Antibody array analysis of labelled proteomes: how should we control specificity?

► We review studies on antibody array analysis of labelled proteomes. ► We point to the limitations of assays based on detection with a single binder and a protein label and argue that direct evidence for specificity is lacking in the literature. ► We present a new variant of the assay referred to as Size-MAP (Size-exclusion chromatography-resolved Microsphere-based Affinity Proteomics). ► Size-MAP resembles a multiplexed western blot and provides internal reference of specificity in highly multiplexed protein analysis.