Al Burlingame, PhD

Phone: +1 415 476-4893
Fax: +1 415 502-1655
600 16th St, Rm N472H
UCSF Box 2240
San Francisco, CA 94158
United States


What I do

My research interests focus on the development of state of the art methodologies in mass spectrometry for use in advancing our global knowledge of human biology, specifically the dynamic, epigenetic modulation and regulation of the proteome.

Departmental research area

My research expertise

bioanalytical chemistry, mass spectrometry

Professional background


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 keywords

  • Proteomics & the Molecular Compositions of Biological Systems
  • Identification of Cell Constituents and Correlation with Gene Expression
  • Posttranslational Modifications of Proteins
  • Molecular Immunochemistry
  • Metabolic Activation and Covalent Binding of Xenobiotics to Cellular Macromolecules
  • mass spectrometry
  • Epigenetics
  • Structures of Modified Macromolecules and protein machines in Structural Biology
  • Molecular Composition of Biological Systems
  • Molecular Structure Determinations
  • Molecular Nature of Chemical Toxicity
  • Antigenic Determinants
  • Glucoconjugates
  • Proteomics
  • Tandem Mass Spectrometry
  • Post-Translational Protein Processing
  • Peptides
  • mass spectrometry
  • Spectrometry, Mass, Electrospray Ionization
  • proteome
  • biochemistry
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Arabidopsis
  • Acetylglucosamine
  • Arabidopsis Proteins
  • proteins
  • Liquid Chromatography
  • Periodicals as Topic