Prion diseases are associated with the accumulation of an abnormal isoform of host-encoded prion protein (PrPSc). A number of prion strains can be distinguished by "glycotyping" analysis of the respective deposited PrPSc compound. In this study, the long-term proteinase It resistance, the molecular mass, and the localization of PrPSc deposits derived from conventional and transgenic mice inoculated with 11 different BSE and scrapie strains or isolates were examined. Differences were found in the long-term proteinase It resistance (50 mu g/ml at 37 degrees C) of PrPSc. For example, scrapie strain Chandler or PrPSc derived from field BSE isolates were destroyed after 6 hr of exposure, whereas PrPSc of strains 87V and ME7 and of the Hessenl isolate were extremely resistant to proteolytic cleavage. Nonglycosylated, proteinase It-treated PrPSc of BSE isolates and of scrapie strain 87V exhibited a 1-2 kD lower molecular mass than PrPSc derived from all other scrapie strains and isolates. With the exception of strain 87V, PrPSc was generally deposited in the cerebrum, cerebellum, and brain stem of different mouse lines at comparable levels. Long-term proteinase resistance, molecular mass, and the analysis of PrPSc deposition therefore provide useful criteria in discriminating prion strains and isolates (e.g., BSE and 87V) that are otherwise indistinguishable by the PrPSc "glycotyping" technique.