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. 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.  View on PubMed
  2. 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.  View on PubMed
  3. 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.  View on PubMed
  4. 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.  View on PubMed
  5. 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.  View on PubMed
  6. Trnka MJ, Baker PR, Robinson PJJ, Burlingame AL, Chalkley RJ Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification.  View on PubMed
  7. Gierasch LM, Davidson NO, Rye KA, Burlingame AL For the Sake of Science.  View on PubMed
  8. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation.  View on PubMed
  9. 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.  View on PubMed
  10. 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.  View on PubMed
  11. Maynard JC, Fujihira H, Dolgonos GE, Suzuki T, Burlingame AL Cytosolic N-GlcNAc proteins are formed by the action of endo-ß-N-acetylglucosaminidase.  View on PubMed
  12. Petkovic M, Oses-Prieto J, Burlingame A, Jan LY, Jan YN TMEM16K is an interorganelle regulator of endosomal sorting.  View on PubMed
  13. Gierasch LM, Davidson NO, Rye KA, Burlingame AL Opening ASBMB publications freely to all.  View on PubMed
  14. Gierasch LM, Davidson NO, Rye KA, Burlingame AL Opening ASBMB publications freely to all.  View on PubMed
  15. Garcia VJ, Xu SL, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Burlingame A, Assaad FF, Wang ZY TRIPP Is a Plant-Specific Component of the Arabidopsis TRAPPII Membrane Trafficking Complex with Important Roles in Plant Development.  View on PubMed
  16. von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation.  View on PubMed
  17. Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS.  View on PubMed
  18. Gingras AC, Carr SA, Burlingame AL Virtual Issue: Technological Innovations.  View on PubMed
  19. Burlingame AL, Carr S, Gingras AC Compliance Checklists No Longer Required at Initial Manuscript Submission.  View on PubMed
  20. Yang Z, Guo G, Yang N, Pun SS, Ho TKL, Ji L, Hu I, Zhang J, Burlingame AL, Li N The change of gravity vector induces short-term phosphoproteomic alterations in Arabidopsis.  View on PubMed

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