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    Al Burlingame, PhD

    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address600 16th Street
    San Francisco CA 94158

       Awards and Honors
      1970John Simon Guggenheim Memorial Fellowship
      Academia Sinica, People's Republic of China1981Official Guest
      Japanese Society for Medical Mass Spectrometry1982Honorary Member
      Academy of Sciences of the USSR1986Official Guest, Academy of Sciences of the USSR
      American Association for the Advancement of Science1990Fellow, American Association for the Advancement of Science
      Virginia Polytechnic University1996The Peters Lecturer
      Northeastern University1999Barnett Lectureship
      Indiana University2001Lilly Distinguished Lecturer
      Nobel Forum, Stockholm, Sweden2007Lecturer, Proteomics in Medicine
      International Forum of Proteomics2012Achievement Award

      My group has long-standing, extensive expertise and experience in mass spectrometry, proteomics and systems biology, especially focused on sequencing, identification and study of unknown proteins, and the detection, assignment and site-specific dynamics of posttranslational modifications of proteins, particularly OGlcNAcylation, phosphorylation, acetylation, methylation and ubiquitinylation. Over many years we have collaborated with the neurobiological community extensively, including structural characterization of the GPI membrane anchor of the prion protein, structure of the lysyl oxidase co-factor, identification and PTM regulation of proteins in the retrograde signaling complexes in damaged axons, the O-GlcNAc/phosphorylation dynamics at the murine synapse, identification of new proteins involved in the Nodes of Ranvier, etc.

      In addition to the work in proteomics and epigenetics above, we have focused significant effort on other studies concerning the architecture of protein complexes and machines for which angstrom resolution structural information has not yet been tractable. For example we have developed a new lysine-lysine cross-linking strategy based on chemical reductive amination that provides comprehensive sequence and cross-link site assignments using electron transfer dissociation (ETD). This information provides accurate distance constraints that complement cryoEM and computer modeling efforts. In parallel software algorithms and scoring strategies have been developed that greatly facilitates the assignment of cross-linked peptides in general. Very recently we have initiated a thrust into development and application of methodology to measure protein complexes directly in the gas phase using a newly acquired high mass Orbitrap Exactive instrument (m/z < 22,000). This effort will complement our long-standing work on chemical cross-linking of protein complexes and machines.

      Finally, we have developed a general suite of programs and software tools required for processing large scale mass spectral data sets (HCD, ETD, etc) and stable isotopic labeling experiments (SILAC, iTRAQ, etc) called Protein Prospector.

      Proteomics & the Molecular Compositions of Biological Systems, Molecular Structure Determinations, Identification of Cell Constituents and Correlation with Gene Expression, Structures of Modified Macromolecules and protein machines in Structural Biology, e.g., Posttranslational Modifications of Proteins, Epigenetics, Glucoconjugates, Antigenic Determinants, Molecular Immunochemistry, Metabolic Activation and Covalent Binding of Xenobiotics to Cellular Macromolecules, Molecular Nature of Chemical Toxicity, Mass Spectrometry, Molecular Composition of Biological Systems

       ORNG Applications 
       Awarded Grants

      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Muller M, Hutin S, Marigold O, Li KH, Burlingame A, Glaunsinger BA. A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases. PLoS Pathog. 2015 May; 11(5):e1004899.
        View in: PubMed
      2. Bradshaw RA, Burlingame AL. Minireviews revisited. Mol Cell Proteomics. 2015 Mar; 14(3):455.
        View in: PubMed
      3. Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A. A20 Restricts Ubiquitination of Pro-Interleukin-1ß Protein Complexes and Suppresses NLRP3 Inflammasome Activity. Immunity. 2015 Jan 20; 42(1):55-67.
        View in: PubMed
      4. Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol. 2015 Jan 16; 10(1):63-71.
        View in: PubMed
      5. Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human Liver Cytochrome P450 3A4 Ubiquitination: MOLECULAR RECOGNITION BY UBC7-gp78 AUTOCRINE MOTILITY FACTOR RECEPTOR AND UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 UBIQUITIN LIGASE COMPLEXES. J Biol Chem. 2015 Feb 6; 290(6):3308-32.
        View in: PubMed
      6. Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H. NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. Adv Biol Regul. 2015 May; 58:16-27.
        View in: PubMed
      7. Ultanir SK, Yadav S, Hertz NT, Oses-Prieto JA, Claxton S, Burlingame AL, Shokat KM, Jan LY, Jan YN. MST3 Kinase Phosphorylates TAO1/2 to Enable Myosin Va Function in Promoting Spine Synapse Development. Neuron. 2014 Dec 3; 84(5):968-82.
        View in: PubMed
      8. Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48.
        View in: PubMed
      9. Pando-Robles V, Oses-Prieto JA, Rodríguez-Gandarilla M, Meneses-Romero E, Burlingame AL, Batista CV. Quantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC-MS. J Proteomics. 2014 Dec 5; 111:16-29.
        View in: PubMed
      10. Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY, Quail PH. A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science. 2014 Jun 6; 344(6188):1160-4.
        View in: PubMed
      11. Deng Z, Oses-Prieto JA, Kutschera U, Tseng TS, Hao L, Burlingame AL, Wang ZY, Briggs WR. Blue light-induced proteomic changes in etiolated Arabidopsis seedlings. J Proteome Res. 2014 May 2; 13(5):2524-33.
        View in: PubMed PMC4015686
      12. Cho Y, Di Liberto V, Carlin D, Abe N, Li KH, Burlingame AL, Guan S, Michaelevski I, Cavalli V. Syntaxin13 expression is regulated by mammalian target of rapamycin (mTOR) in injured neurons to promote axon regeneration. J Biol Chem. 2014 May 30; 289(22):15820-32.
        View in: PubMed PMC4140936
      13. Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA. Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell. Crit Care. 2014; 18(2):R50.
        View in: PubMed PMC4056080
      14. Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014 Mar; 13(3):907-17.
        View in: PubMed PMC3945918
      15. Abernathy E, Clyde K, Yeasmin R, Krug LT, Burlingame A, Coscoy L, Glaunsinger B. Gammaherpesviral gene expression and virion composition are broadly controlled by accelerated mRNA degradation. PLoS Pathog. 2014 Jan; 10(1):e1003882.
        View in: PubMed PMC3894220
      16. Asmussen J, Lasater EA, Tajon C, Oses-Prieto J, Jun YW, Taylor BS, Burlingame A, Craik CS, Shah NP. MEK-dependent negative feedback underlies BCR-ABL-mediated oncogene addiction. Cancer Discov. 2014 Feb; 4(2):200-15.
        View in: PubMed
      17. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34.
        View in: PubMed PMC3916644
      18. Young LC, Hartig N, Muñoz-Alegre M, Oses-Prieto JA, Durdu S, Bender S, Vijayakumar V, Vietri Rudan M, Gewinner C, Henderson S, Jathoul AP, Ghatrora R, Lythgoe MF, Burlingame AL, Rodriguez-Viciana P. An MRAS, SHOC2, and SCRIB complex coordinates ERK pathway activation with polarity and tumorigenic growth. Mol Cell. 2013 Dec 12; 52(5):679-92.
        View in: PubMed
      19. Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA. Global cellular response to chemotherapy-induced apoptosis. Elife. 2013; 2:e01236.
        View in: PubMed PMC3808542
      20. Xu P, Xu SL, Li ZJ, Tang W, Burlingame AL, Wang ZY. A brassinosteroid-signaling kinase interacts with multiple receptor-like kinases in Arabidopsis. Mol Plant. 2014 Feb; 7(2):441-4.
        View in: PubMed PMC3900014
      21. Wang C, Shang JX, Chen QX, Oses-Prieto JA, Bai MY, Yang Y, Yuan M, Zhang YL, Mu CC, Deng Z, Wei CQ, Burlingame AL, Wang ZY, Sun Y. Identification of BZR1-interacting proteins as potential components of the brassinosteroid signaling pathway in Arabidopsis through tandem affinity purification. Mol Cell Proteomics. 2013 Dec; 12(12):3653-65.
        View in: PubMed PMC3861714
      22. Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell. 2013 Aug 15; 154(4):737-47.
        View in: PubMed PMC3950538
      23. Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell. 2013 Jul; 25(7):2679-98.
        View in: PubMed PMC3753391
      24. Nishino M, Choy JW, Gushwa NN, Oses-Prieto JA, Koupparis K, Burlingame AL, Renslo AR, McKerrow JH, Taunton J. Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei [corrected]. Elife. 2013; 2:e00712.
        View in: PubMed PMC3707081
      25. Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF. N- and O-glycosylation in the murine synaptosome. Mol Cell Proteomics. 2013 Dec; 12(12):3474-88.
        View in: PubMed PMC3861701
      26. Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Mol Cell Proteomics. 2013 Sep; 12(9):2381-2.
        View in: PubMed PMC3769317
      27. Xu J, Wang AH, Oses-Prieto J, Makhijani K, Katsuno Y, Pei M, Yan L, Zheng YG, Burlingame A, Brückner K, Derynck R. Arginine Methylation Initiates BMP-Induced Smad Signaling. Mol Cell. 2013 Jul 11; 51(1):5-19.
        View in: PubMed PMC3951972
      28. Bellodi C, McMahon M, Contreras A, Juliano D, Kopmar N, Nakamura T, Maltby D, Burlingame A, Savage SA, Shimamura A, Ruggero D. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. Cell Rep. 2013 May 30; 3(5):1493-502.
        View in: PubMed PMC3857015
      29. Susuki K, Chang KJ, Zollinger DR, Liu Y, Ogawa Y, Eshed-Eisenbach Y, Dours-Zimmermann MT, Oses-Prieto JA, Burlingame AL, Seidenbecher CI, Zimmermann DR, Oohashi T, Peles E, Rasband MN. Three mechanisms assemble central nervous system nodes of Ranvier. Neuron. 2013 May 8; 78(3):469-82.
        View in: PubMed PMC3756512
      30. Gautam V, Trinidad JC, Rimerman RA, Costa BM, Burlingame AL, Monaghan DT. Nedd4 is a specific E3 ubiquitin ligase for the NMDA receptor subunit GluN2D. Neuropharmacology. 2013 Nov; 74:96-107.
        View in: PubMed PMC3855079
      31. Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9.
        View in: PubMed PMC3704229
      32. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem. 2013 Jun 7; 288(23):16606-18.
        View in: PubMed PMC3675596
      33. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. MBio. 2013; 4(2):e00098-13.
        View in: PubMed PMC3622926
      34. Bessat M, Knudsen G, Burlingame AL, Wang CC. A minimal anaphase promoting complex/cyclosome (APC/C) in Trypanosoma brucei. PLoS One. 2013; 8(3):e59258.
        View in: PubMed PMC3606461
      35. Liu W, Baker SS, Trinidad J, Burlingame AL, Baker RD, Forte JG, Virtuoso LP, Egilmez NK, Zhu L. Inhibition of lysosomal enzyme activities by proton pump inhibitors. J Gastroenterol. 2013 Dec; 48(12):1343-52.
        View in: PubMed
      36. Myers SA, Daou S, Affar el B, Burlingame A. Electron transfer dissociation (ETD): the mass spectrometric breakthrough essential for O-GlcNAc protein site assignments-a study of the O-GlcNAcylated protein host cell factor C1. Proteomics. 2013 Mar; 13(6):982-91.
        View in: PubMed PMC3988289
      37. Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc. 2013 Feb 27; 135(8):2879-82.
        View in: PubMed
      38. Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH. Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock. Cell Metab. 2013 Feb 5; 17(2):291-302.
        View in: PubMed PMC3597447
      39. Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS. Rearrangements within human spliceosomes captured after exon ligation. RNA. 2013 Mar; 19(3):400-12.
        View in: PubMed PMC3677250
      40. Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25.
        View in: PubMed PMC3566858
      41. Ouellet H, Chow ED, Guan S, Cox JS, Burlingame AL, de Montellano PR. Genetic and mass spectrometric tools for elucidating the physiological function(s) of cytochrome P450 enzymes from Mycobacterium tuberculosis. Methods Mol Biol. 2013; 987:79-94.
        View in: PubMed
      42. Just S, Illing S, Trester-Zedlitz M, Lau EK, Kotowski SJ, Miess E, Mann A, Doll C, Trinidad JC, Burlingame AL, von Zastrow M, Schulz S. Differentiation of opioid drug effects by hierarchical multi-site phosphorylation. Mol Pharmacol. 2013 Mar; 83(3):633-9.
        View in: PubMed PMC3583494
      43. Zhuang M, Guan S, Wang H, Burlingame AL, Wells JA. Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator. Mol Cell. 2013 Jan 24; 49(2):273-82.
        View in: PubMed PMC3557559
      44. Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL. Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics. Adv Biol Regul. 2013 Jan; 53(1):87-96.
        View in: PubMed PMC3577974
      45. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD. Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17931-5.
        View in: PubMed PMC3497735
      46. Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R. Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins. Mol Cell Proteomics. 2013 Jan; 12(1):29-41.
        View in: PubMed PMC3536907
      47. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100.
        View in: PubMed PMC3707110
      48. Nagano K, Akpan A, Warnasuriya G, Corless S, Totty N, Yang A, Stein R, Zvelebil M, Stensballe A, Burlingame A, Waterfield M, Cramer R, Timms JF, Naaby-Hansen S. Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase coactivation in Swiss 3T3 fibroblasts. Mol Cell Proteomics. 2012 Dec; 11(12):1690-708.
        View in: PubMed PMC3518109
      49. Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA. Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death Differ. 2012 Dec; 19(12):2040-8.
        View in: PubMed PMC3504717
      50. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25.
        View in: PubMed PMC3404735
      51. Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA. Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12432-7.
        View in: PubMed PMC3412033
      52. Stowe IB, Mercado EL, Stowe TR, Bell EL, Oses-Prieto JA, Hernández H, Burlingame AL, McCormick F. A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1. Genes Dev. 2012 Jul 1; 26(13):1421-6.
        View in: PubMed PMC3403010
      53. Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics. 2012 Aug; 11(8):215-29.
        View in: PubMed PMC3412957
      54. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay MA, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia. Am J Physiol Lung Cell Mol Physiol. 2012 Jul 1; 303(1):L12-9.
        View in: PubMed PMC3426434
      55. Guan S, Price JC, Ghaemmaghami S, Prusiner SB, Burlingame AL. Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling. Anal Chem. 2012 May 1; 84(9):4014-21.
        View in: PubMed PMC3923578
      56. Burlingame AL, Stults JT. Mass spectrometry: reconnaissance at the Frontiers of biology. Mol Cell Proteomics. 2012 May; 11(5):1-2.
        View in: PubMed PMC3418840
      57. Ruperez P, Gago-Martinez A, Burlingame AL, Oses-Prieto JA. Quantitative phosphoproteomic analysis reveals a role for serine and threonine kinases in the cytoskeletal reorganization in early T cell receptor activation in human primary T cells. Mol Cell Proteomics. 2012 May; 11(5):171-86.
        View in: PubMed PMC3418841
      58. Sivaramakrishnan S, Ouellet H, Matsumura H, Guan S, Moënne-Loccoz P, Burlingame AL, Ortiz de Montellano PR. Proximal ligand electron donation and reactivity of the cytochrome P450 ferric-peroxo anion. J Am Chem Soc. 2012 Apr 18; 134(15):6673-84.
        View in: PubMed PMC3329582
      59. Sherman J, Molloy MP, Burlingame AL. Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity. Proteomics. 2012 Apr; 12(8):1147-50.
        View in: PubMed
      60. Ultanir SK, Hertz NT, Li G, Ge WP, Burlingame AL, Pleasure SJ, Shokat KM, Jan LY, Jan YN. Chemical genetic identification of NDR1/2 kinase substrates AAK1 and Rabin8 Uncovers their roles in dendrite arborization and spine development. Neuron. 2012 Mar 22; 73(6):1127-42.
        View in: PubMed PMC3333840
      61. Agard NJ, Mahrus S, Trinidad JC, Lynn A, Burlingame AL, Wells JA. Global kinetic analysis of proteolysis via quantitative targeted proteomics. Proc Natl Acad Sci U S A. 2012 Feb 7; 109(6):1913-8.
        View in: PubMed PMC3277568
      62. Hengeveld RC, Hertz NT, Vromans MJ, Zhang C, Burlingame AL, Shokat KM, Lens SM. Development of a chemical genetic approach for human aurora B kinase identifies novel substrates of the chromosomal passenger complex. Mol Cell Proteomics. 2012 May; 11(5):47-59.
        View in: PubMed PMC3418839
      63. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIß. J Virol. 2012 Apr; 86(7):3605-16.
        View in: PubMed PMC3302542
      64. Xu SL, Chalkley RJ, Wang ZY, Burlingame AL. Identification of O-linked ß-D-N-acetylglucosamine-modified proteins from Arabidopsis. Methods Mol Biol. 2012; 876:33-45.
        View in: PubMed PMC3699408
      65. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70.
        View in: PubMed PMC3310911
      66. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Nature. 2012 Jan 19; 481(7381):371-5.
        View in: PubMed PMC3310910
      67. Deng Z, Xu S, Chalkley RJ, Oses-Prieto JA, Burlingame AL, Wang ZY, Kutschera U. Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth. Plant Biol (Stuttg). 2012 May; 14(3):420-7.
        View in: PubMed PMC3312047
      68. Wang Y, Guan S, Acharya P, Liu Y, Thirumaran RK, Brandman R, Schuetz EG, Burlingame AL, Correia MA. Multisite phosphorylation of human liver cytochrome P450 3A4 enhances Its gp78- and CHIP-mediated ubiquitination: a pivotal role of its Ser-478 residue in the gp78-catalyzed reaction. Mol Cell Proteomics. 2012 Feb; 11(2):M111.010132.
        View in: PubMed PMC3277751
      69. Bohlen CJ, Chesler AT, Sharif-Naeini R, Medzihradszky KF, Zhou S, King D, Sánchez EE, Burlingame AL, Basbaum AI, Julius D. A heteromeric Texas coral snake toxin targets acid-sensing ion channels to produce pain. Nature. 2011 Nov 17; 479(7373):410-4.
        View in: PubMed PMC3226747
      70. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics. 2012 May; 11(5):15-30.
        View in: PubMed PMC3418849
      71. Guan S, Price JC, Prusiner SB, Ghaemmaghami S, Burlingame AL. A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010728.
        View in: PubMed PMC3237081
      72. Kim TW, Guan S, Burlingame AL, Wang ZY. The CDG1 kinase mediates brassinosteroid signal transduction from BRI1 receptor kinase to BSU1 phosphatase and GSK3-like kinase BIN2. Mol Cell. 2011 Aug 19; 43(4):561-71.
        View in: PubMed PMC3206214
      73. Lau EK, Trester-Zedlitz M, Trinidad JC, Kotowski SJ, Krutchinsky AN, Burlingame AL, von Zastrow M. Quantitative encoding of the effect of a partial agonist on individual opioid receptors by multisite phosphorylation and threshold detection. Sci Signal. 2011 Aug 9; 4(185):ra52.
        View in: PubMed PMC3625704
      74. Ge W, Song Y, Zhang C, Zhang Y, Burlingame AL, Guo Y. Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen. Biochim Biophys Acta. 2011 Dec; 1814(12):1964-73.
        View in: PubMed PMC3214693
      75. Francone OL, Ishida BY, de la Llera-Moya M, Royer L, Happe C, Zhu J, Chalkey RJ, Schaefer P, Cox C, Burlingame A, Kane JP, Rothblat GH. Disruption of the murine procollagen C-proteinase enhancer 2 gene causes accumulation of pro-apoA-I and increased HDL levels. J Lipid Res. 2011 Nov; 52(11):1974-83.
        View in: PubMed PMC3196229
      76. Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ. Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10620-5.
        View in: PubMed PMC3127919
      77. Myers SA, Panning B, Burlingame AL. Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells. Proc Natl Acad Sci U S A. 2011 Jun 7; 108(23):9490-5.
        View in: PubMed PMC3111310
      78. Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS. Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate. PLoS One. 2011; 6(4):e19061.
        View in: PubMed PMC3079748
      79. Brennan DF, Dar AC, Hertz NT, Chao WC, Burlingame AL, Shokat KM, Barford D. A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK. Nature. 2011 Apr 21; 472(7343):366-9.
        View in: PubMed
      80. Song Y, Zhang C, Ge W, Zhang Y, Burlingame AL, Guo Y. Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE. J Proteomics. 2011 Jun 10; 74(7):1045-67.
        View in: PubMed PMC3107904
      81. Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 7; 13(41):18288-96.
        View in: PubMed PMC3415327
      82. Tang W, Yuan M, Wang R, Yang Y, Wang C, Oses-Prieto JA, Kim TW, Zhou HW, Deng Z, Gampala SS, Gendron JM, Jonassen EM, Lillo C, DeLong A, Burlingame AL, Sun Y, Wang ZY. PP2A activates brassinosteroid-responsive gene expression and plant growth by dephosphorylating BZR1. Nat Cell Biol. 2011 Feb; 13(2):124-31.
        View in: PubMed PMC3077550
      83. Li T, Xu SL, Oses-Prieto JA, Putil S, Xu P, Wang RJ, Li KH, Maltby DA, An LH, Burlingame AL, Deng ZP, Wang ZY. Proteomics analysis reveals post-translational mechanisms for cold-induced metabolic changes in Arabidopsis. Mol Plant. 2011 Mar; 4(2):361-74.
        View in: PubMed PMC3063518
      84. Wang Y, Guan S, Acharya P, Koop DR, Liu Y, Liao M, Burlingame AL, Correia MA. Ubiquitin-dependent proteasomal degradation of human liver cytochrome P450 2E1: identification of sites targeted for phosphorylation and ubiquitination. J Biol Chem. 2011 Mar 18; 286(11):9443-56.
        View in: PubMed PMC3058980
      85. Chu F, Ren X, Chasse A, Hickman T, Zhang L, Yuh J, Smith MT, Burlingame AL. Quantitative mass spectrometry reveals the epigenome as a target of arsenic. Chem Biol Interact. 2011 Jun 30; 192(1-2):113-7.
        View in: PubMed
      86. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Receptor tyrosine kinase signaling--a proteomic perspective. Adv Enzyme Regul. 2011; 51(1):293-305.
        View in: PubMed PMC3079071
      87. Su T, Bryant DM, Luton F, Vergés M, Ulrich SM, Hansen KC, Datta A, Eastburn DJ, Burlingame AL, Shokat KM, Mostov KE. A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol. 2010 Dec; 12(12):1143-53.
        View in: PubMed PMC3072784
      88. Bradshaw RA, Burlingame AL. Technological innovation revisited. Mol Cell Proteomics. 2010 Nov; 9(11):2335-6.
        View in: PubMed PMC2984236
      89. Wang F, Bai MY, Deng Z, Oses-Prieto JA, Burlingame AL, Lu T, Chong K, Wang ZY. Proteomic study identifies proteins involved in brassinosteroid regulation of rice growth. J Integr Plant Biol. 2010 Dec; 52(12):1075-85.
        View in: PubMed
      90. Ferreyra ML, Biarc J, Burlingame AL, Casati P. Arabidopsis L10 ribosomal proteins in UV-B responses. Plant Signal Behav. 2010 Oct; 5(10):1222-5.
        View in: PubMed PMC3115351
      91. Trnka MJ, Burlingame AL. Topographic studies of the GroEL-GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene: the power of high resolution electron transfer dissociation for determination of both peptide sequences and their attachment sites. Mol Cell Proteomics. 2010 Oct; 9(10):2306-17.
        View in: PubMed PMC2953922
      92. Wang D, Oses-Prieto JA, Li KH, Fernandes JF, Burlingame AL, Walbot V. The male sterile 8 mutation of maize disrupts the temporal progression of the transcriptome and results in the mis-regulation of metabolic functions. Plant J. 2010 Sep; 63(6):939-51.
        View in: PubMed PMC2974755
      93. Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S. Analysis of proteome dynamics in the mouse brain. Proc Natl Acad Sci U S A. 2010 Aug 10; 107(32):14508-13.
        View in: PubMed PMC2922600
      94. David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C. Widespread protein aggregation as an inherent part of aging in C. elegans. PLoS Biol. 2010; 8(8):e1000450.
        View in: PubMed PMC2919420
      95. Michaelevski I, Segal-Ruder Y, Rozenbaum M, Medzihradszky KF, Shalem O, Coppola G, Horn-Saban S, Ben-Yaakov K, Dagan SY, Rishal I, Geschwind DH, Pilpel Y, Burlingame AL, Fainzilber M. Signaling to transcription networks in the neuronal retrograde injury response. Sci Signal. 2010; 3(130):ra53.
        View in: PubMed PMC3645873
      96. Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR. Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol Microbiol. 2010 Aug; 77(3):730-42.
        View in: PubMed PMC2909382
      97. Oda Y, Chalkley RJ, Burlingame AL, Bikle DD. The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation. J Invest Dermatol. 2010 Oct; 130(10):2377-88.
        View in: PubMed PMC4114506
      98. Falcone Ferreyra ML, Pezza A, Biarc J, Burlingame AL, Casati P. Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress. Plant Physiol. 2010 Aug; 153(4):1878-94.
        View in: PubMed PMC2923885
      99. He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell. 2010 May 14; 38(3):428-38.
        View in: PubMed PMC3085314
      100. Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D. Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel. J Biol Chem. 2010 Jul 9; 285(28):21671-8.
        View in: PubMed PMC2898378
      101. Burlingame AL, Stults JT. Mass spectrometry and the evolution of proteomics. Mol Cell Proteomics. 2010 May; 9(5):753.
        View in: PubMed PMC2871410
      102. Kutschera U, Deng Z, Oses-Prieto JA, Burlingame AL, Wang ZY. Cessation of coleoptile elongation and loss of auxin sensitivity in developing rye seedlings: a quantitative proteomic analysis. Plant Signal Behav. 2010 May; 5(5):509-17.
        View in: PubMed
      103. Hertz NT, Wang BT, Allen JJ, Zhang C, Dar AC, Burlingame AL, Shokat KM. Chemical genetic approach for kinase-substrate mapping by covalent capture of thiophosphopeptides and analysis by mass spectrometry. Curr Protoc Chem Biol. 2010 Mar 1; 2(1):15-36.
        View in: PubMed PMC3894912
      104. Phan VT, Ding VW, Li F, Chalkley RJ, Burlingame A, McCormick F. The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans. Mol Cell Biol. 2010 May; 30(9):2264-79.
        View in: PubMed PMC2863595
      105. Eliuk SM, Maltby D, Panning B, Burlingame AL. High resolution electron transfer dissociation studies of unfractionated intact histones from murine embryonic stem cells using on-line capillary LC separation: determination of abundant histone isoforms and post-translational modifications. Mol Cell Proteomics. 2010 May; 9(5):824-37.
        View in: PubMed PMC2871417
      106. Rishal I, Michaelevski I, Rozenbaum M, Shinder V, Medzihradszky KF, Burlingame AL, Fainzilber M. Axoplasm isolation from peripheral nerve. Dev Neurobiol. 2010 Feb; 70(2):126-33.
        View in: PubMed PMC2857660
      107. Ogawa Y, Oses-Prieto J, Kim MY, Horresh I, Peles E, Burlingame AL, Trimmer JS, Meijer D, Rasband MN. ADAM22, a Kv1 channel-interacting protein, recruits membrane-associated guanylate kinases to juxtaparanodes of myelinated axons. J Neurosci. 2010 Jan 20; 30(3):1038-48.
        View in: PubMed PMC2811262
      108. Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL. Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem. 2010 Jan 15; 82(2):579-84.
        View in: PubMed PMC2836188
      109. Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF. Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides. Eur J Mass Spectrom (Chichester, Eng). 2010; 16(3):421-8.
        View in: PubMed PMC2963623
      110. Guan S, Burlingame AL. High mass selectivity for top-down proteomics by application of SWIFT technology. J Am Soc Mass Spectrom. 2010 Mar; 21(3):455-9.
        View in: PubMed PMC3384707
      111. Guan S, Burlingame AL. Data processing algorithms for analysis of high resolution MSMS spectra of peptides with complex patterns of posttranslational modifications. Mol Cell Proteomics. 2010 May; 9(5):804-10.
        View in: PubMed PMC2871415
      112. Michaelevski I, Medzihradszky KF, Lynn A, Burlingame AL, Fainzilber M. Axonal transport proteomics reveals mobilization of translation machinery to the lesion site in injured sciatic nerve. Mol Cell Proteomics. 2010 May; 9(5):976-87.
        View in: PubMed PMC2871428
      113. Chu F, Baker PR, Burlingame AL, Chalkley RJ. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics. 2010 Jan; 9(1):25-31.
        View in: PubMed PMC2808265
      114. Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS. The role of exon sequences in C complex spliceosome structure. J Mol Biol. 2009 Nov 27; 394(2):363-75.
        View in: PubMed PMC2783800
      115. Kim TW, Guan S, Sun Y, Deng Z, Tang W, Shang JX, Sun Y, Burlingame AL, Wang ZY. Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat Cell Biol. 2009 Oct; 11(10):1254-60.
        View in: PubMed PMC2910619
      116. Jo WJ, Ren X, Chu F, Aleshin M, Wintz H, Burlingame A, Smith MT, Vulpe CD, Zhang L. Acetylated H4K16 by MYST1 protects UROtsa cells from arsenic toxicity and is decreased following chronic arsenic exposure. Toxicol Appl Pharmacol. 2009 Dec 15; 241(3):294-302.
        View in: PubMed PMC2784148
      117. Tomizawa M, Talley TT, Park JF, Maltby D, Medzihradszky KF, Durkin KA, Cornejo-Bravo JM, Burlingame AL, Casida JE, Taylor P. Nicotinic agonist binding site mapped by methionine- and tyrosine-scanning coupled with azidochloropyridinyl photoaffinity labeling. J Med Chem. 2009 Jun 25; 52(12):3735-41.
        View in: PubMed PMC2748672
      118. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 2009 Jun 16; 7(6):e1000134.
        View in: PubMed PMC2691599
      119. Chalkley RJ, Thalhammer A, Schoepfer R, Burlingame AL. Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc Natl Acad Sci U S A. 2009 Jun 2; 106(22):8894-9.
        View in: PubMed PMC2690010
      120. Ortiz-Muñoz G, Houard X, Martín-Ventura JL, Ishida BY, Loyau S, Rossignol P, Moreno JA, Kane JP, Chalkley RJ, Burlingame AL, Michel JB, Meilhac O. HDL antielastase activity prevents smooth muscle cell anoikis, a potential new antiatherogenic property. FASEB J. 2009 Sep; 23(9):3129-39.
        View in: PubMed PMC2735359
      121. Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, Walbot V. Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers. Plant J. 2009 Aug; 59(4):622-33.
        View in: PubMed
      122. Fernandez F, Trinidad JC, Blank M, Feng DD, Burlingame AL, Garner CC. Normal protein composition of synapses in Ts65Dn mice: a mouse model of Down syndrome. J Neurochem. 2009 Jul; 110(1):157-69.
        View in: PubMed PMC2735138
      123. Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem. 2009 Apr 9; 52(7):2067-75.
        View in: PubMed PMC2664636
      124. Conrad F, Zhu X, Zhang X, Chalkley RJ, Burlingame AL, Marks JD, Liu B. Human antibodies targeting cell surface antigens overexpressed by the hormone refractory metastatic prostate cancer cells: ICAM-1 is a tumor antigen that mediates prostate cancer cell invasion. J Mol Med (Berl). 2009 May; 87(5):507-14.
        View in: PubMed PMC2796542
      125. Zhang W, St-Gelais F, Grabner CP, Trinidad JC, Sumioka A, Morimoto-Tomita M, Kim KS, Straub C, Burlingame AL, Howe JR, Tomita S. A transmembrane accessory subunit that modulates kainate-type glutamate receptors. Neuron. 2009 Feb 12; 61(3):385-96.
        View in: PubMed PMC2803770
      126. Thalhammer A, Trinidad JC, Burlingame AL, Schoepfer R. Densin-180: revised membrane topology, domain structure and phosphorylation status. J Neurochem. 2009 Apr; 109(2):297-302.
        View in: PubMed PMC2846389
      127. Joubel A, Chalkley RJ, Medzihradszky KF, Hondermarck H, Burlingame AL. Identification of new p53 acetylation sites in COS-1 cells. Mol Cell Proteomics. 2009 Jun; 8(6):1167-73.
        View in: PubMed PMC2690490
      128. McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF. SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair. Aging (Albany NY). 2009 Jan; 1(1):109-21.
        View in: PubMed PMC2815768
      129. Yam AY, Xia Y, Lin HT, Burlingame A, Gerstein M, Frydman J. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol. 2008 Dec; 15(12):1255-62.
        View in: PubMed PMC2658641
      130. Lee SH, Sterling H, Burlingame A, McCormick F. Tpr directly binds to Mad1 and Mad2 and is important for the Mad1-Mad2-mediated mitotic spindle checkpoint. Genes Dev. 2008 Nov 1; 22(21):2926-31.
        View in: PubMed PMC2577792
      131. Casado P, Prado MA, Zuazua-Villar P, Del Valle E, Artime N, Cabal-Hierro L, Rupérez P, Burlingame AL, Lazo PS, Ramos S. Microtubule interfering agents and KSP inhibitors induce the phosphorylation of the nuclear protein p54(nrb), an event linked to G2/M arrest. J Proteomics. 2009 Jan 30; 71(6):592-600.
        View in: PubMed
      132. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell. 2008 Sep 5; 134(5):866-76.
        View in: PubMed PMC2566540
      133. Tang W, Kim TW, Oses-Prieto JA, Sun Y, Deng Z, Zhu S, Wang R, Burlingame AL, Wang ZY. BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis. Science. 2008 Jul 25; 321(5888):557-60.
        View in: PubMed PMC2730546
      134. Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL. In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol Cell Proteomics. 2008 Dec; 7(12):2386-98.
        View in: PubMed PMC2596346
      135. Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS. Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing. Cell Cycle. 2008 Jun 15; 7(12):1795-803.
        View in: PubMed PMC2940709
      136. Li Z, Lee JH, Chu F, Burlingame AL, Günzl A, Wang CC. Identification of a novel chromosomal passenger complex and its unique localization during cytokinesis in Trypanosoma brucei. PLoS One. 2008; 3(6):e2354.
        View in: PubMed PMC2396291
      137. Hirsch J, Niemann CU, Hansen KC, Choi S, Su X, Frank JA, Fang X, Hirose R, Theodore P, Sapru A, Burlingame AL, Matthay MA. Alterations in the proteome of pulmonary alveolar type II cells in the rat after hepatic ischemia-reperfusion. Crit Care Med. 2008 Jun; 36(6):1846-54.
        View in: PubMed PMC2442403
      138. Casati P, Campi M, Chu F, Suzuki N, Maltby D, Guan S, Burlingame AL, Walbot V. Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize. Plant Cell. 2008 Apr; 20(4):827-42.
        View in: PubMed PMC2390752
      139. Tomizawa M, Maltby D, Talley TT, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE. Atypical nicotinic agonist bound conformations conferring subtype selectivity. Proc Natl Acad Sci U S A. 2008 Feb 5; 105(5):1728-32.
        View in: PubMed PMC2234212
      140. Tang W, Deng Z, Oses-Prieto JA, Suzuki N, Zhu S, Zhang X, Burlingame AL, Wang ZY. Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE. Mol Cell Proteomics. 2008 Apr; 7(4):728-38.
        View in: PubMed PMC2401332
      141. Trinidad JC, Thalhammer A, Specht CG, Lynn AJ, Baker PR, Schoepfer R, Burlingame AL. Quantitative analysis of synaptic phosphorylation and protein expression. Mol Cell Proteomics. 2008 Apr; 7(4):684-96.
        View in: PubMed
      142. Walther TC, Aguilar PS, Fröhlich F, Chu F, Moreira K, Burlingame AL, Walter P. Pkh-kinases control eisosome assembly and organization. EMBO J. 2007 Dec 12; 26(24):4946-55.
        View in: PubMed PMC2094096
      143. Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS. Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice. J Cell Biol. 2007 Oct 8; 179(1):151-64.
        View in: PubMed PMC2064744
      144. Deng Z, Zhang X, Tang W, Oses-Prieto JA, Suzuki N, Gendron JM, Chen H, Guan S, Chalkley RJ, Peterman TK, Burlingame AL, Wang ZY. A proteomics study of brassinosteroid response in Arabidopsis. Mol Cell Proteomics. 2007 Dec; 6(12):2058-71.
        View in: PubMed PMC2966871
      145. Iacovides DC, O'Shea CC, Oses-Prieto J, Burlingame A, McCormick F. Critical role for arginine methylation in adenovirus-infected cells. J Virol. 2007 Dec; 81(23):13209-17.
        View in: PubMed PMC2169124
      146. Gampala SS, Kim TW, He JX, Tang W, Deng Z, Bai MY, Guan S, Lalonde S, Sun Y, Gendron JM, Chen H, Shibagaki N, Ferl RJ, Ehrhardt D, Chong K, Burlingame AL, Wang ZY. An essential role for 14-3-3 proteins in brassinosteroid signal transduction in Arabidopsis. Dev Cell. 2007 Aug; 13(2):177-89.
        View in: PubMed PMC2000337
      147. Tomizawa M, Maltby D, Medzihradszky KF, Zhang N, Durkin KA, Presley J, Talley TT, Taylor P, Burlingame AL, Casida JE. Defining nicotinic agonist binding surfaces through photoaffinity labeling. Biochemistry. 2007 Jul 31; 46(30):8798-806.
        View in: PubMed
      148. Medzihradszky KF, Guan S, Maltby DA, Burlingame AL. Sulfopeptide fragmentation in electron-capture and electron-transfer dissociation. J Am Soc Mass Spectrom. 2007 Sep; 18(9):1617-24.
        View in: PubMed
      149. Allen JJ, Li M, Brinkworth CS, Paulson JL, Wang D, Hübner A, Chou WH, Davis RJ, Burlingame AL, Messing RO, Katayama CD, Hedrick SM, Shokat KM. A semisynthetic epitope for kinase substrates. Nat Methods. 2007 Jun; 4(6):511-6.
        View in: PubMed PMC2932705
      150. Tomizawa M, Talley TT, Maltby D, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE. Mapping the elusive neonicotinoid binding site. Proc Natl Acad Sci U S A. 2007 May 22; 104(21):9075-80.
        View in: PubMed PMC1885630
      151. Maloney A, Clarke PA, Naaby-Hansen S, Stein R, Koopman JO, Akpan A, Yang A, Zvelebil M, Cramer R, Stimson L, Aherne W, Banerji U, Judson I, Sharp S, Powers M, deBilly E, Salmons J, Walton M, Burlingame A, Waterfield M, Workman P. Gene and protein expression profiling of human ovarian cancer cells treated with the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin. Cancer Res. 2007 Apr 1; 67(7):3239-53.
        View in: PubMed
      152. Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA. Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome. Am J Respir Crit Care Med. 2007 May 15; 175(10):1006-13.
        View in: PubMed PMC1899270
      153. Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell. 2007 Mar 9; 128(5):1003-12.
        View in: PubMed PMC2932701
      154. Osés-Prieto JA, Zhang X, Burlingame AL. Formation of epsilon-formyllysine on silver-stained proteins: implications for assignment of isobaric dimethylation sites by tandem mass spectrometry. Mol Cell Proteomics. 2007 Feb; 6(2):181-92.
        View in: PubMed
      155. Chu F, Mahrus S, Craik CS, Burlingame AL. Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces. J Am Chem Soc. 2006 Aug 16; 128(32):10362-3.
        View in: PubMed
      156. Chalkley RJ, Brinkworth CS, Burlingame AL. Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom. 2006 Sep; 17(9):1271-4.
        View in: PubMed
      157. Chu F, Maynard JC, Chiosis G, Nicchitta CV, Burlingame AL. Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94. Protein Sci. 2006 Jun; 15(6):1260-9.
        View in: PubMed PMC2242539
      158. Conway MC, Whittal RM, Baldwin MA, Burlingame AL, Balhorn R. Electrospray mass spectrometry of NeuAc oligomers associated with the C fragment of the tetanus toxin. J Am Soc Mass Spectrom. 2006 Jul; 17(7):967-76.
        View in: PubMed
      159. Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics. 2006 May; 5(5):787-8.
        View in: PubMed
      160. Rodriguez-Viciana P, Oses-Prieto J, Burlingame A, Fried M, McCormick F. A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity. Mol Cell. 2006 Apr 21; 22(2):217-30.
        View in: PubMed
      161. Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc Natl Acad Sci U S A. 2006 May 2; 103(18):6988-93.
        View in: PubMed PMC1459006
      162. Zhou Q, Cadrin M, Herrmann H, Chen CH, Chalkley RJ, Burlingame AL, Omary MB. Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker. J Biol Chem. 2006 Jun 16; 281(24):16453-61.
        View in: PubMed
      163. Hirsch J, Hansen KC, Choi S, Noh J, Hirose R, Roberts JP, Matthay MA, Burlingame AL, Maher JJ, Niemann CU. Warm ischemia-induced alterations in oxidative and inflammatory proteins in hepatic Kupffer cells in rats. Mol Cell Proteomics. 2006 Jun; 5(6):979-86.
        View in: PubMed
      164. Trinidad JC, Specht CG, Thalhammer A, Schoepfer R, Burlingame AL. Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol Cell Proteomics. 2006 May; 5(5):914-22.
        View in: PubMed
      165. Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics. 2006 May; 5(5):923-34.
        View in: PubMed
      166. Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse CK, Geraerts WP, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li K. Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability. J Neurosci. 2006 Jan 11; 26(2):518-29.
        View in: PubMed
      167. Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics. 2006 Jan; 5(1):194-203.
        View in: PubMed
      168. Olsen O, Moore KA, Fukata M, Kazuta T, Trinidad JC, Kauer FW, Streuli M, Misawa H, Burlingame AL, Nicoll RA, Bredt DS. Neurotransmitter release regulated by a MALS-liprin-alpha presynaptic complex. J Cell Biol. 2005 Sep 26; 170(7):1127-34.
        View in: PubMed PMC2171538
      169. Baxter BK, Abeliovich H, Zhang X, Stirling AG, Burlingame AL, Goldfarb DS. Atg19p ubiquitination and the cytoplasm to vacuole trafficking pathway in yeast. J Biol Chem. 2005 Nov 25; 280(47):39067-76.
        View in: PubMed
      170. Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Protein identification: the good, the bad, and the ugly. Mol Cell Proteomics. 2005 Sep; 4(9):1221-2.
        View in: PubMed
      171. Burlingame AL, Zhang X, Chalkley RJ. Mass spectrometric analysis of histone posttranslational modifications. Methods. 2005 Aug; 36(4):383-94.
        View in: PubMed
      172. Casati P, Zhang X, Burlingame AL, Walbot V. Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol Cell Proteomics. 2005 Nov; 4(11):1673-85.
        View in: PubMed
      173. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell. 2005 Jun 17; 121(6):859-72.
        View in: PubMed
      174. Chalkley RJ, Baker PR, Huang L, Hansen KC, Allen NP, Rexach M, Burlingame AL. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol Cell Proteomics. 2005 Aug; 4(8):1194-204.
        View in: PubMed
      175. Chalkley RJ, Baker PR, Hansen KC, Medzihradszky KF, Allen NP, Rexach M, Burlingame AL. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines? Mol Cell Proteomics. 2005 Aug; 4(8):1189-93.
        View in: PubMed
      176. Fukata Y, Tzingounis AV, Trinidad JC, Fukata M, Burlingame AL, Nicoll RA, Bredt DS. Molecular constituents of neuronal AMPA receptors. J Cell Biol. 2005 May 9; 169(3):399-404.
        View in: PubMed PMC2171936
      177. Trester-Zedlitz M, Burlingame A, Kobilka B, von Zastrow M. Mass spectrometric analysis of agonist effects on posttranslational modifications of the beta-2 adrenoceptor in mammalian cells. Biochemistry. 2005 Apr 26; 44(16):6133-43.
        View in: PubMed
      178. Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S, Zhang C, Hansen KC, Burlingame AL, Trautman JK, Shokat KM, Adams CL. An unbiased cell morphology-based screen for new, biologically active small molecules. PLoS Biol. 2005 May; 3(5):e128.
        View in: PubMed PMC1073692
      179. Bradshaw RA, Burlingame AL. From proteins to proteomics. IUBMB Life. 2005 Apr-May; 57(4-5):267-72.
        View in: PubMed
      180. Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL. Phosphorylation state of postsynaptic density proteins. J Neurochem. 2005 Mar; 92(6):1306-16.
        View in: PubMed
      181. Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol. Proteomics. 2005 Feb; 5(2):388-98.
        View in: PubMed
      182. Huang L, Burlingame AL. Comprehensive mass spectrometric analysis of the 20S proteasome complex. Methods Enzymol. 2005; 405:187-236.
        View in: PubMed
      183. Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame AL, Unwin RJ. Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics. 2005 Jan; 5(1):101-12.
        View in: PubMed
      184. Smith-Beckerman DM, Fung KW, Williams KE, Auersperg N, Godwin AK, Burlingame AL. Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer. Mol Cell Proteomics. 2005 Feb; 4(2):156-68.
        View in: PubMed
      185. Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Burlingame AL. Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry. Proc Natl Acad Sci U S A. 2004 Nov 23; 101(47):16454-9.
        View in: PubMed PMC528904
      186. Vergés M, Luton F, Gruber C, Tiemann F, Reinders LG, Huang L, Burlingame AL, Haft CR, Mostov KE. The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol. 2004 Aug; 6(8):763-9.
        View in: PubMed
      187. Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol. 2004 Jul; 287(1):L1-23.
        View in: PubMed
      188. Medzihradszky KF, Zhang X, Chalkley RJ, Guan S, McFarland MA, Chalmers MJ, Marshall AG, Diaz RL, Allis CD, Burlingame AL. Characterization of Tetrahymena histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS). Mol Cell Proteomics. 2004 Sep; 3(9):872-86.
        View in: PubMed
      189. Cutillas P, Burlingame A, Unwin R. Proteomic strategies and their application in studies of renal function. News Physiol Sci. 2004 Jun; 19:114-9.
        View in: PubMed
      190. Cutillas PR, Chalkley RJ, Hansen KC, Cramer R, Norden AG, Waterfield MD, Burlingame AL, Unwin RJ. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol. 2004 Sep; 287(3):F353-64.
        View in: PubMed
      191. Jiménez CR, ter Maat A, Pieneman A, Burlingame AL, Smit AB, Li KW. Spatio-temporal dynamics of the egg-laying-inducing peptides during an egg-laying cycle: a semiquantitative matrix-assisted laser desorption/ionization mass spectrometry approach. J Neurochem. 2004 May; 89(4):865-75.
        View in: PubMed
      192. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation. J Steroid Biochem Mol Biol. 2004 May; 89-90(1-5):273-6.
        View in: PubMed
      193. Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics. 2004 Jun; 3(6):531-3.
        View in: PubMed
      194. Perlson E, Medzihradszky KF, Darula Z, Munno DW, Syed NI, Burlingame AL, Fainzilber M. Differential proteomics reveals multiple components in retrogradely transported axoplasm after nerve injury. Mol Cell Proteomics. 2004 May; 3(5):510-20.
        View in: PubMed
      195. Perlson E, Hanz S, Medzihradszky KF, Burlingame AL, Fainzilber M. From snails to sciatic nerve: Retrograde injury signaling from axon to soma in lesioned neurons. J Neurobiol. 2004 Feb 5; 58(2):287-94.
        View in: PubMed
      196. Medzihradszky KF, Darula Z, Perlson E, Fainzilber M, Chalkley RJ, Ball H, Greenbaum D, Bogyo M, Tyson DR, Bradshaw RA, Burlingame AL. O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes. Mol Cell Proteomics. 2004 May; 3(5):429-40.
        View in: PubMed
      197. Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Urinary proteomics of renal Fanconi syndrome. Contrib Nephrol. 2004; 141:155-69.
        View in: PubMed
      198. Wignall SM, Gray NS, Chang YT, Juarez L, Jacob R, Burlingame A, Schultz PG, Heald R. Identification of a novel protein regulating microtubule stability through a chemical approach. Chem Biol. 2004 Jan; 11(1):135-46.
        View in: PubMed
      199. Ishida BY, Bailey KR, Duncan KG, Chalkley RJ, Burlingame AL, Kane JP, Schwartz DM. Regulated expression of apolipoprotein E by human retinal pigment epithelial cells. J Lipid Res. 2004 Feb; 45(2):263-71.
        View in: PubMed
      200. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation. Mol Endocrinol. 2003 Nov; 17(11):2329-39.
        View in: PubMed
      201. Burlingame AL. Toward deciphering the knowledge encrypted in large datasets. Mol Cell Proteomics. 2003 Jul; 2(7):425.
        View in: PubMed
      202. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics. 2003 May; 2(5):299-314.
        View in: PubMed
      203. Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond). 2003 May; 104(5):483-90.
        View in: PubMed
      204. Kotite L, Zhang LH, Yu Z, Burlingame AL, Havel RJ. Human apoC-IV: isolation, characterization, and immunochemical quantification in plasma and plasma lipoproteins. J Lipid Res. 2003 Jul; 44(7):1387-94.
        View in: PubMed
      205. Chalkley RJ, Burlingame AL. Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry. Mol Cell Proteomics. 2003 Mar; 2(3):182-90.
        View in: PubMed
      206. Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec; 1(12):930-46.
        View in: PubMed
      207. Williams KE, Carver TA, Miranda JJ, Kautiainen A, Vogel JS, Dingley K, Baldwin MA, Turteltaub KW, Burlingame AL. Attomole detection of in vivo protein targets of benzene in mice: evidence for a highly reactive metabolite. Mol Cell Proteomics. 2002 Nov; 1(11):885-95.
        View in: PubMed
      208. Hart SR, Waterfield MD, Burlingame AL, Cramer R. Factors governing the solubilization of phosphopeptides retained on ferric NTA IMAC beads and their analysis by MALDI TOFMS. J Am Soc Mass Spectrom. 2002 Sep; 13(9):1042-51.
        View in: PubMed
      209. Zhang K, Tang H, Huang L, Blankenship JW, Jones PR, Xiang F, Yau PM, Burlingame AL. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal Biochem. 2002 Jul 15; 306(2):259-69.
        View in: PubMed
      210. Zhang K, Williams KE, Huang L, Yau P, Siino JS, Bradbury EM, Jones PR, Minch MJ, Burlingame AL. Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry. Mol Cell Proteomics. 2002 Jul; 1(7):500-8.
        View in: PubMed
      211. Zanata SM, Lopes MH, Mercadante AF, Hajj GN, Chiarini LB, Nomizo R, Freitas AR, Cabral AL, Lee KS, Juliano MA, de Oliveira E, Jachieri SG, Burlingame A, Huang L, Linden R, Brentani RR, Martins VR. Stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection. EMBO J. 2002 Jul 1; 21(13):3307-16.
        View in: PubMed PMC125391
      212. Michels J, Geyer A, Mocanu V, Welte W, Burlingame AL, Przybylski M. Structure and functional characterization of the periplasmic N-terminal polypeptide domain of the sugar-specific ion channel protein (ScrY porin). Protein Sci. 2002 Jun; 11(6):1565-74.
        View in: PubMed PMC2373611
      213. Huang L, Baldwin MA, Maltby DA, Medzihradszky KF, Baker PR, Allen N, Rexach M, Edmondson RD, Campbell J, Juhasz P, Martin SA, Vestal ML, Burlingame AL. The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. Mol Cell Proteomics. 2002 Jun; 1(6):434-50.
        View in: PubMed
      214. Hawkes DB, Adams GW, Burlingame AL, Ortiz de Montellano PR, De Voss JJ. Cytochrome P450(cin) (CYP176A), isolation, expression, and characterization. J Biol Chem. 2002 Aug 2; 277(31):27725-32.
        View in: PubMed
      215. Benvenuti S, Cramer R, Quinn CC, Bruce J, Zvelebil M, Corless S, Bond J, Yang A, Hockfield S, Burlingame AL, Waterfield MD, Jat PS. Differential proteome analysis of replicative senescence in rat embryo fibroblasts. Mol Cell Proteomics. 2002 Apr; 1(4):280-92.
        View in: PubMed
      216. Liu B, Huang L, Sihlbom C, Burlingame A, Marks JD. Towards proteome-wide production of monoclonal antibody by phage display. J Mol Biol. 2002 Feb 1; 315(5):1063-73.
        View in: PubMed
      217. Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M. Chemical approaches for functionally probing the proteome. Mol Cell Proteomics. 2002 Jan; 1(1):60-8.
        View in: PubMed
      218. Chalkley RJ, Burlingame AL. Identification of GlcNAcylation sites of peptides and alpha-crystallin using Q-TOF mass spectrometry. J Am Soc Mass Spectrom. 2001 Oct; 12(10):1106-13.
        View in: PubMed
      219. Person MD, Brown KC, Mahrus S, Craik CS, Burlingame AL. Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci. 2001 Aug; 10(8):1549-62.
        View in: PubMed PMC2374083
      220. Allen NP, Huang L, Burlingame A, Rexach M. Proteomic analysis of nucleoporin interacting proteins. J Biol Chem. 2001 Aug 3; 276(31):29268-74.
        View in: PubMed
      221. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Sample preparation for MALDI mass analysis of peptides and proteins. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.3.
        View in: PubMed
      222. Jiménez CR, Huang L, Qiu Y, Burlingame AL. In-gel digestion of proteins for MALDI-MS fingerprint mapping. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.4.
        View in: PubMed
      223. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Searching sequence databases over the internet: protein identification using MS-Fit. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.5.
        View in: PubMed
      224. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Searching sequence databases over the internet: protein identification using MS-tag. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.6.
        View in: PubMed
      225. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Enzymatic approaches for obtaining amino acid sequence: on-target ladder sequencing. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.7.
        View in: PubMed
      226. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC. Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J Biol Chem. 2001 Jul 27; 276(30):28327-39.
        View in: PubMed
      227. Baldwin MA, Medzihradszky KF, Lock CM, Fisher B, Settineri TA, Burlingame AL. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis. Anal Chem. 2001 Apr 15; 73(8):1707-20.
        View in: PubMed
      228. Hoang VM, Foulk R, Clauser K, Burlingame A, Gibson BW, Fisher SJ. Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire. Biochemistry. 2001 Apr 3; 40(13):4077-86.
        View in: PubMed
      229. Polson AG, Huang L, Lukac DM, Blethrow JD, Morgan DO, Burlingame AL, Ganem D. Kaposi's sarcoma-associated herpesvirus K-bZIP protein is phosphorylated by cyclin-dependent kinases. J Virol. 2001 Apr; 75(7):3175-84.
        View in: PubMed PMC114111
      230. Habelhah H, Shah K, Huang L, Burlingame AL, Shokat KM, Ronai Z. Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue. J Biol Chem. 2001 May 25; 276(21):18090-5.
        View in: PubMed
      231. Habelhah H, Shah K, Huang L, Ostareck-Lederer A, Burlingame AL, Shokat KM, Hentze MW, Ronai Z. ERK phosphorylation drives cytoplasmic accumulation of hnRNP-K and inhibition of mRNA translation. Nat Cell Biol. 2001 Mar; 3(3):325-30.
        View in: PubMed
      232. Medzihradszky KF, Leffler H, Baldwin MA, Burlingame AL. Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: peptide analysis by complementary ionization techniques. J Am Soc Mass Spectrom. 2001 Feb; 12(2):215-21.
        View in: PubMed
      233. Qiu Y, Benet LZ, Burlingame AL. Identification of hepatic protein targets of the reactive metabolites of the non-hepatotoxic regioisomer of acetaminophen, 3'-hydroxyacetanilide, in the mouse in vivo using two-dimensional gel electrophoresis and mass spectrometry. Adv Exp Med Biol. 2001; 500:663-73.
        View in: PubMed
      234. Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem Biol. 2000 Aug; 7(8):569-81.
        View in: PubMed
      235. Whittal RM, Benz CC, Scott G, Semyonov J, Burlingame AL, Baldwin MA. Preferential oxidation of zinc finger 2 in estrogen receptor DNA-binding domain prevents dimerization and, hence, DNA binding. Biochemistry. 2000 Jul 25; 39(29):8406-17.
        View in: PubMed
      236. Williamson TL, Corson LB, Huang L, Burlingame A, Liu J, Bruijn LI, Cleveland DW. Toxicity of ALS-linked SOD1 mutants. Science. 2000 Apr 21; 288(5465):399.
        View in: PubMed
      237. Laiko VV, Baldwin MA, Burlingame AL. Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem. 2000 Feb 15; 72(4):652-7.
        View in: PubMed
      238. Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem. 2000 Feb 1; 72(3):552-8.
        View in: PubMed
      239. Whittal RM, Ball HL, Cohen FE, Burlingame AL, Prusiner SB, Baldwin MA. Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Sci. 2000 Feb; 9(2):332-43.
        View in: PubMed PMC2144551
      240. Chang WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK. Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol. 2000 Feb; 122(2):295-318.
        View in: PubMed PMC58868
      241. Cramer R, Burlingame AL. Employing target modifications for the investigation of liquid infrared matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom. 2000; 14(2):53-60.
        View in: PubMed
      242. Yao Y, Toth CR, Huang L, Wong ML, Dias P, Burlingame AL, Coffino P, Wang CC. alpha5 subunit in Trypanosoma brucei proteasome can self-assemble to form a cylinder of four stacked heptamer rings. Biochem J. 1999 Dec 1; 344 Pt 2:349-58.
        View in: PubMed PMC1220650
      243. Yao Y, Huang L, Krutchinsky A, Wong ML, Standing KG, Burlingame AL, Wang CC. Structural and functional characterizations of the proteasome-activating protein PA26 from Trypanosoma brucei. J Biol Chem. 1999 Nov 26; 274(48):33921-30.
        View in: PubMed
      244. Bossi A, Patel MJ, Webb EJ, Baldwin MA, Jacob RJ, Burlingame AL, Righetti PG. Analysis of cross-linked human hemoglobin by conventional isoelectric focusing, immobilized pH gradients, capillary electrophoresis, and mass spectrometry. Electrophoresis. 1999 Oct; 20(14):2810-7.
        View in: PubMed
      245. Huang L, Shen M, Chernushevich I, Burlingame AL, Wang CC, Robertson CD. Identification and isolation of three proteasome subunits and their encoding genes from Trypanosoma brucei. Mol Biochem Parasitol. 1999 Aug 20; 102(2):211-23.
        View in: PubMed
      246. Clauser KR, Baker P, Burlingame AL. Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem. 1999 Jul 15; 71(14):2871-82.
        View in: PubMed
      247. Stimson E, Hope J, Chong A, Burlingame AL. Site-specific characterization of the N-linked glycans of murine prion protein by high-performance liquid chromatography/electrospray mass spectrometry and exoglycosidase digestions. Biochemistry. 1999 Apr 13; 38(15):4885-95.
        View in: PubMed
      248. Wolfender JL, Chu F, Ball H, Wolfender F, Fainzilber M, Baldwin MA, Burlingame AL. Identification of tyrosine sulfation in Conus pennaceus conotoxins alpha-PnIA and alpha-PnIB: further investigation of labile sulfo- and phosphopeptides by electrospray, matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry. J Mass Spectrom. 1999 Apr; 34(4):447-54.
        View in: PubMed
      249. Swanson KD, Taylor LK, Haung L, Burlingame AL, Landreth GE. Transcription factor phosphorylation by pp90(rsk2). Identification of Fos kinase and NGFI-B kinase I as pp90(rsk2). J Biol Chem. 1999 Feb 5; 274(6):3385-95.
        View in: PubMed
      250. Talrose VL, Person MD, Whittal RM, Walls FC, Burlingame AL, Baldwin MA. Insight into absorption of radiation/energy transfer in infrared matrix-assisted laser desorption/ionization: the roles of matrices, water and metal substrates. Rapid Commun Mass Spectrom. 1999; 13(21):2191-8.
        View in: PubMed
      251. Cramer R, Richter WJ, Stimson E, Burlingame AL. Analysis of phospho- and glycopolypeptides with infrared matrix-assisted laser desorption and ionization. Anal Chem. 1998 Dec 1; 70(23):4939-44.
        View in: PubMed
      252. Jiménez CR, Burlingame AL. Ultramicroanalysis of peptide profiles in biological samples using MALDI mass spectrometry. Exp Nephrol. 1998 Sep-Oct; 6(5):421-8.
        View in: PubMed
      253. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1998 Aug 15; 70(16):647R-716R.
        View in: PubMed
      254. Qiu Y, Benet LZ, Burlingame AL. Identification of the hepatic protein targets of reactive metabolites of acetaminophen in vivo in mice using two-dimensional gel electrophoresis and mass spectrometry. J Biol Chem. 1998 Jul 10; 273(28):17940-53.
        View in: PubMed
      255. Prakobphol A, Thomsson KA, Hansson GC, Rosen SD, Singer MS, Phillips NJ, Medzihradszky KF, Burlingame AL, Leffler H, Fisher SJ. Human low-molecular-weight salivary mucin expresses the sialyl lewisx determinant and has L-selectin ligand activity. Biochemistry. 1998 Apr 7; 37(14):4916-27.
        View in: PubMed
      256. Brown KC, Yu Z, Burlingame AL, Craik CS. Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein. Biochemistry. 1998 Mar 31; 37(13):4397-406.
        View in: PubMed
      257. Qiu Y, Burlingame AL, Benet LZ. Mechanisms for covalent binding of benoxaprofen glucuronide to human serum albumin. Studies By tandem mass spectrometry. Drug Metab Dispos. 1998 Mar; 26(3):246-56.
        View in: PubMed
      258. Jiménez CR, Li KW, Dreisewerd K, Spijker S, Kingston R, Bateman RH, Burlingame AL, Smit AB, van Minnen J, Geraerts WP. Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network. Biochemistry. 1998 Feb 17; 37(7):2070-6.
        View in: PubMed
      259. Fainzilber M, Nakamura T, Lodder JC, Zlotkin E, Kits KS, Burlingame AL. gamma-Conotoxin-PnVIIA, a gamma-carboxyglutamate-containing peptide agonist of neuronal pacemaker cation currents. Biochemistry. 1998 Feb 10; 37(6):1470-7.
        View in: PubMed
      260. Medzihradszky KF, Besman MJ, Burlingame AL. Reverse-phase capillary high performance liquid chromatography/high performance electrospray ionization mass spectrometry: an essential tool for the characterization of complex glycoprotein digests. Rapid Commun Mass Spectrom. 1998; 12(8):472-8.
        View in: PubMed
      261. Yu Z, Friso G, Miranda JJ, Patel MJ, Lo-Tseng T, Moore EG, Burlingame AL. Structural characterization of human hemoglobin crosslinked by bis(3,5-dibromosalicyl) fumarate using mass spectrometric techniques. Protein Sci. 1997 Dec; 6(12):2568-77.
        View in: PubMed PMC2143614
      262. Grogan A, Reeves E, Keep N, Wientjes F, Totty NF, Burlingame AL, Hsuan JJ, Segal AW. Cytosolic phox proteins interact with and regulate the assembly of coronin in neutrophils. J Cell Sci. 1997 Dec; 110 ( Pt 24):3071-81.
        View in: PubMed
      263. Machesky LM, Reeves E, Wientjes F, Mattheyse FJ, Grogan A, Totty NF, Burlingame AL, Hsuan JJ, Segal AW. Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins. Biochem J. 1997 Nov 15; 328 ( Pt 1):105-12.
        View in: PubMed PMC1218893
      264. Caldera PS, Yu Z, Knegtel RM, McPhee F, Burlingame AL, Craik CS, Kuntz ID, Ortiz de Montellano PR. Alkylation of a catalytic aspartate group of the SIV protease by an epoxide inhibitor. Bioorg Med Chem. 1997 Nov; 5(11):2019-27.
        View in: PubMed
      265. Medzihradszky KF, Besman MJ, Burlingame AL. Structural characterization of site-specific N-glycosylation of recombinant human factor VIII by reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry. Anal Chem. 1997 Oct 1; 69(19):3986-94.
        View in: PubMed
      266. Talwar N, Pilz RB, Yu Z, Burlingame A, Boss GR. A low molecular weight substance purified from human placenta inhibits cAMP-dependent protein kinase and activates protein kinase C. Mol Cell Biochem. 1997 May; 170(1-2):75-83.
        View in: PubMed
      267. Sullivan CM, Smith DM, Matsui NM, Andrews LE, Clauser KR, Chapeaurouge A, Burlingame AL, Epstein LB. Identification of constitutive and gamma-interferon- and interleukin 4-regulated proteins in the human renal carcinoma cell line ACHN. Cancer Res. 1997 Mar 15; 57(6):1137-43.
        View in: PubMed
      268. Matsui NM, Smith DM, Clauser KR, Fichmann J, Andrews LE, Sullivan CM, Burlingame AL, Epstein LB. Immobilized pH gradient two-dimensional gel electrophoresis and mass spectrometric identification of cytokine-regulated proteins in ME-180 cervical carcinoma cells. Electrophoresis. 1997 Mar-Apr; 18(3-4):409-17.
        View in: PubMed
      269. Epstein LB, Smith DM, Matsui NM, Tran HM, Sullivan C, Raineri I, Burlingame AL, Clauser KR, Hall SC, Andrews LE. Identification of cytokine-regulated proteins in normal and malignant cells by the combination of two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, Edman degradation and immunoblotting and approaches to the analysis of their functional roles. Electrophoresis. 1996 Nov; 17(11):1655-70.
        View in: PubMed
      270. Yates JR, Eng JK, Clauser KR, Burlingame AL. Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides. J Am Soc Mass Spectrom. 1996 Nov; 7(11):1089-98.
        View in: PubMed
      271. Wang SX, Mure M, Medzihradszky KF, Burlingame AL, Brown DE, Dooley DM, Smith AJ, Kagan HM, Klinman JP. A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains. Science. 1996 Aug 23; 273(5278):1078-84.
        View in: PubMed
      272. Fainzilber M, Lodder JC, van der Schors RC, Li KW, Yu Z, Burlingame AL, Geraerts WP, Kits KS. A novel hydrophobic omega-conotoxin blocks molluscan dihydropyridine-sensitive calcium channels. Biochemistry. 1996 Jul 2; 35(26):8748-52.
        View in: PubMed
      273. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1996 Jun 15; 68(12):599R-651R.
        View in: PubMed
      274. Buckley N, Maltby D, Burlingame AL, Oppenheimer NJ. Reactions of Charged Substrates. 4. The Gas-Phase Dissociation of (4-Substituted benzyl)dimethylsulfoniums and -pyridiniums. J Org Chem. 1996 Apr 19; 61(8):2753-2762.
        View in: PubMed
      275. Nakamura T, Yu Z, Fainzilber M, Burlingame AL. Mass spectrometric-based revision of the structure of a cysteine-rich peptide toxin with gamma-carboxyglutamic acid, TxVIIA, from the sea snail, Conus textile. Protein Sci. 1996 Mar; 5(3):524-30.
        View in: PubMed PMC2143357
      276. Burlingame AL. Characterization of protein glycosylation by mass spectrometry. Curr Opin Biotechnol. 1996 Feb; 7(1):4-10.
        View in: PubMed
      277. Lipniunas PH, Townsend RR, Burlingame AL, Hindsgaul O. High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides. J Am Soc Mass Spectrom. 1996 Feb; 7(2):182-8.
        View in: PubMed
      278. Medzihradszky KF, Adams GW, Burlingame AL, Bateman RH, Green MR. Peptide sequence determination by matrix-assisted laser desorption ionization employing a tandem double focusing magnetic-Orthogonal acceleration time-of-flight mass spectrometer. J Am Soc Mass Spectrom. 1996 Jan; 7(1):1-10.
        View in: PubMed
      279. Settineri CA, Burlingame AL. Structural characterization of protein glycosylation using HPLC/electrospray ionization mass spectrometry and glycosidase digestion. Methods Mol Biol. 1996; 61:255-78.
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      280. Tsutakawa SE, Medzihradszky KF, Flint AJ, Burlingame AL, Koshland DE. Determination of in vivo phosphorylation sites in protein kinase C. J Biol Chem. 1995 Nov 10; 270(45):26807-12.
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      281. Iwahara S, Satoh H, Song DX, Webb J, Burlingame AL, Nagae Y, Muller-Eberhard U. Purification, characterization, and cloning of a heme-binding protein (23 kDa) in rat liver cytosol. Biochemistry. 1995 Oct 17; 34(41):13398-406.
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      282. Zia-Amirhosseini P, Ding A, Burlingame AL, McDonagh AF, Benet LZ. Synthesis and mass-spectrometric characterization of human serum albumins modified by covalent binding of two non-steroidal anti-inflammatory drugs: tolmetin and zomepirac. Biochem J. 1995 Oct 15; 311 ( Pt 2):431-5.
        View in: PubMed PMC1136018
      283. Pongracz K, Pathak DN, Nakamura T, Burlingame AL, Bodell WJ. Activation of the tamoxifen derivative metabolite E to form DNA adducts: comparison with the adducts formed by microsomal activation of tamoxifen. Cancer Res. 1995 Jul 15; 55(14):3012-5.
        View in: PubMed
      284. Fainzilber M, Nakamura T, Gaathon A, Lodder JC, Kits KS, Burlingame AL, Zlotkin E. A new cysteine framework in sodium channel blocking conotoxins. Biochemistry. 1995 Jul 11; 34(27):8649-56.
        View in: PubMed
      285. Clauser KR, Hall SC, Smith DM, Webb JW, Andrews LE, Tran HM, Epstein LB, Burlingame AL. Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc Natl Acad Sci U S A. 1995 May 23; 92(11):5072-6.
        View in: PubMed PMC41850
      286. Schindler PA, Settineri CA, Collet X, Fielding CJ, Burlingame AL. Site-specific detection and structural characterization of the glycosylation of human plasma proteins lecithin:cholesterol acyltransferase and apolipoprotein D using HPLC/electrospray mass spectrometry and sequential glycosidase digestion. Protein Sci. 1995 Apr; 4(4):791-803.
        View in: PubMed PMC2143102
      287. Ding A, Zia-Amirhosseini P, McDonagh AF, Burlingame AL, Benet LZ. Reactivity of tolmetin glucuronide with human serum albumin. Identification of binding sites and mechanisms of reaction by tandem mass spectrometry. Drug Metab Dispos. 1995 Mar; 23(3):369-76.
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      288. Adams GW, Mayer P, Medzihradszky KF, Burlingame AL. Mass spectrometric studies of the primary sequence and structure of bovine liver and serum amine oxidase. Methods Enzymol. 1995; 258:90-114.
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      289. Robertson JG, Adams GW, Medzihradszky KF, Burlingame AL, Villafranca JJ. Complete assignment of disulfide bonds in bovine dopamine beta-hydroxylase. Biochemistry. 1994 Sep 27; 33(38):11563-75.
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      290. Brown JD, Hann BC, Medzihradszky KF, Niwa M, Burlingame AL, Walter P. Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression. EMBO J. 1994 Sep 15; 13(18):4390-400.
        View in: PubMed PMC395366
      291. Fainzilber M, Hasson A, Oren R, Burlingame AL, Gordon D, Spira ME, Zlotkin E. New mollusc-specific alpha-conotoxins block Aplysia neuronal acetylcholine receptors. Biochemistry. 1994 Aug 16; 33(32):9523-9.
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      292. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1994 Jun 15; 66(12):634R-683R.
        View in: PubMed
      293. Medzihradszky KF, Maltby DA, Hall SC, Settineri CA, Burlingame AL. Characterization of protein iv-glycosylation by reversed-phase microbore liquid chromatography / electrospray mass spectrometry, complementary mobile phases, and sequential exoglycosidase digestion. J Am Soc Mass Spectrom. 1994 May; 5(5):350-8.
        View in: PubMed
      294. Salto R, Babé LM, Li J, Rosé JR, Yu Z, Burlingame A, De Voss JJ, Sui Z, Ortiz de Montellano P, Craik CS. In vitro characterization of nonpeptide irreversible inhibitors of HIV proteases. J Biol Chem. 1994 Apr 8; 269(14):10691-8.
        View in: PubMed
      295. Mu D, Medzihradszky KF, Adams GW, Mayer P, Hines WM, Burlingame AL, Smith AJ, Cai D, Klinman JP. Primary structures for a mammalian cellular and serum copper amine oxidase. J Biol Chem. 1994 Apr 1; 269(13):9926-32.
        View in: PubMed
      296. Herrmann J, Turck CW, Atchison RE, Huflejt ME, Poulter L, Gitt MA, Burlingame AL, Barondes SH, Leffler H. Primary structure of the soluble lactose binding lectin L-29 from rat and dog and interaction of its non-collagenous proline-, glycine-, tyrosine-rich sequence with bacterial and tissue collagenase. J Biol Chem. 1993 Dec 15; 268(35):26704-11.
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      297. Mel SF, Falick AM, Burlingame AL, Stroud RM. Mapping a membrane-associated conformation of colicin Ia. Biochemistry. 1993 Sep 14; 32(36):9473-9.
        View in: PubMed
      298. Ding A, Ojingwa JC, McDonagh AF, Burlingame AL, Benet LZ. Evidence for covalent binding of acyl glucuronides to serum albumin via an imine mechanism as revealed by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1993 May 1; 90(9):3797-801.
        View in: PubMed PMC46392
      299. Oda Y, Herrmann J, Gitt MA, Turck CW, Burlingame AL, Barondes SH, Leffler H. Soluble lactose-binding lectin from rat intestine with two different carbohydrate-binding domains in the same peptide chain. J Biol Chem. 1993 Mar 15; 268(8):5929-39.
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      300. Stahl N, Baldwin MA, Teplow DB, Hood L, Gibson BW, Burlingame AL, Prusiner SB. Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry. 1993 Mar 2; 32(8):1991-2002.
        View in: PubMed
      301. Hall SC, Smith DM, Masiarz FR, Soo VW, Tran HM, Epstein LB, Burlingame AL. Mass spectrometric and Edman sequencing of lipocortin I isolated by two-dimensional SDS/PAGE of human melanoma lysates. Proc Natl Acad Sci U S A. 1993 Mar 1; 90(5):1927-31.
        View in: PubMed PMC45993
      302. Kaur S, Pongracz K, Bodell WJ, Burlingame AL. Bis(hydroxyphenylethyl)deoxyguanosine adducts identified by [32P]-postlabeling and four-sector tandem mass spectrometry: unanticipated adducts formed upon treatment of DNA with styrene 7,8-oxide. Chem Res Toxicol. 1993 Jan-Feb; 6(1):125-32.
        View in: PubMed
      303. Wen DX, Livingston BD, Medzihradszky KF, Kelm S, Burlingame AL, Paulson JC. Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. J Biol Chem. 1992 Oct 15; 267(29):21011-9.
        View in: PubMed
      304. Sanders DA, Gillece-Castro BL, Burlingame AL, Koshland DE. Phosphorylation site of NtrC, a protein phosphatase whose covalent intermediate activates transcription. J Bacteriol. 1992 Aug; 174(15):5117-22.
        View in: PubMed PMC206329
      305. Burlingame AL, Baillie TA, Russell DH. Mass spectrometry. Anal Chem. 1992 Jun 15; 64(12):467R-502R.
        View in: PubMed
      306. Stahl N, Baldwin MA, Hecker R, Pan KM, Burlingame AL, Prusiner SB. Glycosylinositol phospholipid anchors of the scrapie and cellular prion proteins contain sialic acid. Biochemistry. 1992 Jun 2; 31(21):5043-53.
        View in: PubMed
      307. Hines WM, Falick AM, Burlingame AL, Gibson BW. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra. J Am Soc Mass Spectrom. 1992 May; 3(4):326-36.
        View in: PubMed
      308. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. Identification of N2-substituted 2'-deoxyguanosine-3'-phosphate adducts detected by 32P-postlabeling of styrene-oxide-treated DNA. Carcinogenesis. 1992 Mar; 13(3):315-9.
        View in: PubMed
      309. Buechter DD, Medzihradszky KF, Burlingame AL, Kenyon GL. The active site of creatine kinase. Affinity labeling of cysteine 282 with N-(2,3-epoxypropyl)-N-amidinoglycine. J Biol Chem. 1992 Feb 5; 267(4):2173-8.
        View in: PubMed
      310. Medzihradszky KF, Gibson BW, Kaur S, Yu ZH, Medzihradszky D, Burlingame AL, Bass NM. The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family. Eur J Biochem. 1992 Feb 1; 203(3):327-39.
        View in: PubMed
      311. Gillece-Castro BL, Prakobphol A, Burlingame AL, Leffler H, Fisher SJ. Structure and bacterial receptor activity of a human salivary proline-rich glycoprotein. J Biol Chem. 1991 Sep 15; 266(26):17358-68.
        View in: PubMed
      312. Poulter L, Karrer R, Burlingame AL. n-Alkyl p-aminobenzoates as derivatizing agents in the isolation, separation, and characterization of submicrogram quantities of oligosaccharides by liquid secondary ion mass spectrometry. Anal Biochem. 1991 May 15; 195(1):1-13.
        View in: PubMed
      313. Kaur S, Hall SC, Burlingame AL. Strategies for identification of covalent xenobiotic modifications in proteins by mass spectrometry. Prog Clin Biol Res. 1991; 372:107-17.
        View in: PubMed
      314. Medzihradszky KF, Gillece-Castro BL, Settineri CA, Townsend RR, Masiarz FR, Burlingame AL. Structure determination of O-linked glycopeptides by tandem mass spectrometry. Biomed Environ Mass Spectrom. 1990 Dec 5; 19(12):777-81.
        View in: PubMed
      315. Baldwin MA, Stahl N, Reinders LG, Gibson BW, Prusiner SB, Burlingame AL. Permethylation and tandem mass spectrometry of oligosaccharides having free hexosamine: analysis of the glycoinositol phospholipid anchor glycan from the scrapie prion protein. Anal Biochem. 1990 Nov 15; 191(1):174-82.
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      316. Settineri CA, Medzihradszky KF, Masiarz FR, Burlingame AL, Chu C, George-Nascimento C. Characterization of O-glycosylation sites in recombinant B-chain of platelet-derived growth factor expressed in yeast using liquid secondary ion mass spectrometry, tandem mass spectrometry and Edman sequence analysis. Biomed Environ Mass Spectrom. 1990 Nov; 19(11):665-76.
        View in: PubMed
      317. Stahl N, Baldwin MA, Burlingame AL, Prusiner SB. Identification of glycoinositol phospholipid linked and truncated forms of the scrapie prion protein. Biochemistry. 1990 Sep 25; 29(38):8879-84.
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      318. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. Detection of (3'-hydroxy)-3,N4-benzetheno-2'-deoxycytidine-3'-phosphate by 32P-postlabeling of DNA reacted with p-benzoquinone. Carcinogenesis. 1990 Sep; 11(9):1469-72.
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      319. Burlingame AL, Millington DS, Norwood DL, Russell DH. Mass spectrometry. Anal Chem. 1990 Jun 15; 62(12):268R-303R.
        View in: PubMed
      320. Janes SM, Mu D, Wemmer D, Smith AJ, Kaur S, Maltby D, Burlingame AL, Klinman JP. A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase. Science. 1990 May 25; 248(4958):981-7.
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      321. Poulter L, Burlingame AL. Desorption mass spectrometry of oligosaccharides coupled with hydrophobic chromophores. Methods Enzymol. 1990; 193:661-89.
        View in: PubMed
      322. Bodell WJ, Pongracz K, Kaur S, Burlingame AL, Liu SF, Rappaport SM. Investigation of styrene oxide-DNA adducts and their detection in workers exposed to styrene. Prog Clin Biol Res. 1990; 340C:271-82.
        View in: PubMed
      323. Gillece-Castro BL, Burlingame AL. Oligosaccharide characterization with high-energy collision-induced dissociation mass spectrometry. Methods Enzymol. 1990; 193:689-712.
        View in: PubMed
      324. Sanders DA, Gillece-Castro BL, Stock AM, Burlingame AL, Koshland DE. Identification of the site of phosphorylation of the chemotaxis response regulator protein, CheY. J Biol Chem. 1989 Dec 25; 264(36):21770-8.
        View in: PubMed
      325. Kaur S, Hollander D, Haas R, Burlingame AL. Characterization of structural xenobiotic modifications in proteins by high sensitivity tandem mass spectrometry. Human hemoglobin treated in vitro with styrene 7,8-oxide. J Biol Chem. 1989 Oct 15; 264(29):16981-4.
        View in: PubMed
      326. Haraguchi T, Fisher S, Olofsson S, Endo T, Groth D, Tarentino A, Borchelt DR, Teplow D, Hood L, Burlingame A, et al. Asparagine-linked glycosylation of the scrapie and cellular prion proteins. Arch Biochem Biophys. 1989 Oct; 274(1):1-13.
        View in: PubMed
      327. Poulter L, Earnest JP, Stroud RM, Burlingame AL. Structure, oligosaccharide structures, and posttranslationally modified sites of the nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A. 1989 Sep; 86(17):6645-9.
        View in: PubMed PMC297901
      328. Hernández LM, Ballou L, Alvarado E, Gillece-Castro BL, Burlingame AL, Ballou CE. A new Saccharomyces cerevisiae mnn mutant N-linked oligosaccharide structure. J Biol Chem. 1989 Jul 15; 264(20):11849-56.
        View in: PubMed
      329. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. O6-substituted-2'-deoxyguanosine-3'-phosphate adducts detected by 32P post-labeling of styrene oxide treated DNA. Carcinogenesis. 1989 Jun; 10(6):1009-13.
        View in: PubMed
      330. Gibson BW, Webb JW, Yamasaki R, Fisher SJ, Burlingame AL, Mandrell RE, Schneider H, Griffiss JM. Structure and heterogeneity of the oligosaccharides from the lipopolysaccharides of a pyocin-resistant Neisseria gonorrhoeae. Proc Natl Acad Sci U S A. 1989 Jan; 86(1):17-21.
        View in: PubMed PMC286394
      331. Poulter L, Earnest JP, Stroud RM, Burlingame AL. Cesium ion liquid secondary ion mass spectrometry of membrane-bound glycoproteins: structural and topological considerations of acetylcholine receptor from Torpedo californica. Biomed Environ Mass Spectrom. 1988 Oct; 16(1-12):25-30.
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      332. Xu XB, Burlingame AL. Environmental applications of organic mass spectrometry in China. Biomed Environ Sci. 1988 Oct; 1(3):253-69.
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      333. Aberth WH, Burlingame AL. Effect of primary beam energy on the secondary ion sputtering efficiency of liquid secondary ionization mass spectrometry in the 5-30-keV range. Anal Chem. 1988 Jul 15; 60(14):1426-8.
        View in: PubMed
      334. Burlingame AL, Maltby D, Russell DH, Holland PT. Mass spectrometry. Anal Chem. 1988 Jun 15; 60(12):294R-342R.
        View in: PubMed
      335. Gibson BW, Yu ZG, Aberth W, Burlingame AL, Bass NM. Revision of the blocked N terminus of rat heart fatty acid-binding protein by liquid secondary ion mass spectrometry. J Biol Chem. 1988 Mar 25; 263(9):4182-5.
        View in: PubMed
      336. Webb JW, Jiang K, Gillece-Castro BL, Tarentino AL, Plummer TH, Byrd JC, Fisher SJ, Burlingame AL. Structural characterization of intact, branched oligosaccharides by high performance liquid chromatography and liquid secondary ion mass spectrometry. Anal Biochem. 1988 Mar; 169(2):337-49.
        View in: PubMed
      337. Gillece-Castro BL, Fisher SJ, Tarentino AL, Peterson DL, Burlingame AL. Structure of the oligosaccharide portion of human hepatitis B surface antigen. Arch Biochem Biophys. 1987 Jul; 256(1):194-201.
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      338. Burlingame AL, Baillie TA, Derrick PJ. Mass spectrometry. Anal Chem. 1986 Apr; 58(5):165R-211R.
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      339. Wickramanayake PP, Deinzer ML, Burlingame AL. Positive and negative liquid secondary ion mass spectrometry of chloro- and nitrophenylglucuronides. Biomed Mass Spectrom. 1985 Mar; 12(3):127-33.
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      340. Aberth W, Burlingame AL. Comparison of three geometries for a cesium primary beam liquid secondary ion mass spectrometry source. Anal Chem. 1984 Dec; 56(14):2915-8.
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      341. Latini R, Reginato R, Burlingame AL, Kates RE. High-performance liquid chromatographic isolation and fast atom bombardment mass spectrometric identification of Di-N-desethylamiodarone, a new metabolite of amiodarone in the dog. Biomed Mass Spectrom. 1984 Sep; 11(9):466-71.
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      342. Lampe MA, Burlingame AL, Whitney J, Williams ML, Brown BE, Roitman E, Elias PM. Human stratum corneum lipids: characterization and regional variations. J Lipid Res. 1983 Feb; 24(2):120-30.
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      343. Straub KM, Burlingame AL. Carcinogen binding to DNA. Biomed Mass Spectrom. 1981 Sep; 8(9):431-5.
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      344. Xu XB, Nachtman JP, Rappaport SM, Wei ET, Lewis S, Burlingame AL. Identification of 2-nitrofluorene in diesel exhaust particulates. J Appl Toxicol. 1981 Jun; 1(3):196-8.
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      345. Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH, Oppenheimer NJ. Structural identification of autoinducer of Photobacterium fischeri luciferase. Biochemistry. 1981 Apr 28; 20(9):2444-9.
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      346. Linscheid M, D'Angona J, Burlingame AL, Dell A, Ballou CE. Field desorption mass spectrometry of oligosaccharides. Proc Natl Acad Sci U S A. 1981 Mar; 78(3):1471-5.
        View in: PubMed PMC319152
      347. Cronholm T, Sjövall J, Wilson DM, Burlingame AL. Exchange of methyl hydrogens in ethanol during incorporation in bile acids in vivo. Biochim Biophys Acta. 1979 Nov 21; 575(2):193-203.
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      348. Lewis S, Kenyon CN, Meili J, Burlingame AL. High resolution gas chromatographic/real-time high resolution mass spectrometric identification of organic acids in human urine. Anal Chem. 1979 Jul; 51(8):1275-85.
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      349. Straub KM, Meehan T, Burlingame AL, Calvin M. Identification of the major adducts formed by reaction of benzo(a)pyrene diol epoxide with DNA in vitro. Proc Natl Acad Sci U S A. 1977 Dec; 74(12):5285-9.
        View in: PubMed PMC431688
      350. Burlingame AL. Assessment of the trace organic molecular composition of industrial and municipal wastewater effluents by capillary gas chromatography/real-time high-resolution mass spectrometry: a preliminary report. Ecotoxicol Environ Saf. 1977 Jun; 1(1):111-50.
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      351. Bowes CW, Mulvihill MJ, Simoneit BR, Burlingame AL, Risebrough RW. Identification of chlorinated dibenzofurans in American polychlorinated biphenyls. Nature. 1975 Jul 24; 256(5515):305-7.
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      352. Cronholm T, Burlingame AL, Sjövall J. Utilization of the carbon and hydrogen atoms of ethanol in the biosynthesis of steroids and bile acids. Eur J Biochem. 1974 Dec 2; 49(3):497-510.
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      353. Wilson DM, Burlingame AL. Deuterium and carbon-13 tracer studies of ethanol metabolism in the rat by 2H, 1H-decoupled 13C nuclear magnetic resonance. Biochem Biophys Res Commun. 1974 Feb 4; 56(3):828-35.
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      354. Burlingame AL, McPherron RV, Wilson DM. Nonheuristic computer determination of molecular structure based upon carbon-13 nuclear magnetic resonance data: branched alkanes. Proc Natl Acad Sci U S A. 1973 Dec; 70(12):3419-22.
        View in: PubMed PMC427249
      355. Simoneit BR, Smith DH, Eglinton G, Burlingame AL. Application of real-time mass spectrometric techniques to environmental organic geochemistry. II. Organic matter in San Francisco Bay area water. Arch Environ Contam Toxicol. 1973 Oct; 1(3):193-208.
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      356. Bowes GW, Simoneit BR, Burlingame AL, de Lappe BW, Risebrough RW. The search for chlorinated dibenzofurans and chlorinated dibenzodioxins in wildlife populations showing elevated levels of embryonic death. Environ Health Perspect. 1973 Sep; 5:191-8.
        View in: PubMed PMC1474954
      357. Welch JW, Burlingame AL. Very long-chain fatty acids in yeast. J Bacteriol. 1973 Jul; 115(1):464-6.
        View in: PubMed PMC246264
      358. Holland PT, Simoneit BR, Wszolek PC, Burlingame AL. Study of carbon compounds in Apollo 12 and 14 lunar samples. Space Life Sci. 1972 Oct; 3(4):551-61.
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      359. Burlingame AL, Johanson GA. Mass spectrometry. Anal Chem. 1972 Apr 1; 44(5):337-78.
        View in: PubMed
      360. Balogh B, Wilson DM, Burlingame AL. Carbon-13 NMR study of the stereochemistry of steranes from oil shale of the Green River formation (Eocene). Nature. 1971 Sep 24; 233(5317):261-3.
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      361. van Tamelen EE, Hanzlik RP, Clayton RB, Burlingame AL. Minimal substrate structural requirements for lanosterol-squalene 2,3-oxide cyclase action. 10'-norsqualene 2,3-oxide. J Am Chem Soc. 1970 Apr 8; 92(7):2137-9.
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      362. Simoneit BR, Schnoes HK, Haug P, Burlingame AL. Nitrogenous compounds of the Colorado Green River Formation oil shale: a preliminary analysis by mass spectrometry. Nature. 1970 Apr 4; 226(5240):75-6.
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      363. Burlingame AL, Calvin M, Han J, Henderson W, Reed W, Simoneit BR. Lunar organic compounds: search and characterization. Science. 1970 Jan 30; 167(3918):751-2.
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      364. Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL. Tumor inhibitors. 43. Solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitium. J Org Chem. 1969 Dec; 34(12):3888-93.
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      365. Kupchan SM, Anderson WK, Bollinger P, Doskotch RW, Smith RM, Renauld JA, Schnoes HK, Burlingame AL, Smith DH. Tumor inhibitors. XXXIX. Active principles of Acnistus arborescens. Isolation and structural and spectral studies of withaferin A and withacnistin. J Org Chem. 1969 Dec; 34(12):3858-66.
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      366. Kupchan SM, Aynehchi Y, Cassady JM, Schnoes HK, Burlingame AL. Tumor inhibitors XL. The isolation and structural elucidation of elephantin and elephantopin, two novel sesquiterpenoid tumor inhibitors from Elephantopus elatus. J Org Chem. 1969 Dec; 34(12):3867-75.
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      367. Simoneit BR, Burlingame AL, Flory DA, Smith ID. Apollo lunar module engine exhaust products. Science. 1969 Nov 7; 166(3906):733-8.
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      368. Burlingame AL, Simoneit BR. Isoprenoid Fatty acids isolated from the kerogen matrix of the green river formation (eocene). Science. 1968 May 3; 160(3827):531-3.
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      369. van Tamelen EE, Sharpless KB, Hanzlik R, Clayton RB, Burlingame AL, Wszolek PC. Enzymic cyclization of trans,trans,trans-18,19-dihydrosqualene 2,3-oxide. J Am Chem Soc. 1967 Dec 20; 89(26):7150-1.
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      370. Haug P, Schnoes HK, Burlingame AL. Isoprenoid and dicarboxylic acids isolated from colorado green river shale (eocene). Science. 1967 Nov 10; 158(3802):772-3.
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      371. Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL. The isolation, structural elucidation, and synthesis of solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitum. J Am Chem Soc. 1967 Oct 25; 89(22):5718-9.
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      372. Urey HC, Lewis JS, Burlingame AL, Schnoes HK, Studier MH, Hayatsu R, Anders E. Organic matter in carbonaceous chondrites. Science. 1966 Apr 1; 152(3718):102-7.
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        View in: PubMed PMC219916
      374. Eglinton G, Scott PM, Belsky T, Burlingame AL, Calvin M. Hydrocarbons of Biological Origin from a One-Billion-Year-Old Sediment. Science. 1964 Jul 17; 145(3629):263-4.
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