Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases.

INTRODUCTION

Thirty years ago George Smith introduced ‘phage display’ as a means to express vast collections of recombinant proteins and peptides to be screened by affinity selection (1) (a process coined ‘biopanning’ (2)). Two basic systems evolved: (i) phage display of random peptide libraries and (ii) the production of phage displayed antibodies. The latter has been used extensively to generate human monoclonal antibodies, replacing to some extent the production of murine monoclonal antibodies via classical hybridoma technology. The first system, random peptide libraries, was initially applied to the epitope analysis of a specific monoclonal antibody with the ultimate intent of affinity selection of a peptide-mimetic assumed to simulate and represent the cognate epitope of the antibody being studied (7,8). Cortese et al. went on to implement random peptide phage display to study polyclonal sera, demonstrating that pathogen related peptides could be isolated through biopanning peptide-libraries with disease-defining polyclonal serum.

In many cases the application of phage display libraries was performed to clone out a specific peptide or antibody for further development and study. More recently, phage display has also served as the basis for computational prediction of epitope-structures, as reviewed by Sun et al. and for the critical profiling of the repertoire of antibody specificities of polyclonal sera, i.e. profiling the IgOme .