Abstract: The present invention describes diagnostic calibration methods and related compositions for flow cytometry instruments using synthetic control particles as an internal reference standard. The invention provides synthetic control beads which substantially reduce the drawbacks of conventional control beads. Synthetic beads coated with C3, C4 or CR1 and a non-specific spacer protein such as ovalbumin provide a control bead without the positive reactivity seen in conventional BSA controls. The present invention further provides a buffer system containing non-specific blockers and assay performance enhancers that do not interfere with analyte detection. The invention provides advantageous improvements over prior instrument calibration procedures, and provides control beads that enable consistent, reproducible data for diagnostic assays using flow cytometry.