This invention provides methods of using ion-detecting microspheres containing an ionphore and a chromoionphore in clinical laboratory instrumentation such as flow cytometry for sample analysis. In one embodiment, the microspheres are contacted with a flowing stream of a sample under conditions that allow the ion-selective ionophores to complex with the ions in the sample, and to cause deprotonation of the chromoionophore. The complexes are then exposed to an excitation wavelength light source suitable for exciting the deprotonated chromoionophore to emit a fluorescence signal pattern. Detection of the fluorescence signal pattern emitted by the deprotonated chromoionophore in microspheres containing the complexes allows for determination of the presence of the target ions in the sample. In one embodiment, lead ion-detecting microspheres are provided that can detect nanomolar levels of lead ions with response times on the order of minutes.