Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods

J Proteome Res. 2023 Sep 1;22(9):3096-3102. doi: 10.1021/acs.jproteome.3c00159. Epub 2023 Aug 1.


Structural proteomics techniques are useful for the determination of protein interaction interfaces. Each technique provides orthogonal structural information on the structure and the location of protein interaction sites. Here, we have characterized a monoclonal antibody epitope for a protein antigen by a combination of differential photoreactive surface modification (SM), cross-linking (CL), differential hydrogen-deuterium exchange (HDX), and epitope extraction/excision. We found that experimental data from different approaches agree with each other in determining the epitope of the monoclonal antibody on the protein antigens using the HIV-1 p24-mAb E complex as an illustrative example. A combination of these multiple structural proteomics approaches results in a detailed picture of the interaction of the proteins and increases confidence in the determination of the final structure of the protein interaction interface. Data are available via ProteomeXchange with identifier PXD040902.

Keywords: HIV-1 p24; HIV-1 p24−mAb E complex; cross-linking; epitope mapping; hydrogen-deuterium exchange; surface modification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies, Monoclonal* / chemistry
  • Epitope Mapping / methods
  • Epitopes / chemistry
  • Mass Spectrometry / methods
  • Proteomics*


  • Epitopes
  • Antibodies, Monoclonal