This chapter describes the development and use of bead-based miniaturized multiplexed sandwich immunoassays for focused protein profiling. Bead-based protein arrays or suspension microarrays allow simultaneous analysis of a variety of parameters within a single experiment. In suspension microarrays capture antibodies are coupled onto color-coded microspheres. The applications of suspension microarrays are described, which allow to analyze proteins present in different types of body fluids, such as serum or plasma, cerebrospinal, pleural and synovial fluids, as well as cell culture supernatants. The chapter is divided into the generation of suspension microarrays, sample preparation, processing of suspension microarrays, validation of analytical performance, and finally pattern generation using bioinformatics tools.