UNIT 9.5 Identification of B Cell and T Cell Epitopes Using Synthetic Peptide Combinatorial Libraries

  1. Clemencia Pinilla,
  2. Jon R. Appel,
  3. Valeria Judkowski,
  4. Richard A. Houghten

Published Online: 1 NOV 2012

DOI: 10.1002/0471142735.im0905s99

Current Protocols in Immunology

Current Protocols in Immunology

How to Cite

Pinilla, C., Appel, J. R., Judkowski, V. and Houghten, R. A. 2012. Identification of B Cell and T Cell Epitopes Using Synthetic Peptide Combinatorial Libraries. Current Protocols in Immunology. 99:9.5:9.5.1–9.5.16.

Author Information

  1. Torrey Pines Institute for Molecular Studies, San Diego, California

Publication History

  1. Published Online: 1 NOV 2012
  2. Published Print: NOV 2012


This unit presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries of peptide molecules. The protocols employ peptide libraries to identify peptides recognized by MAbs and T cells. The first protocol uses a positional scanning peptide library made up of hexapeptides to identify antigenic determinants recognized by MAbs. The 120 mixtures in the hexapeptide library are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide library to identify T cell peptide ligands. The 200 mixtures of the decapeptide library are tested for their ability to induce T cell activation. Support protocols cover optimization of the assay conditions for each MAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide library, along with deconvolution approaches. Curr. Protoc. Immunol. 99:9.5.1-9.5.16. © 2012 by John Wiley & Sons, Inc.


  • combinatorial libraries;
  • monoclonal antibodies;
  • T cells;
  • peptides