Transmissible spongiform encephalopathies (TSEs) or prion diseases are characterized by the accumulation of an aggregated isoform of the prion protein (PrP). This pathological isoform, termed PrPSc, appears to be the primary component of the TSE infectious agent or prion. However, it is not clear to what extent other protein co-factors may be involved in TSE pathogenesis or whether there are PrPSc-associated proteins which help to determine TSE strain-specific disease phenotypes. We enriched PrPSc from the brains of mice infected with either 22L or Chandler TSE strains and examined the protein content of these samples using nanospray liquid chromatography-tandem mass spectrometry. These samples were compared to “mock” PrPSc preparations from uninfected brains. Prion protein was the major component of the infected samples and ferritin was the most abundant impurity. By contrast, mock enrichments contained no detectable prion protein but did contain a significant amount of ferritin. Of the total proteins identified, 32% were found in both mock and infected samples. The similarities between PrPSc samples from 22L and Chandler TSE strains suggest that the non-PrPSc protein components found in standard enrichment protocols are not strain-specific.