Peptide Array-Based Epitope Mapping Service


Epitope mapping is a method that is often employed to identify the antigen binding sites of an antibody. However, epitope mapping can also be used in other protein interactions with high affinity, including those with proteins, chemicals, and DNA. RayBiotech’s peptide array-based epitope mapping service uses high-quality peptides that are chemically synthesized, thereby negating many of the steps and time required with the traditional approach that involves recombinant cloning, expression, and purification of different regions of the target gene.

RayBiotech’s comprehensive epitope mapping service includes peptide design and synthesis, array printing, sample testing, and report generation. Just send us your samples, and we’ll send you the report!

Epitope mapping array detection image
Detection of antibody binding to a RayBiotech peptide-based epitope mapping array. Array was incubated with A) buffer or B) monoclonal antibody.


  • Identify high antigenicity epitopes for antibody production & vaccine development
  • Locate (auto)antigen epitopes of (auto)antibodies
  • Define the best antibody clone against the protein-of-interest
  • Perform epitope mutant analysis
  • Map B cell epitopes

Service Features

  • Small serum sample volume required (2 µl)
  • High density (simultaneously analyze hundreds of overlapping peptides)
  • High sensitivity
  • Large dynamic range
  • Suitable for high-throughput assays
  • High efficiency and accuracy
  • Affordable, quick and simple to use

Available Pre-made Epitope Mapping Arrays

In addition to custom epitope mapping arrays, RayBiotech offers pre-made arrays for popular targets. For more information, please contact our technical support team at

Programmed Cell Death 1 (PD-1)
F24-L288, no signal peptide
Programmed Death Ligand 1 (PD-L1)
F19-T290, no signal peptide
Cytotoxic T-Lymphocyte Associated Protein 4 (CTLA4)
K36-N223, no signal peptide

How It Works

Epitope mapping array - how it works

RayBiotech’s peptide-based epitope mapping arrays are prepared by first printing overlapping, chemically-synthesized peptides(> 95% purity) spanning the length of the protein-of-interest onto a glass slide surface in an arrayed format, with each peptide spotted in triplicate. Multiple positive and negative controls are also printed onto the array to monitor each incubation step. Purified antibodies or bodily fluids containing antibodies are then diluted and incubated on the peptide arrays, during which the antibodies specifically bind to the peptides displaying their sequence-of-interest. After unbound antibodies are washed off the array, a biotin-conjugated secondary antibody (e.g., anti-human IgG, mouse IgG) and a fluorescence dye-conjugated streptavidin molecule are added to the array to enable the detection of bound antibodies bound. Fluorescent signal is then captured using a laser scanner. Since the peptide sequence of each spot is known, the antibody’s potential epitope(s) can be ascertained.

Array Format

  • Number of replicates per peptide: Triplicate
  • Array substrate: Glass slide
  • Number of subarrays per slide: 4
  • Printed controls: Biotin-BSA, human IgG, mouse IgG, full-length target protein (unless otherwise specified)

Assay Format

  • Compatible Sample Types: Antibodies (serum, plasma, ascites, recombinant antibodies, purified antibodies), chemicals, aptamer, or any other binders.
  • Antibody Type: Human IgG and mouse IgG. Other isotypes (IgA, IgM, IgE, etc.) derived from most animals, upon request.
  • Method of Detection: Fluorescence captured by laser scanner
  • Data: Semi-Quantitative

Representative Data

Results are presented as a fluorescent scan of the array (Figure 1) and in a table format (Table 1).

Epitope mapping results
Figure 1. Peptide array images showing antibody binding to its peptide epitope using a RayBiotech's peptide-based epitope mapping array. All target peptides were printed in triplicate. Biotin-BSA and mouse IgG were printed and used as positive controls. Arrays S1, S2, and S3 were incubated with the monoclonal antibody (mAb) at 200, 400, and 800-fold dilutions, respectively. CTL array was incubated without the mAb. The epitope sequence, represented by Peptide #8, is indicated with an arrow in array S1.
Epitope mapping chart
Table 1. Fluorescence signal of the peptide array probed with the mAb. Background signal is represented by data from the CTRL array (see Figure 1). Of the 11 peptides, Peptide #8 had the strongest signal, which significantly increased with an increase in the mAb antibody concentration. The normalized data is shown on left and the signal to noise (S:N) ratio is shown on the right.

RayBiotech would like to thank Dr. Clemens Duerrschmid (Baylor College of Medicine, Houston, TX) for allowing us to present this data.