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

  • July 1, 1985 - May 31, 2023 - UCSF Liver Center , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P30DK026743
  • 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
  • June 15, 2013 - June 14, 2014 - Purchase of Q-Exactive Mass Spectrometer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: S10OD016229
  • September 30, 1999 - May 31, 2014 - Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS) , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P41RR013461
  • June 1, 1976 - September 14, 2012 - Resource for Biocomputing, Visualization, and Informatics , Co-Investigator . Sponsor: NIH/NCRR, Sponsor Award ID: P41RR001081
  • May 6, 2010 - May 5, 2011 - Purchase of Applied Biosystems QTRAP 5500 Mass Spectrometer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: S10RR026662
  • September 30, 2003 - June 30, 2010 - SCCOR in translational research in Acute Lung Injury , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P50HL074005
  • July 1, 2004 - June 30, 2008 - Purchase of LTQ FT-ICR Hybrid Mass Spectrometer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: S10RR019934
  • April 15, 2001 - April 14, 2005 - PURCHASE OF MICRO LC/NANO ESIQQTOF MASS SPECTROMETER , Principal Investigator . Sponsor: NIH, Sponsor Award ID: S10RR015804
  • February 15, 2000 - February 14, 2004 - MALDI TOF/TOF TANDEM MASS SPECTROMETER , Principal Investigator . Sponsor: NIH, Sponsor Award ID: S10RR014606
  • August 15, 1994 - August 14, 1995 - INTERNATIONAL SYMPOSIUM ON MS IN HEALTH &LIFE SCIENCES , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R13RR009774
  • September 15, 1988 - September 14, 1989 - 2ND INTERNATIONAL SYMPOSIUM ON MASS SPECTROMETRY , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R13RR004298
  • April 1, 1983 - November 30, 1986 - ELECTRON COLLISION-INDUCED DISSOCIATION FOR MASS SPECTRO , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM032067

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. Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen identifies RBM42 as a mediator of oncogenic mRNA translation specificity. Nat Cell Biol. 2025 Feb 04.  View on PubMed
  2. Bastola S, Pavlyukov MS, Sharma N, Ghochani Y, Nakano MA, Muthukrishnan SD, Yu SY, Kim MS, Sohrabi A, Biscola NP, Yamashita D, Anufrieva KS, Kovalenko TF, Jung G, Ganz T, O'Brien B, Kawaguchi R, Qin Y, Seidlits SK, Burlingame AL, Oses-Prieto JA, Havton LA, Goldman SA, Hjelmeland AB, Nakano I, Kornblum HI. Endothelial-secreted Endocan activates PDGFRA and regulates vascularity and spatial phenotype in glioblastoma. Nat Commun. 2025 Jan 07; 16(1):471.  View on PubMed
  3. Leana-Sandoval G, Kolli AV, Sandoval MA, Saavedra E, Li KH, Chen LY, Burlingame AL, Ramírez-Franco J, Díaz-Alonso J. The VGCC auxiliary subunit α2δ1 is an extracellular GluA1 interactor and regulates LTP, spatial memory, and seizure susceptibility. bioRxiv. 2024 Dec 02.  View on PubMed
  4. Roychowdhury T, McNutt SW, Pasala C, Nguyen HT, Thornton DT, Sharma S, Botticelli L, Digwal CS, Joshi S, Yang N, Panchal P, Chakrabarty S, Bay S, Markov V, Kwong C, Lisanti J, Chung SY, Ginsberg SD, Yan P, De Stanchina E, Corben A, Modi S, Alpaugh ML, Colombo G, Erdjument-Bromage H, Neubert TA, Chalkley RJ, Baker PR, Burlingame AL, Rodina A, Chiosis G, Chu F. Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation. Nat Commun. 2024 Oct 16; 15(1):8912.  View on PubMed
  5. Melton AJ, Palfini VL, Ogawa Y, Oses Prieto JA, Vainshtein A, Burlingame AL, Peles E, Rasband MN. TRIM46 Is Required for Microtubule Fasciculation In Vivo But Not Axon Specification or Axon Initial Segment Formation. J Neurosci. 2024 Oct 16; 44(42).  View on PubMed
  6. He L, Kwon D, Trnka MJ, Liu Y, Yang J, Li K, Totah RA, Johnson EF, Burlingame AL, Correia MA. Liver CYP4A autophagic-lysosomal degradation (ALD): A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site. bioRxiv. 2024 Oct 14.  View on PubMed
  7. Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen for mediators of onco-mRNA translation specificity. bioRxiv. 2024 Oct 11.  View on PubMed
  8. Ferreccio A, Byeon S, Cornell M, Oses-Prieto J, Deshpande A, Weiss LA, Burlingame A, Yadav S. TAOK2 Drives Opposing Cilia Length Deficits in 16p11.2 Deletion and Duplication Carriers. bioRxiv. 2024 Oct 07.  View on PubMed
  9. Susanto TT, Hung V, Levine AG, Chen Y, Kerr CH, Yoo Y, Oses-Prieto JA, Fromm L, Zhang Z, Lantz TC, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages. Mol Cell. 2024 Sep 19; 84(18):3545-3563.e25.  View on PubMed
  10. Yang H, Zingaro VA, Lincoff J, Tom H, Oikawa S, Oses-Prieto JA, Edmondson Q, Seiple I, Shah H, Kajimura S, Burlingame AL, Grabe M, Ruggero D. Remodelling of the translatome controls diet and its impact on tumorigenesis. Nature. 2024 Sep; 633(8028):189-197.  View on PubMed
  11. Estevez P, Oses-Prieto J, Castro D, Penin A, Burlingame A, Gago-Martinez A. First Detection of Algal Caribbean Ciguatoxin in Amberjack Causing Ciguatera Poisoning in the Canary Islands (Spain). Toxins (Basel). 2024 Apr 13; 16(4).  View on PubMed
  12. McNutt SW, Roychowdhury T, Pasala C, Nguyen HT, Thornton DT, Sharma S, Botticelli L, Digwal CS, Joshi S, Yang N, Panchal P, Chakrabarty S, Bay S, Markov V, Kwong C, Lisanti J, Chung SY, Ginsberg SD, Yan P, DeStanchina E, Corben A, Modi S, Alpaugh M, Colombo G, Erdjument-Bromage H, Neubert TA, Chalkley RJ, Baker PR, Burlingame AL, Rodina A, Chiosis G, Chu F. Phosphorylation-Driven Epichaperome Assembly: A Critical Regulator of Cellular Adaptability and Proliferation. Res Sq. 2024 Apr 03.  View on PubMed
  13. Darula Z, McCabe MC, Barrett A, Schmitt LR, Maslanka MD, Saviola AJ, Orgel J, Burlingame A, Staab-Weijnitz CA, Stenmark K, Weaver V, Chalkley RJ, Hansen KC. Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry. bioRxiv. 2024 Mar 31.  View on PubMed
  14. Passino R, Finneran MC, Hafner H, Feng Q, Huffman LD, Zhao XF, Johnson CN, Kawaguchi R, Oses-Prieto JA, Burlingame AL, Geschwind DH, Benowitz LI, Giger RJ. Neutrophil-inflicted vasculature damage suppresses immune-mediated optic nerve regeneration. Cell Rep. 2024 03 26; 43(3):113931.  View on PubMed
  15. Yang N, Ren J, Dai S, Wang K, Leung M, Lu Y, An Y, Burlingame A, Xu S, Wang Z, Yu W, Li N. The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism. Mol Cell Proteomics. 2024 Mar; 23(3):100738.  View on PubMed
  16. Susanto TT, Hung V, Levine AG, Kerr CH, Yoo Y, Chen Y, Oses-Prieto JA, Fromm L, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages. bioRxiv. 2023 Dec 07.  View on PubMed
  17. Tsusaka T, Najar MA, Schwarz B, Bohrnsen E, Oses-Prieto JA, Lee C, Burlingame AL, Bosio CM, Burslem GM, Goldberg EL. Reversible histone deacetylase activity catalyzes lysine acylation. bioRxiv. 2023 Nov 17.  View on PubMed
  18. Okoh J, Mays J, Bacq A, Oses-Prieto JA, Tyanova S, Chen CJ, Imanbeyev K, Doladilhe M, Zhou H, Jafar-Nejad P, Burlingame A, Noebels J, Baulac S, Costa-Mattioli M. Targeted suppression of mTORC2 reduces seizures across models of epilepsy. Nat Commun. 2023 11 14; 14(1):7364.  View on PubMed
  19. Ogawa Y, Lim BC, George S, Oses-Prieto JA, Rasband JM, Eshed-Eisenbach Y, Hamdan H, Nair S, Boato F, Peles E, Burlingame AL, Van Aelst L, Rasband MN. Antibody-directed extracellular proximity biotinylation reveals that Contactin-1 regulates axo-axonic innervation of axon initial segments. Nat Commun. 2023 10 26; 14(1):6797.  View on PubMed
  20. Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol. 2023 Nov; 25(11):1600-1615.  View on PubMed

Go to UCSF Profiles, powered by CTSI