The Enzyme-Linked Immunosorbent Assay (ELISA) and Western Blot analysis have been workhorse techniques for the analysis of protein levels and state, such as phosphorylation. The ELISA is also useful for measuring the affinity of a molecule for its ligand. The disadvantage of these techniques is that only a single protein can be analyzed for ELISA and a few (up to three) proteins for Western Blotting. Exact quantification is difficult with Western Blotting and changes are often reported as fold differences. We present here protocols for using fluorescent microspheres coated with the selected capture molecule to perform in essence several hundred mini ELISAs with each microsphere representing an ELISA; this reduces the variability of the assay. In addition, it is possible to analyze up to 100 analytes simultaneously using microspheres because each fluorescent microsphere exhibits distinct fluorescence in the red and far red channels: the fluorescence intensity in the channels in the red and far red channels (up to ten different intensities for each channel leading to a 10 � 10 matrix of intensities) constitutes the address for each analyte.