The interaction of a series of water-soluble conjugated polyelectrolytes with varying backbone structure, charge type (cationic and anionic), and charge density with a set of seven different proteins is explored by using fluorescence correlation spectroscopy (FCS). The FCS method affords the diffusion time for a particular CPE/protein pair, and this diffusion time is a reflection of the aggregation state of the polymer/protein in the solution. The diffusion time is larger for oppositely charged CPE/protein combinations, reflecting the tendency toward the formation of CPE/protein aggregates in these systems. However, by careful analysis of the data, other factors emerge, including possible effects of hydrophobic interaction in specific CPE/protein systems. The final diffusion time for each CPE/protein mixture varies and the diffusion time response pattern created by the six-CPE array for a typical protein is unique, and this effect was leveraged to develop a sensor array for protein identification by using linear-discriminant analysis (LDA) methods. By application of multimode linear discrimination analysis, the unknown protein samples have been successfully identified with a total accuracy of 93%.Keywords: conjugated polyelectrolyte; fluorescence correlation spectroscopy; protein identification; protein/polymer aggregation;