Antibody Epitope Mapping Service

What is Antibody Epitope Mapping?

Antibodies are an important component of the immune system. They are glycoproteins produced by B cells that can bind to antigens such as viruses, bacteria, and cancer cells, and neutralize or label them for destruction by other immune cells. Antibodies have different structures, affinities, and specificities, allowing them to recognize and respond to a wide range of antigens. However, to use antibodies for diagnostic, therapeutic, or research purposes, it is necessary to determine the precise epitopes on the antigen that the antibody binds to. This is where antibody epitope mapping comes in.

Antibody epitope mapping is the process of identifying and characterizing specific regions or sites on an antigen that are recognized and bound by antibodies. This information can be used to design better vaccines, diagnostic assays, or antibody-based therapies, as well as to understand the molecular basis of antibody-antigen interactions.

Epitope mapping on the 3D structureEpitope mapping on the 3D structure (Leoni et al., 2019)

Antibody Epitope Mapping Techniques in Creative Proteomics

At Creative Proteomics, we offer a range of services for antibody epitope mapping, including peptide scanning, targeted mutagenesis, hydrogen-deuterium exchange mass spectrometry, X-ray crystallography, NMR spectroscopy, and computational modeling. Our team of experienced biologists, chemists, and bioinformaticians can help you identify and characterize antibody epitopes with high precision and accuracy. Whether you are conducting basic research, designing vaccines or optimizing antibody-based therapies, we can provide you with the insights and solutions you need to succeed.

  • Peptide scanning: Overlapping peptides covering the entire antigen sequence are synthesized and tested for their binding to antibodies using techniques such as enzyme-linked immunosorbent assays (ELISA) or surface plasmon resonance (SPR). By comparing the binding patterns of different peptides, specific amino acid residues that contribute to antibody-epitope interactions can be inferred. This method is relatively simple and cost-effective, but it may miss conformational epitopes that require an intact folded antigen.
  • Alanine scan: A single amino acid in the target molecule is substituted with alanine and the resulting peptide is tested for its ability to bind to the antibody. This method identifies key amino acids involved in antibody-target interactions.
  • Site-specific mutagenesis: Specific amino acid mutations are introduced into the antigen and tested for their effect on antibody binding. By identifying key residues necessary for antibody-epitope interactions, an accurate map of the epitope can be constructed.
  • Hydrogen deuterium exchange mass spectrometry (HDX-MS): This technique can be used to identify regions of an antigen that are protected by antibody binding. By measuring the rate of deuterium atom exchange on the antigen in the presence and absence of antibodies, it can reveal which regions of the antigen are involved in antibody binding and thus represent potential epitopes.

Epitope Mapping of Polyclonal Antibodies by HDX-MSEpitope Mapping of Polyclonal Antibodies by HDX-MS (Stander et al., 2021)

  • X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy: These techniques allow the three-dimensional structure of antigen-antibody complexes to be determined with atomic resolution, revealing the precise interactions between epitopes and complementary sites (the complementary determining regions of antibodies).

Our services are provided with the highest standards of quality, reliability, and confidentiality and are backed by a dedicated team of experts committed to providing personalized and responsive support. With our comprehensive antibody epitope mapping service, you can be sure that you will receive the most accurate and detailed information about your antibody, enabling you to make informed decisions about your development program.


  1. Leoni, Claudia, et al. "Chitinases as food allergens." Molecules 24.11 (2019): 2087.
  2. Stander, Susanne, et al. "Epitope mapping of polyclonal antibodies by hydrogen–deuterium exchange mass spectrometry (HDX-MS)." Analytical Chemistry 93.34 (2021): 11669-11678.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.