Mapping protein-protein interactions by affinity-directed mass spectrometry

Yingming Zhao, Tom W. Muir, Stephen B.H. Kent, E. D. Tischer, Jan Marian Scardina, Brian T. Chait

Research output: Contribution to journalArticlepeer-review

91 Scopus citations


A precise and rapid method for identifying sites of interaction between proteins was demonstrated; the basis of the method is direct mass spectrometric readout from the complex to determine the specific components of the proteins that interact-a method termed affinity-directed mass spectrometry. The strategy was used to define the region of interaction of a protein growth factor with a monoclonal antibody. A combination of proteolytic digestion and affinity-directed mass spectrometry was used to rapidly determine the approximate location of a continuous binding epitope within the growth factor. The precise boundaries of the binding epitope were determined by affinity-directed mass spectrometric analysis of sets of synthetic peptide ladders that span the approximate binding region. In addition to the mapping of such linear epitopes, affinity-directed mass spectrometry can be applied to the mapping of other types of molecule- molecule contacts, including ligand-receptor and protein-oligonucleotide interactions.

Original languageEnglish (US)
Pages (from-to)4020-4024
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number9
StatePublished - Apr 30 1996
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General


  • antibody
  • epitope
  • protein ladder


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