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In the analysis of gene expression, DNA microarrays have found widespread application. However, expression on the mRNA level does not provide an accurate account of the functional state of a cell or tissue. First, mRNA levels do not reflect expression levels of proteins. Second, proteins are subject to a variety of post-translational modifications and enter into dynamically regulated molecular complexes. Because of their relative ease of handling, microarray-based approaches are gaining significance for the highly parallel analysis of proteins, complementing the more established proteomics approaches, such as mass spectrometry and gel electrophoresis. However, in comparison to DNA microarrays, protein microarrays are confronted with two major challenges: First, proteins possess very different physico-chemical characteristics, and activity depends on the preservation of their native conformation. Second, it is more difficult to identify a specific binder for a protein than to generate a highly specific DNA probe. To this point, protein array technology has focused on applications in auto-immunity, cancer, and microbiology. Many labs have collectively constructed arrays for studying three major classes of biomolecules: antibodies, cytokines and chemokines, and signaling molecules involved in activation of blood cells. Antibody profiling allows the identification of novel, unidentified targets of the immune response, as well as the ability to study epitope spreading. Other array platforms have been developed to study intracellular signaling molecules in lymphocytes, either by immobilizing monoclonal antibodies on planar surfaces to capture analytes, or by printing lysates and using existing phospho-specific antibodies (termed reverse-phase protein lysate microarrays). In addition, peptide microarrays have been employed for epitope mapping of antibodies and for defining binding specificities of protein domains. Like oligonucleotide microarrays, peptide microarrays offer the advantage of probe generation by parallel synthesis procedures. This session will cover protein and peptide array technologies and their applications, and the methods for interrogating datasets.