of the presence of altered proteins or other agents that may be the result of disease. Specifically, post-translational modifications, which are typically altered as a result of disease can be detected using RPAs. Functional protein microarrays Functional protein microarrays (also known as target protein arrays) are constructed by immobilising large numbers of purified proteins and are used to identify protein–protein, protein–DNA, protein–RNA, protein–phospholipid, and protein–small-molecule interactions, to assay enzymatic activity and to detect antibodies and demonstrate their specificity. They differ from analytical arrays in that functional protein arrays are composed of arrays containing full-length functional proteins or protein domains. These protein chips are used to study the biochemical activities of the entire proteome in a single experiment. The key element in any functional protein microarray-based assay is the arrayed proteins must retain their native structure, such that meaningful functional interactions can take place on the array surface. The advantages of controlling the precise mode of surface attachment through use of an appropriate affinity tag are that the immobilised proteins will have a homogeneous orientation resulting in a higher specific activity and higher signal-to-noise ratio in assays, with less interference from non-specific interactions. Detection Protein array detection methods must give a high signal and a low background. The most common and widely used method for detection is fluorescence labeling which is highly sensitive, safe and compatible with readily available microarray laser scanners. Other labels can be used, such as affinity, photochemical or radioisotope tags. These labels are attached to the probe itself and can interfere with the probe-target protein reaction. Therefore, a number of label free detection methods are available, such as surface plasmon resonance (SPR), carbon nanotubes, carbon nanowire sensors (where detection occurs via changes in conductance) and microelectromechanical system (MEMS) cantilevers. All these label free detection methods are relatively new and are not yet suitable for high-throughput protein interaction detection; however, they do offer much promise for the future. Immunoassays on thiol-ene "synthetic paper" micropillar scaffolds have shown to generate a superior fluorescence signal. Protein quantitation on nitrocellulose coated glass slides can use near-IR fluorescent detection. This limits interferences due to auto-fluorescence of the nitrocellulose at the UV wavelengths used for standard fluorescent detection probes. Applications There are five major areas where protein arrays are being applied: diagnostics, proteomics, protein functional analysis, antibody characterization, and treatment development. Diagnostics involves the detection of antigens and antibodies in blood samples; the