Peptides and Anti-peptide Antibodies for Small and Medium Scale Peptide and Anti-peptide Affinity Microarrays: Antigenic Peptide Selection, Immobilization, and Processing

Part of the Methods in Molecular Biology book series (MIMB, volume 1352)


This chapter describes the principles of selection of antigenic peptides for the development of anti-peptide antibodies for use in microarray-based multiplex affinity assays and also with mass-spectrometry detection. The methods described here are mostly applicable to small to medium scale arrays. Although the same principles of peptide selection would be suitable for larger scale arrays (with 100+ features) the actual informatics software and printing methods may well be different. Because of the sheer number of proteins/peptides to be processed and analyzed dedicated software capable of processing all the proteins and an enterprise level array robotics may be necessary for larger scale efforts. This report aims to provide practical advice to those who develop or use arrays with up to ~100 different peptide or protein features.

Key words

Proteomics Peptidomics Peptide array Antibody array Affinity assay Antigenicity Immunization Polyclonal antibodies 


  1. 1.
    Soloviev M, Finch P (2006) Peptidomics: bridging the gap between proteome and metabolome. Proteomics 6:744–747CrossRefPubMedGoogle Scholar
  2. 2.
    Soloviev M, Finch P (2005) Peptidomics, current status. J Chromatogr B 815:11–24CrossRefGoogle Scholar
  3. 3.
    Scrivener E, Barry R, Platt A et al (2003) Peptidomics: a new approach to affinity protein microarrays. Proteomics 3:122–128CrossRefPubMedGoogle Scholar
  4. 4.
    Soloviev M, Terrett J (2005) Practical guide to protein microarrays: assay systems, methods and algorithms. In: Schena M (ed) Protein microarrays. Jones and Bartlett, Sudbury, MA, pp 43–56Google Scholar
  5. 5.
    Barry R, Diggle T, Terrett J, Soloviev M (2003) Competitive assay formats for high-throughput affinity arrays. J Biomol Screen 8:257–263CrossRefPubMedGoogle Scholar
  6. 6.
    Zhang F, Dulneva A, Bailes J et al (2010) Affinity peptidomics: peptide selection and affinity capture on hydrogels and microarrays. Methods Mol Biol 615:313–344CrossRefPubMedGoogle Scholar
  7. 7.
    Artimo P, Jonnalagedda M, Arnold K et al (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res 40:W597–W603CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Dietrich JB (1985) Antibodies against synthetic peptides—their interest in biology. Annee Biol 24:129–152Google Scholar
  9. 9.
    Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino-acid sequences. Proc Natl Acad Sci U S A 78:3824–3828CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Westhof E, Altschuh D, Moras D et al (1984) Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature 311:123–126CrossRefPubMedGoogle Scholar
  11. 11.
    Hofmann HJ, Hädge D (1987) On the theoretical prediction of protein antigenic determinants from amino acid sequences. Biomed Biochim Acta 46:855–866PubMedGoogle Scholar
  12. 12.
    Pellequer JL, Westhof E (1993) PREDITOP: a program for antigenicity prediction. J Mol Graph 11:204–210CrossRefPubMedGoogle Scholar
  13. 13.
    Ponomarenko JV, Bourne PE (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Flower DR (2007) Immunoinformatics and the in silico prediction of immunogenicity. An introduction. Methods Mol Biol 409:1–15CrossRefPubMedGoogle Scholar
  15. 15.
    Ponomarenko J, Bui HH, Li W et al (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9:514CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Hancock DC, O’Reilly NJ (2005) Synthetic peptides as antigens for antibody production. Methods Mol Biol 295:13–26PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.School of Biological Sciences, Centre for Biomedical SciencesRoyal Holloway University of LondonSurreyUK

Personalised recommendations