Epitope mapping

Peptide library synthesis is useful for epitope mapping. Epitope mapping allows to identify the peptide sequences on an antigen that elicit an immune response. For example, you might be interested in our SARS-CoV-2 peptide libraries.

Peptide libraries will display multiple peptide fragments to deduce epitopes. The most common applications of epitope mapping are T-cells and antibody epitope mapping. Peptide libraries for epitope mapping are used for developing vaccines (for viral diseases and cancer).

T-cell epitope mapping

T-cell cultures or purified receptors are added to the peptide library. If there is binding, the peptide can be considered as capable of being immunogenic. Binding events can be monitored via flow cytometry.

Antibody epitope mapping

Antibodies are added to the peptide library and binding can be assessed by ELISA.

Recommended settings

Overlapping, positional and truncated peptide libraries are frequently used for epitope mapping
– To discover epitope, unpurified peptides with standard quality control are usually sufficient
– To characterize epitopes : purity >70% and in-depth quality control is recommended

For more information about our peptide library synthesis service, please visit this link.



Reineke U. vol 524. Humana Press (2009)
Antibody epitope mapping using de novo generated synthetic peptide libraries


ABSTRACT: Identification of antibody binding peptides may be based on the primary structure of the protein antigens used to raise the antibodies (knowledge- or sequence-based approach). This involves scanning the entire sequence of the antigen with overlapping peptides (peptidescan), which are then probed for binding to the respective antibody. If a natural protein binding partner is not known, one has to use combinatorial synthetic libraries with peptide mixtures, randomly generated chemically synthesized libraries of single individual sequences, or biologically produced libraries (e.g., phage display libraries, see Chapter « Epitope Mapping Using Phage Display Peptide Libraries »). This chapter describes chemically synthesized combinatorial, as well as randomly generated peptide libraries, collectively called de novo approaches, and their application for antibody epitope mapping.

Gershoni, J.M., Roitburd-Berman, A., Siman-Tov, D.D. et al. Epitope Mapping. BioDrugs 21, 145–156 (2007)
Epitope mapping: the first step in developing epitope-based vaccines.

ABSTRACT: Antibodies are an effective line of defense in preventing infectious diseases. Highly potent neutralizing antibodies can intercept a virus before it attaches to its target cell and, thus, inactivate it. This ability is based on the antibodies’ specific recognition of epitopes, the sites of the antigen to which antibodies bind. Thus, understanding the antibody/epitope interaction provides a basis for the rational design of preventive vaccines. It is assumed that immunization with the precise epitope, corresponding to an effective neutralizing antibody, would elicit the generation of similarly potent antibodies in the vaccinee. Such a vaccine would be a ‘B-cell epitope-based vaccine’, the implementation of which requires the ability to backtrack from a desired antibody to its corresponding epitope. In this article we discuss a range of methods that enable epitope discovery based on a specific antibody. Such a reversed immunological approach is the first step in the rational design of an epitope-based vaccine. Undoubtedly, the gold standard for epitope definition is x-ray analyses of crystals of antigen:antibody complexes. This method provides atomic resolution of the epitope; however, it is not readily applicable to many antigens and antibodies, and requires a very high degree of sophistication and expertise. Most other methods rely on the ability to monitor the binding of the antibody to antigen fragments or mutated variations. In mutagenesis of the antigen, loss of binding due to point modification of an amino acid residue is often considered an indication of an epitope component. In addition, computational combinatorial methods for epitope mapping are also useful. These methods rely on the ability of the antibody of interest to affinity isolate specific short peptides from combinatorial phage display peptide libraries. The peptides are then regarded as leads for the definition of the epitope corresponding to the antibody used to screen the peptide library. For epitope mapping, computational algorithms have been developed, such as Mapitope, which has recently been found to be effective in mapping conformational discontinuous epitopes. The pros and cons of various approaches towards epitope mapping are also discussed.

Fack F et al. J. Immunol. Methods 206, 43–52. (1997)
Epitope mapping by phage display: random versus gene-fragment libraries.

ABSTRACT: We present a comparative study on epitope mapping of four monoclonal antibodies directed against four different antigens using alternative phage display techniques and peptide scanning: mAb215 reacts with the largest subunit of RNA polymerase II, mAbBp53-11 with the tumor suppressor protein p53, mAbGDO5 with the Hantaan virus glycoprotein G2 and mAbL13F3 with the Hantaan virus nucleocapsid protein. Epitopes were determined (i) by gene-fragment phage display libraries, constructed by DNaseI digested random gene fragments cloned into the 5′ terminus of the pIII-gene of fd phage and (ii) by random peptide phage libraries displaying 6mer and 15mer peptides at the N-terminus of the pIII protein. Using the gene-fragment phage display libraries a single round of affinity selection resulted in the determination of the corresponding epitopes for all monoclonal antibodies tested. In contrast, biopanning of 6mer and 15mer random peptide libraries was only successful for two of the antibodies (mAbBp53-11 and mAbGDO5) after three or four rounds of selection. For the anti-p53 antibody we recovered the epitope from both the 6mer and 15mer library, for mAbGDO5 only the 6mer library displayed the epitope sequence. However, screening of the random peptide libraries with mAb215 and mAbL13F3 failed to yield immunopositive clones. Fine mapping of the epitopes by peptide scan revealed that the minimal epitopes recognized by mAbBp53-11 and mAbGDO5 consist of four and five amino acids, respectively, whereas mAb215 requires a minimal epitope of 11 amino acids for antigen recognition. In contrast, mAbL13F3 did not react with any of the synthesized 15mer peptides. The limits of the different methods of epitope mapping tested in this study are compared and the advantages of the gene-fragment phage display system are discussed.