The goal of the project is to develop and demonstrate two related approaches to molecular analysis and separation that employ flow based analytical instrumentation and magnetic microsphere technology: a magnetic flow spectrometer for separation, and a magnetic flow cytometer for identification. The flow spectrometer system will be unique in enabling highly parallel continuous flow biomolecular separations on a preparative scale, streamlining downstream analysis and revolutionizing our ability to identify potential diagnostic or therapeutic targets. The magnetic flow cytometer will combine a novel magnetic target- molecule tagging concept with fluorescence-based analyte detection. The instrumentation proposed will contribute significantly to a broad range of applications improving human health and quality of life including drug discovery, molecular targeting, DNA analysis, proteomics, and understanding the pathways of cell cycle regulation. We will validate the new instrument by conventional molecular analysis methods and apply it to the study of intracellular vesicle traffic. A product for commercialization is anticipated. Operation of the proposed instrument involves three steps. 1) Magnetically encoded microspheres are prepared by encapsulating strong ferromagnetic material with high remnant magnetization and coercivity, never before used for such applications, in polymer spheres. The distribution of microspheres can be sorted into different bins depending on their intrinsic magnetic moment by flowing through a chamber where a magnetic field gradient induces a force such that they are collected in different bins with narrow distributions of magnetic moment. Microspheres from each bin are chemically bound to target molecules so that each species of magnetic moment is bound to one unique kind of molecule. The collection of microspheres and associated target molecules are then mixed together and incubated with analytes. 2) The incubated collection of microspheres are flowed through a SQUID detector system which identifies the target molecule by measuring the magnetic moment of the microsphere to which it is attached. 3) The analytes will be chemically prepared with molecular groups that fluoresce when illuminated by a laser beam, indicating the target-analyte binding. Combining SQUIDs for target identification with laser diagnostics to assess binding provides an efficient, high throughput multiplexed bioassay method based on traditional flow cytometry.