Table 2. Acetylated proteins with decreased acetylation in the CypD^−/− mitochondria.

#	Protein	Peptide	WT	SE	KO	SE	KO/WT	p
1	ADT1 MOUSE (P48962) ADP/ATP translocase 1	gDQALSFLADFLAGGIAAAVSK	0.978	0.022	0.603	0.014	0.616	0.00
2	ANXA2_MOUSE (P07356) Annexin A2	SVcHLQAVFER	0.910	0.092	0.565	0.021	0.621	0.02
3	CISY_MOUSE (Q9CZU6) Citrate synthase	SMSTDGLMAFVDSK	0.973	0.020	0.612	0.018	0.629	0.00
4	DHSA_MOUSE (Q8K2B3) Succinate dehydrogenase [ubiquinone] flavoprotein subunit	AAFGLSEAGFNTAcLTALFPTR	0.965	0.128	0.372	0.145	0.386	0.04
5	KCRS_MOUSE (Q6P8J7) Creatine kinase S-type	YYALSEMTEQDQQR	0.950	0.116	0.480	0.018	0.505	0.02
6	SUCA_MOUSE (Q9WUM5) Succinyl-CoA ligase [GDP-forming] subunit alpha	NTkIIcQGFTGK	0.853	0.073	0.530	0.048	0.621	0.02
		HLGLPVFNTVAEAK	0.829	0.092	0.564	0.012	0.681	0.05
7	THIL_MOUSE (Q8QZT1) Acetyl-CoA acetyltransferase	VLkYAGLK	0.955	0.025	0.459	0.178	0.481	0.05
8	VDAC1_MOUSE (Q60932) Voltage-dependent anion-selective channel protein 1	LTFDSSFSPNTGAK	0.923	0.041	0.658	0.032	0.713	0.02
9	VDAC2_MOUSE (Q60930) Voltage-dependent anion-selective channel protein 2	YkWcEYGLTFTEK	1.035	0.021	0.717	0.080	0.693	0.02
10	VDAC3_MOUSE (Q60931) Voltage-dependent anion-selective channel protein 3	cNTPTYcDLGAAAK	0.992	0.068	0.715	0.053	0.720	0.03

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 chronic or acute inhibition 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. The acetylated lysine residue is in bold and italicized. SE, standard error; p, p-value.