Table 3. Acetylated proteins from electron transport chain complexes with increased in acetylation in the CypD-/- mitochondria.

#	Accession	Protein ID	Protein Name	# of acetylated peptides
1	AT5F1	Q9CQQ7	ATP synthase subunit b	4
2	ATP5H	Q9DCX2	ATP synthase subunit d	6
3	ATP5J	P97450	ATP synthase-coupling factor 6	4
4	ATP5L	Q9CPQ8	ATP synthase subunit g	3
5	ATP8	P03930	ATP synthase protein 8	2
6	ATPB	P56480	ATP synthase subunit beta	3
7	ATPG	Q91VR2	ATP synthase subunit gamma	1
8	ATPK	Q03265	ATP synthase subunit f	1
9	ATPO	Q9DB20	ATP synthase subunit O	4
10	COX5B	P19536	Cytochrome c oxidase subunit 5B	2
11	COX7C	P17665	Cytochrome c oxidase subunit 7C	1
12	CX7A1	P56392	Cytochrome c oxidase subunit 7A1	1
13	CYC	P62897	Cytochrome c, somatic	1
14	NDUA5	Q9CPP6	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	2
15	NDUAA	Q99LC3	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10	1
16	NDUAD	Q9ERS2	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	1
17	NDUV1	Q91YT0	NADH dehydrogenase [ubiquinone] flavoprotein 1	2
18	QCR1	Q9CZ13	Cytochrome b-c1 complex subunit 1	1
19	QCR7	Q9D855	Cytochrome b-c1 complex subunit 7	3

Relative quantification of acetylated peptides were performed using QUOIL (QUantification withOut Isotope Labeling), an in-house software program designed as a label-free approach to peptide quantification by LC-MS/MS. The following criteria were used to determine the effect of ablation of CypD on acetylated peptides: at least greater than 20% change and p <0.05 vs. WT samples. Accession numbers are from the SWISSPROT/Uniprot database.