Research Summary

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.

Research Funding

  • August 1, 2002 - April 30, 2020 - Genetic Biochemical Studies of Plant Steroid Signaling, Principal Investigator. Sponsor: NIH, Sponsor Award ID: R01GM066258
  • September 30, 1987 - March 31, 2017 - Toxic Substances in the Environment, Co-Investigator. Sponsor: NIH, Sponsor Award ID: P42ES004705
  • March 15, 1997 - May 31, 2016 - Bio-Organic Biomedical Mass Spectrometry Resource, Principal Investigator. Sponsor: NIH, Sponsor Award ID: P41GM103481
  • March 1, 1982 - May 31, 2015 - Bio-Organic Biomedical Mass Spectrometry Resource, Principal Investigator. Sponsor: NIH, Sponsor Award ID: P41RR001614

Education

University of Rhode Island, Kingston, RI, B.S. 1959, Chemistry
MIT, Cambridge, MA, Ph.D., 1962, Chemistry, Physics

Honors & Awards

  • 1970-72
    Guggenheim Fellow, Karolinska Institute, Stockholm
  • 1990-
    Elected Fellow, American Association for the Advancement of Science1999-2006
    Deputy Editor, Molecular and Cellular Proteomics
  • 2002-04
    Physiological Chemistry Study Section CSR, NIH
  • 2006-
    Co-editor, Molecular and Cellular Proteomics
  • 2013-
    Editor-in-chief, Molecular and Cellular Proteomics
  • 2012
    International Forum of Proteomics, Achievement Award
  • 2013
    Awarded the MCP lectureship Plenary at the Society for Glycobiology, St Petersburg, FL, November 17-20, 2013
  • 2018
    Albert Nelson Marquis Lifetime Achievement Award

Selected Publications

  1. Roehrig AE, Klupsch K, Oses-Prieto JA, Chaib S, Henderson S, Emmett W, Young LC, Surinova S, Blees A, Pfeiffer A, Tijani M, Brunk F, Hartig N, Muñoz-Alegre M, Hergovich A, Jennings BH, Burlingame AL, Rodriguez-Viciana P. Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex. PLoS One. 2021; 16(8):e0254697.  View on PubMed
  2. Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N. Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars. Biomolecules. 2021 08 16; 11(8).  View on PubMed
  3. Mohan S, Sampognaro PJ, Argouarch AR, Maynard JC, Welch M, Patwardhan A, Courtney EC, Zhang J, Mason A, Li KH, Huang EJ, Seeley WW, Miller BL, Burlingame A, Jacobson MP, Kao AW. Processing of progranulin into granulins involves multiple lysosomal proteases and is affected in frontotemporal lobar degeneration. Mol Neurodegener. 2021 08 03; 16(1):51.  View on PubMed
  4. Stevens SR, Longley CM, Ogawa Y, Teliska LH, Arumanayagam AS, Nair S, Oses-Prieto JA, Burlingame AL, Cykowski MD, Xue M, Rasband MN. Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels. Elife. 2021 06 28; 10.  View on PubMed
  5. Qu J, Fourman S, Fitzgerald M, Liu M, Nair S, Oses-Prieto J, Burlingame A, Morris JH, Davidson WS, Tso P, Bhargava A. Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue. Sci Rep. 2021 Jun 24; 11(1):13289.  View on PubMed
  6. Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep. 2021 Jun 22; 11(1):13084.  View on PubMed
  7. Ruiz-Saenz A, Zahedi F, Peterson E, Yoo A, Dreyer CA, Spassov DS, Oses-Prieto J, Burlingame A, Moasser MM. Proteomic Analysis of Src Family Kinase Phosphorylation States in Cancer Cells Suggests Deregulation of the Unique Domain. Mol Cancer Res. 2021 Jun; 19(6):957-967.  View on PubMed
  8. Conn CS, Yang H, Tom HJ, Ikeda K, Oses-Prieto JA, Vu H, Oguri Y, Nair S, Gill RM, Kajimura S, DeBerardinis RJ, Burlingame AL, Ruggero D. The major cap-binding protein eIF4E regulates lipid homeostasis and diet-induced obesity. Nat Metab. 2021 02; 3(2):244-257.  View on PubMed
  9. Bi Y, Deng Z, Ni W, Shrestha R, Savage D, Hartwig T, Patil S, Hong SH, Zhang Z, Oses-Prieto JA, Li KH, Quail PH, Burlingame AL, Xu SL, Wang ZY. Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions. Nat Commun. 2021 02 11; 12(1):945.  View on PubMed
  10. Ballard PL, Oses-Prieto J, Chapin C, Segal MR, Ballard RA, Burlingame AL. Composition and origin of lung fluid proteome in premature infants and relationship to respiratory outcome. PLoS One. 2020; 15(12):e0243168.  View on PubMed
  11. Chen YC, Oses-Prieto JA, Pope LE, Burlingame AL, Dixon SJ, Renslo AR. Reactivity-Based Probe of the Iron(II)-Dependent Interactome Identifies New Cellular Modulators of Ferroptosis. J Am Chem Soc. 2020 11 11; 142(45):19085-19093.  View on PubMed
  12. Trnka MJ, Baker PR, Robinson PJJ, Burlingame AL, Chalkley RJ. Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-434.  View on PubMed
  13. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. For the Sake of Science. Mol Cell Proteomics. 2019 Mar; 18(3):406-407.  View on PubMed
  14. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA. A Novel Mechanism for NF-?B-activation via I?B-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation. Mol Cell Proteomics. 2020 12; 19(12):1968-1986.  View on PubMed
  15. White CW, Fan X, Maynard JC, Wheatley EG, Bieri G, Couthouis J, Burlingame AL, Villeda SA. Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation. Proc Natl Acad Sci U S A. 2020 09 08; 117(36):22214-22224.  View on PubMed
  16. McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. An ER translocon for multi-pass membrane protein biogenesis. Elife. 2020 08 21; 9.  View on PubMed
  17. Maynard JC, Fujihira H, Dolgonos GE, Suzuki T, Burlingame AL. Cytosolic N-GlcNAc proteins are formed by the action of endo-ß-N-acetylglucosaminidase. Biochem Biophys Res Commun. 2020 10 01; 530(4):719-724.  View on PubMed
  18. Petkovic M, Oses-Prieto J, Burlingame A, Jan LY, Jan YN. TMEM16K is an interorganelle regulator of endosomal sorting. Nat Commun. 2020 07 03; 11(1):3298.  View on PubMed
  19. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. Opening ASBMB publications freely to all. J Lipid Res. 2020 07; 61(7):969-970.  View on PubMed
  20. Gierasch LM, Davidson NO, Rye KA, Burlingame AL. Opening ASBMB publications freely to all. Mol Cell Proteomics. 2020 06; 19(6):914-915.  View on PubMed

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