Abstract: Automated protein assay apparatus and methods suitable for use in a reference lab are described. A screening test for a pathogen or disease condition is performed at the reference lab. If the results of the screening test are positive, a definitive assay is performed. One or more analytes are resolved in a fluid path such as that of a capillary by isoelectric focusing. The resolved analytes are immobilized in the capillary by photoimmobilization. A typical analyte is a protein of a biological sample of a subject. Detection agents such as antibodies are flowed through the capillary which bind to or interact with the analytes, forming antibody-protein complexes. A chemiluminescent substrate is flowed through the capillary and detected with a photon detector. The detected locations of the analytes are recorded and the results sent to the referring physician.