Prion protein allotype profiling by mass spectrometry*

Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative pathologies characterized by the formation in the central nervous system of the amyloid protein PrPSc, which derives from a cellular precursor called PrPc. Epidemiological and laboratory studies have shown that in species where the PrPc gene is polymorphic, the genotype composition is an important factor for the development of the disease. Identification of PrPSc allotypes accumulated in the brain during the disease proved valuable to investigate whether these polymorphisms are critical for the pathological conversion. These analyses are complicated by the heterogeneity and the insolubility of the prion amyloid extracted from affected brains, which have been obviated by extensive digestion of extracted fractions and analysis of peptide fragment composition. We have developed an optimized protocol of liquid chromatography/mass spectrometry (LC/MS) that can reliably map PrP peptides in digested fractions with a low PrPSc/contaminants ratio. This approach has been successfully applied to the analysis of amyloidogenesis in experimentally infected PrP-heterozygous laboratory animals.