai MJ, Hall DB, Stabb EV
• Small-scale immunopurification of cytochrome c oxidase for a high-throughput multiplexing analysis of enzyme activity and amount.
  Biotechnology and applied biochemistry 2007 Murray J, Schilling B, Row RH, Yoo CB, Gibson BW, Marusich MF, Capaldi RA
• Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019.
  The Journal of biological chemistry 2007 Johnston JW, Coussens NP, Allen S, Houtman JC, Turner KH, Zaleski A, Ramaswamy S, Gibson BW, Apicella MA
• Regulation of sialic acid transport and catabolism in Haemophilus influenzae.
  Molecular microbiology 2007 Johnston JW, Zaleski A, Allen S, Mootz JM, Armbruster D, Gibson BW, Apicella MA, Munson RS
• Proposed second class of Haemophilus ducreyi strains show altered protein and lipooligosaccharide profiles.
  Proteomics 2007 Post DM, Gibson BW
• Identification of LpxL, a late acyltransferase of Francisella tularensis.
  Infection and immunity 2007 McLendon MK, Schilling B, Hunt JR, Apicella MA, Gibson BW
• Proteomic analysis of plasma membrane and secretory vesicles from human neutrophils.
  Proteome science 2007 Jethwaney D, Islam MR, Leidal KG, de Bernabe DB, Campbell KP, Nauseef WM, Gibson BW
• Quantification of cysteine oxidation in human estrogen receptor by mass spectrometry.
  Analytical chemistry 2007 Atsriku C, Benz CC, Scott GK, Gibson BW, Baldwin MA
• Characterization of lipid A acylation patterns in Francisella tularensis, Francisella novicida, and Francisella philomiragia using multiple-stage mass spectrometry and matrix-assisted laser desorption/ionization on an intermediate vacuum source linear ion trap.
  Analytical chemistry 2007 Schilling B, McLendon MK, Phillips NJ, Apicella MA, Gibson BW
• Identification of genes involved in the expression of atypical lipooligosaccharide structures from a second class of Haemophilus ducreyi.
  Infection and immunity 2006 Post DM, Munson RS, Baker B, Zhong H, Bozue JA, Gibson BW
• Role of lgtC in resistance of nontypeable Haemophilus influenzae strain R2866 to human serum.
  Infection and immunity 2006 Erwin AL, Allen S, Ho DK, Bonthuis PJ, Bonthius PJ, Jarisch J, Nelson KL, Tsao DL, Unrath WC, Watson ME, Gibson BW, Apicella MA, Smith AL
• DAF-12-dependent rescue of dauer formation in Caenorhabditis elegans by (25S)-cholestenoic acid.
  Aging cell 2006 Held JM, White MP, Fisher AL, Gibson BW, Lithgow GJ, Gill MS
• Huntingtin phosphorylation sites mapped by mass spectrometry. Modulation of cleavage and toxicity.
  The Journal of biological chemistry 2006 Schilling B, Gafni J, Torcassi C, Cong X, Row RH, LaFevre-Bernt MA, Cusack MP, Ratovitski T, Hirschhorn R, Ross CA, Gibson BW, Ellerby LM
• Novel pathways associated with quinone-induced stress in breast cancer cells.
  Drug metabolism reviews 2006 Benz CC, Atsriku C, Yau C, Britton D, Schilling B, Gibson BW, Baldwin MA, Scott GK
• Stable isotope metabolic labeling of Neisseria meningitidis lipooligosaccharide.
  Journal of endotoxin research 2006 Post DM, Zhang D, Weiss JP, Gibson BW
• Identification of a novel sialic acid transporter in Haemophilus ducreyi.
  Infection and immunity 2005 Post DM, Mungur R, Gibson BW, Munson RS
• Novel sialic acid transporter of Haemophilus influenzae.
  Infection and immunity 2005 Allen S, Zaleski A, Johnston JW, Gibson BW, Apicella MA
• Biochemical and functional characterization of membrane blebs purified from Neisseria meningitidis serogroup B.
  The Journal of biological chemistry 2005 Post DM, Zhang D, Eastvold JS, Teghanemt A, Gibson BW, Weiss JP
• Proteomic analysis of succinate dehydrogenase and ubiquinol-cytochrome c reductase (Complex II and III) isolated by immunoprecipitation from bovine and mouse heart mitochondria.
  Biochimica et biophysica acta 2005 Schilling B, Murray J, Yoo CB, Row RH, Cusack MP, Capaldi RA, Gibson BW
• Characterization of a cluster of three glycosyltransferase enzymes essential for Moraxella catarrhalis lipooligosaccharide assembly.
  Journal of bacteriology 2005 Edwards KJ, Allen S, Gibson BW, Campagnari AA
• Mass spectrometric identification of a novel phosphorylation site in subunit NDUFA10 of bovine mitochondrial complex I.
  FEBS letters 2005 Schilling B, Aggeler R, Schulenberg B, Murray J, Row RH, Capaldi RA, Gibson BW
• The human mitochondrial proteome: oxidative stress, protein modifications and oxidative phosphorylation.
  The international journal of biochemistry & cell biology 2005 Gibson BW
• Rapid purification and mass spectrometric characterization of mitochondrial NADH dehydrogenase (Complex I) from rodent brain and a dopaminergic neuronal cell line.
  Molecular & cellular proteomics : MCP 2004 Schilling B, Bharath M M S, Row RH, Murray J, Cusack MP, Capaldi RA, Freed CR, Prasad KN, Andersen JK, Gibson BW
• Lipophilic regulator of a developmental switch in Caenorhabditis elegans.
  Aging cell 2004 Gill MS, Held JM, Fisher AL, Gibson BW, Lithgow GJ
• Novel modification of lipid A of Francisella tularensis.
  Infection and immunity 2004 Phillips NJ, Schilling B, McLendon MK, Apicella MA, Gibson BW
• Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry of lipopolysaccharide species separated by slab-polyacrylamide gel electrophoresis: high-resolution separation and molecular weight determination of lipooligosaccharides from Vibrio fischeri strain HMK.
  Electrophoresis 2004 Pupo E, Phillips NJ, Gibson BW, Apicella MA, Hardy E
• Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry.
  Journal of proteome research 2004 Gaucher SP, Taylor SW, Fahy E, Zhang B, Warnock DE, Ghosh SS, Gibson BW
• Exploiting proteomics in the discovery of drugs that target mitochondrial oxidative damage.
  Science of aging knowledge environment : SAGE KE 2004 Gibson BW
• Proteomic and immunochemical characterization of a role for stathmin in adult neurogenesis.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2004 Jin K, Mao XO, Cottrell B, Schilling B, Xie L, Row RH, Sun Y, Peel A, Childs J, Gendeh G, Gibson BW, Greenberg DA
• The Streptococcus gordonii platelet binding protein GspB undergoes glycosylation independently of export.
  Journal of bacteriology 2004 Bensing BA, Gibson BW, Sullam PM
• Identification of a 3-deoxy-D-manno-octulosonic acid biosynthetic operon in Moraxella catarrhalis and analysis of a KdsA-deficient isogenic mutant.
  Infection and immunity 2003 Luke NR, Allen S, Gibson BW, Campagnari AA
• Molecular components of a cell death pathway activated by endoplasmic reticulum stress.
  The Journal of biological chemistry 2003 Rao RV, Poksay KS, Castro-Obregon S, Schilling B, Row RH, del Rio G, Gibson BW, Ellerby HM, Bredesen DE
• Proteome of Haemophilus ducreyi by 2-D SDS-PAGE and mass spectrometry: strain variation, virulence, and carbohydrate expression.
  Journal of proteome research 2003 Scheffler NK, Falick AM, Hall SC, Ray WC, Post DM, Munson RS, Gibson BW
• Phosphospecific proteolysis for mapping sites of protein phosphorylation.
  Nature biotechnology 2003 Knight ZA, Schilling B, Row RH, Kenski DM, Gibson BW, Shokat KM
• MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides.
  Journal of the American Society for Mass Spectrometry 2003 Schilling B, Row RH, Gibson BW, Guo X, Young MM
• Primary sequence characterization of catestatin intermediates and peptides defines proteolytic cleavage sites utilized for converting chromogranin a into active catestatin secreted from neuroendocrine chromaffin cells.
  Biochemistry 2003 Lee JC, Taylor CV, Gaucher SP, Toneff T, Taupenot L, Yasothornsrikul S, Mahata SK, Sei C, Parmer RJ, Neveu JM, Lane WS, Gibson BW, O'Connor DT, Hook VY
• Metabolic incorporation of unnatural sialic acids into Haemophilus ducreyi lipooligosaccharides.
  Proceedings of the National Academy of Sciences of the United States of America 2003 Goon S, Schilling B, Tullius MV, Gibson BW, Bertozzi CR
• Characterization of the human heart mitochondrial proteome.
  Nature biotechnology 2003 Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS
• The msbB mutant of Neisseria meningitidis strain NMB has a defect in lipooligosaccharide assembly and transport to the outer membrane.
  Infection and immunity 2003 Post DM, Ketterer MR, Phillips NJ, Gibson BW, Apicella MA
• Identification and characterization of the N-acetylglucosamine glycosyltransferase gene of Haemophilus ducreyi.
  Infection and immunity 2002 Sun S, Scheffler NK, Gibson BW, Wang J, Munson RS
• An alternative strategy to determine the mitochondrial proteome using sucrose gradient fractionation and 1D PAGE on highly purified human heart mitochondria.
  Journal of proteome research 2002 Taylor SW, Warnock DE, Glenn GM, Zhang B, Fahy E, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS
• Characterization of lipooligosaccharides from Haemophilus ducreyi containing polylactosamine repeats.
  Journal of the American Society for Mass Spectrometry 2002 Schilling B, Gibson BW, Filiatrault M, Campagnari AA
• The lbgAB gene cluster of Haemophilus ducreyi encodes a beta-1,4-galactosyltransferase and an alpha-1,6-DD-heptosyltransferase involved in lipooligosaccharide biosynthesis.
  Infection and immunity 2002 Tullius MV, Phillips NJ, Scheffler NK, Samuels NM, Munson Jr RS, Hansen EJ, Stevens-Riley M, Campagnari AA, Gibson BW
• Haemophilus influenzae type b strain A2 has multiple sialyltransferases involved in lipooligosaccharide sialylation.
  The Journal of biological chemistry 2002 Jones PA, Samuels NM, Phillips NJ, Munson RS, Bozue JA, Arseneau JA, Nichols WA, Zaleski A, Gibson BW, Apicella MA
• Intracellular survival of Neisseria gonorrhoeae in male urethral epithelial cells: importance of a hexaacyl lipid A.
  Infection and immunity 2002 Post DM, Phillips NJ, Shao JQ, Entz DD, Gibson BW, Apicella MA