Table 6.

Carbonylated proteins identified in liver. Protein Spot No. refers to the numbered spots in 2-D gels shown in Figure 3. Green arrows indicate decrease in protein carbonylation. Red arrows indicate increase in protein carbonylation. The oxidative levels of other proteins were not affected by the dietary interventions. * Pb.05; ** Pb.01.

Spot No.	Identification	Gene Name	UniProtKB Code	Coverage (%)	Peptides	Unique	Avg. Mass	STD	HFHS	HFHS + ω3	HFHS/STD	HFHS + ω3/HFHS	Function
1	Carbamoyl-phosphate synthase [ammonia] mitochondrial	Cps1	P07756|CPSM	81	395	390	164,579	0.39 (0.20)	0.76 (0.10)	0.44 (0.06)	**	**	Urea cycle
2	Pyruvate carboxylase mitochondrial	Pc	P52873|PYC	40	63	63	129,777	1.01 (0.27)	0.99 (0.14)	0.61 (0.02)		**	Gluconeogenesis Lipid biosynthesis Lipid metabolism
3	Dimethylglycine dehydrogenase mitochondrial	Dmgdh	Q63342|M2GD	61	100	100	96,047	0.44 (0.14)	0.67 (0.10)	0.60 (0.08)	*		Amino-acid synthesis
4	Serum albumin	Alb	P02770|ALBU	83	149	149	68,731	0.88 (0.18)	1.49 (0.04)	0.91 (0.07)	**	**	Protein metabolic and post-translational modification Fatty acids transport
5	Transketolase	Tkt	P50137|TKT	51	37	37	67,644	0.80 (0.21)	0.85 (0.12)	0.53 (0.08)		**	Glyceraldehyde-3-phosphate Biosynthetic process pentose-phosphate
6	Catalase	Cat	P04762|CATA	85	149	149	59,757	0.64 (0.16)	0.91 (0.01)	0.52 (0.00)	**	**	Hydrogen peroxide
7	Protein disulfide-isomerase A3	Pdia3	P11598|PDIA3	60	43	43	56,623	1.28 (0.19)	0.77 (0.20)	1.28 (0.03)	**	**	Cell redox homeostasis Protein folding
8	60 kDa heat shock protein mitochondrial	Hspd1	P63039|CH60	66	76	76	60,956	0.59 (0.15)	0.36 (0.03)	0.24 (0.06)	*	*	Host-virus interaction Protein folding
9	Glycerol kinase	Gk	Q63060|GLPK	47	29	26	57,477	0.62 (0.06)	0.53 (0.13)	0.32 (0.06)		*	Glycerol metabolism Glycolysis
10	Formimidoyltransferase-cyclodeaminase	Ftcd	O88618|FTCD	48	35	35	58,914	0.54 (0.05)	0.43 (0.13)	0.29 (0.07)	*		Histidine metabolism
11	Aldehyde dehydrogenase mitochondrial	Aldh2	P11884|ALDH2	82	135	120	56,488	0.59 (0.03)	0.85 (0.05)	0.65 (0.03)	**	**	Alcohol metabolic process, Ethanol oxidation Carbohydrate metabolic process
12	Phenylalanine-4-hydroxylase	Pah	P04176|PH4H	54	40	39	51,822	1.23 (0.22)	1.19 (0.14)	0.82 (0.05)		**	Amino-acid synthesis
13	Methylmalonate-semialdehyde dehydrogenase [acylating] mitochondrial	Aldh6a1	Q02253|MMSA	82	110	110	57,808	1.14 (0.58)	1.00 (0.45)	1.03 (0.08)
	Dihydrolipoyl dehydrogenase mitochondrial	Dld	Q6P6R2|DLDH	67	50	50	54,038
14	Alpha-aminoadipic semialdehyde dehydrogenase	Aldh7a1	Q64057|AL7A1	64	101	101	58,749	1.00 (0.08)	1.08 (0.21)	0.74 (0.02)		*	Cellular aldehyde metabolic Glutamate biosynthetic process Positive regulation of insulin secretion Tricarboxylic acid metabolic process
	Glutamate dehydrogenase 1 mitochondrial	Glud1	P10860|DHE3	76	150	150	61,416
15	4-aminobutyrate aminotransferase mitochondrial	Abat	P50554|GABT	40	20	20	56,456	1.26 (0.46)	0.93 (0.28)	0.95 (0.38)
16	Hydroxymethylglutaryl-CoA synthase mitochondrial	Hmgcs2	P22791|HMCS2	61	76	76	56,912	0.95 (0.37)	1.01 (0.41)	1.02 (0.12)
17	6-phosphogluconate dehydrogenase decarboxylating	Pgd	P85968|6PGD	75	54	54	53,236	0.71 (0.11)	0.63 (0.13)	0.59 (0.17)
18	Actin cytoplasmic 1	Actb	P60711|ACTB	85	104	10	41,737	1.15 (0.31)	1.19 (0.19)	0.67 (0.32)		*	Cell motility Membrane organization
19	Isocitrate dehydrogenase [NADP] cytoplasmic	Idh1	P41562|IDHC	61	45	41	46,734	0.31 (0.16)	0.40 (0.16)	0.24 (0.04)
	Beta-ureidopropionase	Upb1	Q03248|BUP1	51	54	54	44,042
	Long-chain specific acyl-CoA dehydrogenase mitochondrial	Acadl	P15650|ACADL	69	67	67	47,873
20	Fumarylacetoacetase	Fah	P25093|FAAA	68	64	64	45,976	0.48 (0.03)	0.75 (0.10)	0.50 (0.08)	**	*	Amino-acid synthesis
21	Argininosuccinate synthase	Ass1	P09034|ASSY	76	101	101	46,496	1.00 (0.16)	1.87 (0.03)	0.90 (0.11)	**	**	Urea cycle Amino-acid synthesis
22	Phosphoglycerate kinase 1	Pgk1	P16617|PGK1	77	62	25	44,538	0.52 (0.11)	0.89 (0.04)	0.59 (0.14)	**	**	Glycolysis Fatty acid metabolism Lipid metabolism
	3-ketoacyl-CoA thiolase mitochondrial	Acaa2	P13437|THIM	69	33	33	41,871
23	Alcohol dehydrogenase 1	Adh1	P06757|ADH1	80	123	117	39,645	1.09 (0.13)	1.16 (0.26)	0.59 (0.14)		*	Ethanol oxidation Response to sex hormones Retinoid metabolic process
24	Fructose-bisphosphate aldolase B	Aldob	P00884|ALDOB	90	150	146	39,618	0.91 (0.06)	0.97 (0.04)	0.62 (0.08)	*	**	Glycolysis
25	3-oxo-5-beta-steroid 4-dehydrogenase	Akr1d1	P31210|AK1D1	77	54	50	37,378	0.38 (0.05)	0.32 (0.03)	0.19 (0.05)	*	**	Bile acid catabolism Lipid metabolism Urea cycle
	Ornithine carbamoyltransferase mitochondrial	Otc	P00481|OTC	67	72	72	39,886
26	Regucalcin	Rgn	Q03336|RGN	61	76	76	33,390	0.53 (0.11)	0.72 (0.19)	1.06 (0.27)	*	**	Ascorbate biosynthesis
27	Glyceraldehyde-3-phosphate dehydrogenase	Gapdh	P04797|G3P	53	32	10	35,828	0.59 (0.21)	0.55 (0.14)	0.75 (0.29)	**
28	Thiosulfate sulfurtransferase	Tst	P24329|THTR	50	41	41	33,407	0.50 (0.04)	0.57 (0.10)	0.63 (0.06)
29	Malate dehydrogenase cytoplasmic	Mdh1	O88989|MDHC	66	45	45	36,483	0.41 (0.15)	0.77 (0.09)	0.41 (0.12)	**	**	Tricarboxylic acid cycle
30	3-hydroxyanthranilate 3 4-dioxygenase	Haao	P46953|3HAO	45	21	21	32,582	0.72 (0.42)	0.81 (0.03)	0.51 (0.14)		**	Pyridine nucleotide biosynthesis
31	Omega-amidase NIT2	Nit2	Q497B0|NIT2	33	11	11	30,701	1.89 (0.39)	1.95 (0.30)	1.31 (0.47)		*	Amino-acid synthesis
32	Carbonic anhydrase 3	Ca3	P14141|CAH3	87	74	73	29,431	0.56 (0.12)	0.83 (0.17)	0.43 (0.09)	*	*	Response to oxidative stress
33	Glutathione S-transferase Mu 2	Gstm2	P08010|GSTM2	67	23	15	25,703	1.35 (0.37)	1.98 (0.12)	1.17 (0.31)	**	**	Cellular detoxification of nitrogen compound Glutathione metabolic process
34	Glutathione S-transferase Mu 2	Gstm2	P08010|GSTM2	84	62	43	25,703	0.95 (0.03)	1.35 (0.08)	0.93 (0.01)	**	**	Cellular detoxification of nitrogen compound Glutathione metabolic process
35	Glutathione S-transferase Mu 2	Gstm2	P08010|GSTM2	72	28	18	25,703	0.72 (0.19)	2.25 (0.16)	1.14 (0.07)	**	**	Cellular detoxification of nitrogen compound Glutathione metabolic process
36	3-hydroxyacyl-CoA dehydrogenase type-2	Hsd17b10	O70351|HCD2	80	38	38	27,246	0.56 (0.46)	0.98 (0.12)	0.62 (0.26)	*	*	tRNA processing