The current state of the art in the development of antibody alternatives is fraught with difficulties including mass
production, robustness, and overall cost of production. The isolation of synthetic alternatives using peptide libraries
offers great potential for recognition elements that are more stable and have improved binding affinity and target
specificity. Although recent advances in rapid and automated discovery and synthetic library engineering continue to
show promise for this emerging science, there remains a critical need for an improved fundamental understanding of the
mechanisms of recognition. To better understand the fundamental mechanisms of binding, it is critical to be able to
accurately assess binding between peptide reagents and protein targets. The development of empirical methods to
analyze peptide-protein interactions is often overlooked, since it is often assumed that peptides can easily substitute for
antibodies in antibody-derived immunoassays. The physico-chemical difference between peptides and antibodies
represents a major challenge for developing peptides in standard immunoassays as capture or detection reagents.
Analysis of peptide presents a unique challenge since the peptide has to be soluble, must be capable of target recognition,
and capable of ELISA plate or SPR chip binding. Incorporating a plate-binding, hydrophilic peptide fusion (PS-tag)
improves both the solubility and plate binding capability in a direct peptide ELISA format. Secondly, a solution based
methods, affinity capillary electrophoresis (ACE) method is presented as a solution-based, affinity determination method
that can be used for determining both the association constants and binding kinetics.