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The age of proteomics and resulting advances in technology have resulted in an increase in the number of requests for recombinant protein construction, production, and purification projects. One of the mainstays of the Molecular Biology Core Facility (MBCF) at Trudeau Institute is the production of Major Histocompatibility (MHC) Class I and Class II multimeric fluorescently labeled protein-peptide complexes, which allow the tracking of antigen-specific CD8+ and CD4+ T-cells using fluorescence-activated cell sorting (FACS) analysis. In addition, the MBCF has generated fusion proteins to be utilized for immunization strategies and viral coat proteins from influenza and murine gamma herpes virus 68 for detecting epitope-specific antibodies. Another simple but extremely useful and money-saving protein production project is the production and purification of Taq enzyme for a laboratory that uses large quantities of Taq enzyme in a limiting dilution assay for latent viral detection. Requests for milligram amounts of native, endotoxin-free proteins to be used for in vivo vaccination are increasing. The MBCF utilizes a variety of expression systems, but primarily bacterial (using T7 promoter–based plasmids) and the insect cell–based Drosophila Expression System (DES) (Invitrogen). Recently, the Gateway system (Invitrogen) has been introduced into the MBCF to facilitate the whole procedure. Purification schemes are mainly based on size exclusion or affinity chromatography using either protein A, Ni-NTA, or glutathione sepharose.