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. Liu Y, Wang Z, Sinha T, Li KH, Chalkley RJ, Herranz-Pérez V, Xie C, Yoder BK, Burlingame AL, Black BL, Reiter JF. CDK1 and CEP97 cooperatively control centriole length to orchestrate ciliogenesis and developmental patterning. Genes Dev. 2026 May 15. View on PubMed
  2. Yang N, Sing Pun S, Wong EOY, Dai S, Li X, Leung M, Burlingame A, Wang ZY, Yang M, Lu Y, An Y, Zhang Y, Yang Z, Yu W, Li N. Deciphering the Protein Phosphorylation Dynamics Triggered by Seconds of Force Stimulation. Mol Cell Proteomics. 2026 Apr; 25(4):101532. View on PubMed
  3. Zhao XF, Kohen R, Van Battum EY, Niu X, Zeng Y, Zhang X, Johnson CN, Wang K, Verhagen MG, Lim BC, Oses-Prieto JA, Rasband JM, Burlingame AL, Cai D, Pasterkamp RJ, Rasband MN, Giger RJ. Diverse and location-specific roles of PlexinA2, PlexinA4, and NCAM in developing hippocampal mossy fibers. Transl Psychiatry. 2026 Feb 12; 16(1). View on PubMed
  4. Philp AR, Remesal L, Pratt KJB, Maynard JC, Sahota S, Aghayev T, Bieri G, Chu R, Avillion G, Sucharov-Costa J, Fuseya Y, Misra R, Mandelboum S, Zou B, Couthouis J, Xie XS, Fancy SPJ, Burlingame AL, Maki T, Villeda SA. COUNTERING AGE-ASSOCIATED ALTERATIONS IN OLIGODENDROCYTE-DERIVED EXTRACELLULAR MATRIX REJUVENATES COGNITION. bioRxiv. 2026 Feb 05. View on PubMed
  5. Freund PA, Panayotis N, Yuanxiang P, Samer S, Otikovs L, Kawaguchi R, Oses-Prieto J, Zomorrodinia T, Rishal I, Schweizer M, Tsoory M, Grochowska KM, Karpova A, Burlingame AL, Kreutz MR, Fainzilber M. Subcellular depletion of importin β1 impairs presynaptic local translation and spatial memory. Sci Signal. 2026 Jan 20; 19(921):eady2026. View on PubMed
  6. Zahavi EE, Rishal I, Oses-Prieto JA, Brandis A, Malitsky S, Itkin M, Pokorná Š, Cabrera-Cabrera F, Seeba NN, Risti R, Lõokene A, Futerman AH, Burlingame AL, Fainzilber M, Koppel I. Nucleolin perturbation alters membrane lipid homeostasis. Mol Omics. 2025 Dec 01; 21(6):723-735. View on PubMed
  7. Costa ID, Michenfelder E, Siciliano S, Tapita A, Buchanan CN, Vaughn LS, Lee J, Oses-Prieto J, Ma C, Thames E, Samra N, Ben-Dor S, Haffner-Krausz R, McElveen M, Smith TP, Nawar N, Manaswiyoungkul P, Gunning PT, Fainzilber M, Burlingame AL, Zhu H, Perlson E, Sahoo PK, Twiss JL. Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration. bioRxiv. 2025 Oct 30. View on PubMed
  8. Smeyers J, Oses-Prieto JA, Yadanar L, Wang M, Iadarola M, Lu S, Wang KS, Watanabe TH, Debnath J, Burlingame AL, Mordes DA. Phospho-proteome profiling in human neurons reveals targets of TBK1 in ALS/FTD-associated autophagy networks. Cell Rep. 2025 Nov 25; 44(11):116494. View on PubMed
  9. Guo Y, Li T, Tuomivaara ST, Teo CF, Feng S, Chalkley RJ, Zhu R, Cheng T, Li KH, Chen W, Simon A, Jin P, Younger S, Yong AJH, Li K, Li K, Burlingame AL, Jan LY, Jan YN. Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila. Neuron. 2025 Oct 15; 113(20):3352-3362.e5. View on PubMed
  10. Byeon S, Ferreccio A, Cornell M, Oses-Prieto JA, Deshpande A, Manvi S, Blencowe A, Weiss LA, Burlingame AL, Yadav S. TAOK2 drives opposing cilia length deficits in 16p11.2 deletion and duplication carriers. Stem Cell Reports. 2025 Sep 09; 20(9):102608. View on PubMed
  11. Remesal L, Sucharov-Costa J, Wu Y, Pratt KJB, Bieri G, Philp A, Phan M, Aghayev T, White CW, Wheatley EG, Zou B, Desousa BR, Couthouis J, Jian IH, Xie XS, Lu Y, Maynard JC, Burlingame AL, Villeda SA. Targeting iron-associated protein Ftl1 in the brain of old mice improves age-related cognitive impairment. Nat Aging. 2025 Oct; 5(10):1957-1969. View on PubMed
  12. He L, Kwon D, Trnka MJ, Liu Y, Yang J, Li KH, Totah RA, Johnson EF, Burlingame AL, Correia MA. Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site. Mol Pharmacol. 2025 Sep; 107(9):100061. View on PubMed
  13. Palla AM, Lin CC, Trnka MJ, Leao EM, Petronikolou N, Burlingame AL, McGinty RK, Fujimori DG. An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA. J Mol Biol. 2025 Oct 01; 437(19):169301. View on PubMed
  14. 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. Proteomic characterization of type I collagen N-terminal crosslinked peptides. Matrix Biol Plus. 2025 Aug; 27:100179. View on PubMed
  15. Asmerian H, Diaz AJ, Xu H, Oses-Prieto JA, Alberts J, Sanetra A, Gnanabharathi B, Carr N, Burlingame AL, Edwards RH, Silm K. Synaptic vesicles that store monoamines and glutamate differ in protein composition. bioRxiv. 2025 Jun 10. View on PubMed
  16. Li F, Eriksen J, Oses-Prieto JA, Gomez YK, Xu H, Hareendranath S, Das P, Finer-Moore J, Nguyen P, Bowen A, Nelson A, Burlingame A, Grabe M, Stroud RM, Edwards RH. Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2. Nat Struct Mol Biol. 2025 Aug; 32(8):1479-1487. View on PubMed
  17. Li H, Younger NS, Malik B, Shin HJ, Zhang C, Niknafs Y, Zhao SG, Wilder-Romans K, Pitchiaya S, Han S, Barnard T, Lloyd P, Zhang M, Chesner LN, Calvert M, Egusa EA, Zhu J, Chou J, Das R, Kothari V, Shenoy T, Diolaiti ME, Malik R, Prensner JR, Burlingame A, Ashworth A, Chinnaiyan AM, Feng F, Li H. Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer. bioRxiv. 2025 May 24. View on PubMed
  18. Zahavi EE, Koppel I, Kawaguchi R, Oses-Prieto JA, Briner A, Monavarfeshani A, Dalla Costa I, van Niekerk E, Lee J, Matoo S, Hegarty S, Donahue RJ, Sahoo PK, Ben-Dor S, Feldmesser E, Ryvkin J, Leshkowitz D, Perry RB, Cheng Y, Farber E, Abraham O, Samra N, Okladnikov N, Alber S, Albus CA, Rishal I, Ulitsky I, Tuszynski MH, Twiss JL, He Z, Burlingame AL, Fainzilber M. Repeat-element RNAs integrate a neuronal growth circuit. Cell. 2025 Aug 07; 188(16):4350-4365.e22. View on PubMed
  19. Palla AM, Lin CC, Trnka MJ, Leao EM, Petronikolou N, Burlingame AL, McGinty RK, Fujimori DG. An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA. bioRxiv. 2025 May 02. View on PubMed
  20. Tsusaka T, Najar MA, Schwarz B, Bohrnsen E, Oses-Prieto JA, Neudorf H, Lee C, Little JP, Burlingame AL, Bosio CM, Burslem GM, Goldberg EL. Reversible histone deacetylase activity catalyzes lysine acylation. Nat Chem Biol. 2025 Sep; 21(9):1387-1396. View on PubMed

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