Protein-environment-sensitive computational epitope accessibility analysis from antibody dose-response data

TL;DR

This paper introduces a computational method to analyze antibody epitope accessibility directly within biological systems, enhancing antibody selection, quantification, and multiplexing capabilities in imaging applications.

Contribution

It presents a novel, user-friendly approach to quantify antibody binding and epitope accessibility from immunofluorescence data in specific biological contexts.

Findings

Enables selection of optimal antibody dilutions for specific signals

Allows detection of subcellular nano-environment changes

Expands antibody multiplexing in imaging

Abstract

Antibodies are widely used in life-sciences and medical therapy. Yet, broadly applicable methods are missing to determine, in the biological system of choice, antibody specificity and its quantitative contribution to e.g. immunofluorescence stainings. Thereby, antibody-based data often needs to be seen with caution. Here, we present a simple-to-use approach to characterize and quantify antibody binding properties directly in the system of choice. We determine an epitope accessibility distribution in the system of interest based on a computational analysis of antibody-dilution immunofluorescence stainings. This allows the selection of specific antibodies, the choice of a dilution to maximize signal-specificity, and an improvement of signal quantification. It further expands the scope of antibody-based imaging to detect changes of the subcellular nano-environment and allows for antibody multiplexing.