Disclosed are methods for treating a biological sample for an analyte-staining assay. These methods are conducted with the use of a single aqueous multi-functional composition for the purposes of performing the steps of deparaffinization, rehydration, antigen retrieval and endogenous enzyme blocking simultaneously optionally at an elevated temperature. These methods are alternatively conducted with use of a single aqueous multi-functional composition that contains a thermostable protease for the purpose of deparaffinization, rehydration, antigen retrieval and endogenous enzyme blocking at an elevated temperature.