A cleaning composition includes a detectable substance which is relatively stable in the cleaning composition, for indicating whether the cleaning composition has been thoroughly removed from a vessel following a cleaning process. For pharmaceutical applications, the detectable substance is preferably a low-foaming surfactant that is detectable by high performance liquid chromatography at concentrations of around 10 ppm, or less. The surfactant is thus detectable in the same analytical procedure as are traces of pharmaceutical residues which have not been removed from the vessel. The analytical procedure is used to develop a cleaning protocol for future cleaning processes by determining the number of rinses needed for reducing the surfactant, and hence the cleaning product, and also the pharmaceutical residues, in the rinse water to predetermined acceptable levels.