Comparative Evaluation of Reproducibility of Phage-Displayed Peptide Selections and NGS Data, through High-Fidelity Mapping of Massive Peptide Repertoires

Abstract

Phage-displayed peptide selections generate complex repertoires of several hundred thousand peptides as revealed by next-generation sequencing (NGS). In repeated peptide selections, however, even in identical experimental in vitro conditions, only a very small number of common peptides are found. The repertoire complexities are evidence of the difficulty of distinguishing between effective selections of specific peptide binders to exposed targets and the potential high background noise. Such investigation is even more relevant when considering the plethora of in vivo expressed targets on cells, in organs or in the entire organism to define targeting peptide agents. In the present study, we compare the published NGS data of three peptide repertoires that were obtained by phage display under identical experimental in vitro conditions. By applying the recently developed tool PepSimili we evaluate the calculated similarities of the individual peptides from each of these three repertoires and perform their mappings on the human proteome. The peptide-to-peptide mappings reveal high similarities among the three repertoires, confirming the desired reproducibility of phage-displayed peptide selections.

Advances in Antibody Design and Antigenic Peptide Targeting 2.0

“…Peptides which are suitable for use in generation of peptide antibodies may be identified using bioinformatic tools or phage display [5,6] or carefully selected by studying the protein structure and amino acid sequence, depending on the intended use [7,8]. Following the identification of targets, peptide antibodies are generated using standard procedures, e.g., by immunization of an animal, typically mice, or by phage display [6][7][8][9].…”

“…Peptides which are suitable for use in generation of peptide antibodies may be identified using bioinformatic tools or phage display [5,6] or carefully selected by studying the protein structure and amino acid sequence, depending on the intended use [7,8]. Following the identification of targets, peptide antibodies are generated using standard procedures, e.g., by immunization of an animal, typically mice, or by phage display [6][7][8][9]. For example, Petry and colleagues successfully examined the reproducibility of phage-displayed peptide selection tools for the production of antibodies, whereas Valdovino-Navaro and coworkers described the selection of a peptide antibody to SARS-CoV-2 SP240, which was isolated from a peptide phage library with high stability [6,10].…”

“…Following the identification of targets, peptide antibodies are generated using standard procedures, e.g., by immunization of an animal, typically mice, or by phage display [6][7][8][9]. For example, Petry and colleagues successfully examined the reproducibility of phage-displayed peptide selection tools for the production of antibodies, whereas Valdovino-Navaro and coworkers described the selection of a peptide antibody to SARS-CoV-2 SP240, which was isolated from a peptide phage library with high stability [6,10]. In contrast, studies by AlEraky, Trier and Mughal used carefully selected peptides based on amino acid analysis to generate peptide antibodies using common immunization procedures [7][8][9].…”