LC-MS/MS identification of proteins associated with the mock-SAF preparations of uninfected mouse brains.

The SAF preparation procedure was carried out on both uninfected wildtype mouse brains (WT) or uninfected knockout mouse brains (PrP−/−). Four brains for each mouse strain were homogenised prior to detergent extraction and differential centrifugation to isolate protein species. Precipitated proteins were reduced and alkylated in 6 M guanidine hydrochloride then digested with typsin. Tryptic peptides were separated and detected by online LC-MS/MS and the data searched against the IPI murine database by use of the Mascot search algorithm. Proteins that were below the level of significance or for which only single peptides were identified are not reported.