Table 1. PrP peptides found in MACS + Percoll purified mitochondria by high resolution LC-MS/MS.

Mouse line	PrP peptidea	Residues	Spectral Countsb	Massc	m/zd	ppme
C57BL/6	YPGQGSPGGNR	38–48	1	1088.5	545.255	−3.4
	VVEQMCVTQYQK	208–219	7	1527.706	764.858	−2.8
	ESQAYYDGR	220–228	2	1087.457	544.735	−2.3
RM	PGGWNTGGSR	28–37	3	987.4522	494.733	−0.6
	YPGQGSPGGNR	38–48	77	1088.5	545.256	−2.2
	PIIHFGSDYEDR	137–148	22	1447.673	483.564	−2.7
	YPNQVYYR	157–164	10	1101.524	551.768	−2.6
	GENFTETDVK	195–204	5	1138.514	570.262	−3.8
	VVEQMCITQYER	209–220	13	1570.712	786.360	−3.7
	ESQAYYQR	221–228	27	1043.467	522.740	−1.4
Tg3F4	PGGWNTGGSR	28–37	1	987.4522	494.734	1.5
	YPGQGSPGGNR.Y	38–48	18	1088.5	545.257	−0.2
	HMAGAAAAGAVVGGLGGYMLGSAMSR	110–135	1	2394.124	799.048	−0.7
	PMIHFGNDWEDR	136–147	3	1515.657	506.225	−1.7
	PMIHFGNDWEDR	136–147	3	1531.651	511.557	−0.9
	YPNQVYYR	156–163	5	1101.524	551.769	−1.2
	GENFTETDVK	194–203	11	1138.514	570.264	0
	VVEQMCVTQYQK	208–219	19	1511.711	756.862	−1.1
	VVEQMCVTQYQK	208–219	17	1527.706	764.86	0
	ESQAYYDGR	220–228	16	1087.457	544.736	0.1
Tg44	GENFTETDVK	194–203	4	1138.514	570.265	0.9
	VVEQMCVTQYQK	209–219	1	1511.711	756.863	−0.1
	VVEQMCVTQYQK	208–219	1	1527.706	764.86	−0.1
	ESQAYYDGR	220–228	3	1087.457	544.736	0

^aSamples were analyzed using a high resolution Fusion Orbitrap mass spectrometer. Peptides with unique observed mass over charge (m/z) values identified by PEAKS DB search engine with a 0.1% FDR and a −10 logP threshold value of >30. Oxidized methionine residues are shown in bold.

^bThe number of assigned tandem mass spectra or spectral counts associated with that peptide.

^cThe calculated monoisotopic mass of the intact peptide.

^dExperimentally observed m/z value of the precursor ion.

^eCalculated error in parts per million of the experimentally observed monoisotopic peptide m/z value.