Data-driven evaluation of suitable immunogens for improved antibody selection

ABSTRACT Antibodies are indispensable in laboratory and clinical applications due to their high specificity and affinity for protein antigens. However, selecting the right protein fragments as immunogens for antibody production remains challenging. Leveraging the Human Protein Atlas, this study systematically evaluates immunogen properties aiming to identify key factors that influence their suitability. Antibodies were classified as successful or unsuccessful based on standardized validation experiments, and the structural and functional properties of their immunogens were analyzed. Results indicated that longer immunogens often resulted in more successful but less specific antibodies. Shorter immunogens (50 residues or fewer) with disordered or unfolded regions at the N- or C-terminus and long coil stretches, were more likely to generate successful antibodies. Conversely, immunogens with high beta sheet content, multiple secondary structure elements, transmembrane regions, or disulfide bridges were associated with poorer antibody performance. Post-translational modification sites within immunogens appeared to mark beneficial regions for antibody generation. To support antibody selection, a novel R package, immunogenViewer, was developed, enabling researchers to easily apply these insights when immunogen sequences are disclosed. By providing a deeper understanding of immunogen suitability, this study promotes the development of more effective antibodies, ultimately addressing issues of reproducibility and reliability in antibody-based research. The findings are highly relevant to the research community, as end-users often lack control over the immunogen selection process in antibody production.