A method for the multiplexed diagnostic and genetic analysis of enzymes, DNA fragments, antibodies, and other biomolecules comprises the steps of constructing an appropriately labeled beadset, exposing the beadset to a clinical sample, and analyzing the combined sample/beadset by flow cytometry. Flow cytometric measurements are used to classify, in real-time, beads within an exposed beadset and textual explanations, based on the accumulated data obtained during real-time analysis, are generated for the user. A secondary reagent, such as a metal or magnetic particle, is added to the beadset to assist in the analysis. Detection techniques, such as such as light scatter, Rayleigh scatter, Raman scatter, surface plasmon resonance, magnetic induction, or magnetoresistance are used to detect the particle labels.