Protein arrays are already used in disease profiling, where differential expression of specific proteins is measured and correlated to a particular disease state or drug treatment. They can also be used in many stages of the drug discovery process, including target identification and validation, toxicology, pathway elucidation, mode of action, and analysis of drug resistance and surrogate markers of drug response.

CyDye reagents are important as fluorescent labels for biological compounds. CyDye Fluors are intensely fluorescent and highly water soluble, providing significant advantages over other existing fluorophores. CyDye Fluors form the core of many key technologies and platforms, in fields as diverse as DNA microarrays, 2-D DIGE, DNA sequencing, high-throughput screening, flow cytometry, and now protein arrays, where they are particularly suited to highly sensitive and accurate differential analysis.