Methods and kits for probing multiple targets in a biological sample are provided. The methods include the steps of (a) providing a biological sample containing multiple targets, (b) binding at least one fluorescent probe to one or more targets present in the sample; (c) binding at least one control probe to one or more targets present in the sample; (d) detecting at least one signal from the at least one fluorescent probe bound in step (b) and detecting at least one control signal from the at least one control probe bound in step (c); (e) applying to the sample in step (d) a solution comprising an oxidizing agent that selectively inactivates the fluorescent probe and not the control probe; (f) binding at least one fluorescent probe to one or more targets present in the sample of step (e); and (g) detecting at least one signal from the at least one fluorescent probe bound in step (f). An associated kit is also provided.
