Table 2. Protein spots of differential abundance identified in the liver of AA broiler and Big Bone chickens.^a.

Spot no.	Protein name	Accession no.(NCBInr)	Symbol ID	Theoretical Mr (kDa)/pI	Sequence coverage (%)	Matched/searched	Mascot score	Log 2ratio (treatment/control)
								2 weeks	4 weeks	6 weeks
Carbohydrate metabolism and energy production
4	NADP-dependent malic enzyme	gi|45383538	ME1	62.53/6.45	63	32/62	785	8.93
5	NADP-dependent malic enzyme	gi|45383538	ME1	62.53/6.45	50	16/37	331	8.65	8.85	8.74
7	malic enzyme	gi|45383538	ME1	62.53/6.45	33	10/28	142	9.86
10	sulfotransferase	gi|45384226	CHST3	36.33/5.89	68	22/56	739	8.50		8.17
11	ubiquinol—cytochrome c reductase	gi|50754375	UQCRFS1	53.41/6.58	6	2/5	58	9.38
14	alpha-enolase	gi|46048768	ENO1	47.62/6.17	26	8/25	320	8.38	6.82	8.25
16	sulfotransferase	gi|45384226	CHST3	36.33/5.89	30	3/10	115	7.65
17	sulfotransferase	gi|118088279	CHST3	36.79/5.50	8	1/4	62	9.79	9.01
18	phosphoglycolate phosphatase	gi|71894743	PGP	33.55/5.53	19	4/5	121	8.57
22	sepiapterin reductase	gi|50767570	SPR	29.28/5.82	45	6/13	635	8.42	8.00	8.82
23	phosphoglycerate mutase 1	gi|71895985	PGAM1	29.05/7.03	72	11/30	396	9.42
29	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial	gi|71895853	ETFDH	53.61/8.99	42	7/35	969	-8.19		-9.63
44	malate dehydrogenase, cytoplasmic	gi|57530355	MDH1	36.75/6.92	54	6/32	724	1.10
45	fructose 1,6-bisphosphatase	gi|50762393	FBP2	37.05/8.07	65	16/52	1132	1.02
47	voltage-dependent anion-selective channel protein 1	gi|76443696	VDAC1	30.74/6.85	32	2/15	295	-1.15
80	sorting and assembly machinery component 50 homolog	gi|118083116	SAMM50	52.47/5.99	30	2/17	540		7.37	8.84
83	galactose mutarotase (aldose 1-epimerase)	gi|118087781	GALM	38.18/6.19	18	1/6	166		7.53
84	alcohol dehydrogenase [NADP+]	gi|57529654	ADH5	37.34/7.66	35	11/17	168		7.90
85	L-lactate dehydrogenase B chain	gi|45383766	LDHB	36.69/7.07	40	10/13	249		8.73	9.06
87	ubiquinol-cytochrome c reductase hinge protein	gi|118094600	UQCRH	9.45/5.17	43	1/6	125		8.30	8.15
88	phosphoglucomutase-1	gi|84619526	PGM1	67.06/8.98	65	43/61	1142		1.16
89	fumarate hydratase, mitochondrial	gi|57530433	FH	54.49/9.20	49	27/31	1098		-1.08
98	NADP-dependent malic enzyme	gi/45383538	ME1	62.53/6.45	43	27/68	657		1.73
102	pyruvate carboxylase	gi|45383466	PCX	128.03/6.26	61	81/135	2199		-1.32
104	pyruvate carboxylase	gi|45383466	PCX	128.03/6.26	53	49/99	1099		-1.09
120	carbonic anhydrase II	gi|833606	CA2	28.82/6.51	41	8/12	218			7.31
121	phosphomannomutase 2	gi|71895479	PMM2	28.59/5.79	9	1/2	56			9.06
122	triosephosphate isomerase	gi|45382061	TPI1	26.83/6.71	55	6/14	105			8.70
123	triosephosphate isomerase	gi|45382061	TPI1	26.83/6.71	75	13/23	276			8.66
130	alpha-enolase	gi|46048768	ENO1	47.62/6.17	39	9/22	943			-8.76
132	malate dehydrogenase, cytoplasmic	gi|57530355	MDH1	36.75/6.92	27	1/11	237			-8.76
133	ubiquinol-cytochrome c reductase	gi|50754375	UQCRH	53.41/6.58	26	2/16	430			-9.99
144	L-lactate dehydrogenase A chain	gi|45384208	LDHA	36.78/7.75	36	6/15	271			1.14
145	alpha-enolase	gi|46048769	ENO1	47.62/6.17	49	15/33	644			1.35
Protein and amino acid metabolism
1	elongation factor 2	gi|45382453	EEF2	96.34/6.40	39	24/53	387	8.34
2	glycine dehydrogenase [decarboxylating], mitochondrial precursor	gi|45383510	GLDC	111.78/7.55	19	9/22	246	7.93
3	methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial	gi|57529595	MCCC1	78.88/6.51	17	3/14	95	6.33	6.75	7.20
8	cytosol aminopeptidase	gi|71897015	LAP3	56.92/8.38	27	7/14	239	10.50
21	guanidinoacetate N-methyltransferase	gi|118103242	GAMT	17.46/6.59	48	13/23	551	9.36
26	SH3 domain-binding glutamic acid-rich-like protein	gi|60302796	Q5F3C9	12.79/5.07	90	1/22	325	8.54	7.76	7.81
35	cathepsin B precursor	gi|46195455	CTSB	38.48/5.74	27	6/21	530	-9.02
43	glutamine synthetase	gi|45382781	GLUL	42.75/6.38	11	1/8	108	1.39
50	sarcosine dehydrogenase, mitochondrial	gi|363740469	SARDH	102.26/6.42	27	4/30	633	8.34	-7.10
51	dimethylglycine dehydrogenase, mitochondrial	gi|363744224	DMGDH	96.68/7.33	40	3/41	1091	7.93	-6.91
52	histidine ammonia-lyase	gi|45383354	HAL	73.54/6.17	31	3/26	590		-7.52
53	elongation factor 2	gi|45382453	EEF2	96.34/6.40	25	2/27	499		-7.73
54	glycine dehydrogenase [decarboxylating], mitochondrial precursor	gi|45383510	GLDC	113.26/7.55	23	7/21	122		-6.86
55	elongation factor 2	gi|45382453	EEF2	96.34/6.40	21	6/19	90		-7.63
56	ovoinhibitor precursor	gi|71895337	SPINK5	54.39/6.16	18	6/9	137		-7.53
57	S-adenosylmethionine synthase isoform type-1	gi|313760551	MAT1A	44.24/6.28	30	7/14	137		-7.73
58	fumarylacetoacetase (Fumarylacetoacetate hydrolase)	gi|50753071	FAA	46.80/7.31	43	18/49	259		-9.88
64	guanidinoacetate N-methyltransferase	gi|118103242	GAMT	17.46/6.59	35	4/ 12	249		-8.71
69	glutamine synthetase	gi|45382781	GLUL	42.75/6.38	29	6/15	171		-9.73
74	alanyl-tRNA synthetase, cytoplasmic	gi|57524852	AARS	102.00/5.68	38	25/50	623		8.85
78	trifunctional purine biosynthetic protein adenosine-3	gi|47825387	GART	107.56/7.51	26	6/26	132		7.07
81	glutamine synthetase	gi|45382781	GLUL	42.75/6.38	40	8/24	171		9.64
90	4-hydroxyphenylpyruvate dioxygenase	gi|363739843	HPD	45.05/6.41	59	5/27	374		-1.43
93	eukaryotic translation initiation factor 3 subunit I	gi|256419027	EIF3I	36.87/5.38	32	2/13	338		1.02
94	3-hydroxyanthranilate 3,4-dioxygenase	gi|118087959	HAAO	33.74/6.27	18	1/4	131		-1.82
95	guanidinoacetate N-methyltransferase	gi|118103242	GAMT	17.46/6.59	44	7/18	370		1.17
97	pterin-4-alpha-carbinolamine dehydratase	gi|45382483	PCBD1	12.05/6.04	69	4/20	415		-1.36
103	S-adenosylmethionine synthase isoform type-1	gi|313760551	MAT1A	44.24/6.28	55	28/57	664		-2.67
105	S-adenosylmethionine synthase isoform type-1	gi|313760551	MAT1A	44.24/6.28	10	3/5	94		1.11
108	lysyl-tRNA synthetase	gi|71895483	KARS	68.33/5.89	36	3/28	809			6.775
110	phenylalanine-4-hydroxylase	gi|47604920	PAH	51.51/6.49	53	8/42	1247			8.80
139	cytosolic non-specific dipeptidase	gi|57530409	CNDP2	53.39/5.71	39	4/21	690			1.66
140	aldehyde dehydrogenase 9 family, member A1	gi|118094103	ALDH9A1	57.00/7.81	65	34/53	1215			1.13
Nucleotide metabolism
19	adenosine 5-diphosphosugar pyrophosphatase	gi|118081976	GMPS	35.43/6.36	28	9/15	312	8.78		8.38
39	adenosine kinase	gi|57529848	ADK	40.46/6.06	20	3/8	96	-1.21
40	dihydropyrimidinase	gi|118087274	DPYS	69.50/6.42	19	4/16	108	1.48
61	adenosine 5-diphosphosugar pyrophosphatase	gi|118081976	GMPS	35.43/6.36	22	6/12	504		-9.03
62	ribokinase	gi|118088003	RBKS	36.72/5.39	22	3/7	378		-8.01
99	ribose-phosphate pyrophosphokinase 2	gi|57525515	PRPS2	36.04/6.37	58	31/53	865		-1.35
125	nucleoside diphosphate kinase	gi|45384260	NME5	17.45/7.72	79	16/36	264			8.59
128	nucleolar protein B23/No38	gi|212456	NPM1	10.77/4.38	57	1/6	205			-8.94
135	p32 subunit of splicing factor SF2	gi|5509946	C1QBP	23.78/4.41	23	2/5	238			1.14
141	thiosulfate sulfurtransferase	gi|268370289	TST	33.09/6.80	52	22/34	503			-1.20
143	nucleoside diphosphate kinase	gi|2827446	NME5	17.54/7.11	66	32/45	1004			-1.33
Fatty acid metabolism
27	fatty acid-binding protein	gi|45384320	FABP7	15.03/5.61	56	2/6	85	8.68	8.52	9.24
30	long-chain specific acyl-CoA dehydrogenase, mitochondrial	gi|57529797	ACADL	48.26/8.34	32	10/17	159	-10.58
33	dodecenoyl-Coenzyme A delta isomerase	gi|118098151	ECI1	34.56/9.30	33	18/32	379	-8.52		-7.68
42	3-hydroxy-3-methylglutaryl-coenzyme A synthase	gi|118094097	HMGCS1	52.98/6.57	31	11/26	195	1.69
48	fatty acid-binding protein	gi|45384320	FABP7	15.03/5.61	71	9/16	276	2.16
65	sulfotransferase 1B	gi|118090275	SULT1B1	32.01/6.00	48	1/16	351		-6.71
70	phosphatidylethanolamine-binding protein 1	gi|310772215	PEBP1	21.12/6.96	66	4/17	419		8.23
82	3-ketoacyl-CoA thiolase, mitochondrial	gi|57529492	HADHA	42.17/8.02	18	3/7	89		10.03
111	3-hydroxy-3-methylglutaryl-coenzyme A synthase	gi|118094097	HMGCS1	52.98/6.57	30	16/25	383			10.33
112	3-hydroxy-3-methylglutaryl-coenzyme A synthase	gi|118094097	HMGCS1	52.98/6.57	32	15/27	462			9.48
114	SEC14-like 2	gi|50756739	SEC14L3	46.94/6.73	60	24/43	520			10.40
116	phosphatidylinositol transfer protein beta isoform	gi|86129444	PITPNB	30.86/5.63	71	12/27	224			7.01
Antioxidants
6	epoxide hydrolase 2	gi|45384320	EPHX2	63.72/5.89	45	17/29	448	8.37
46	peroxiredoxin-6	gi|57529797	PRDX6	25.08/5.72	58	4/35	793	1.00
68	thioredoxin	gi|118098151	TXNRD1	11.98/5.10	49	1/12	285		-8.97
76	serum albumin precursor	gi|118094097	ALB	71.87/5.51	26	1/14	362		8.70
77	serum albumin precursor	gi|45384320	ALB	71.87/5.51	48	18/31	455		9.23	9.39
86	glutathione S-transferase 2	gi|118090275	GSTM2	26.05/6.85	80	9/33	746		8.86
118	thioredoxin-like protein	gi|310772215	TXNL1	32.73/4.94	40	5/18	131			8.55
124	peroxiredoxin-1 isoform 1	gi|57529492	PRDX1	22.53/8.24	40	2/15	390			8.19
126	thioredoxin	gi|118094097	TXNRD1	11.98/5.10	49	2/6	61			8.82
127	thioredoxin	gi|118094097	TXNRD1	11.98/5.10	32	1/3	67			8.22
136	protein disulfide-isomerase A3 precursor	gi|50756739	PDIA3	56.55/5.76	32	2/16	507			2.25
142	retinal dehydrogenase 1	gi|86129444	ALDH1A1	56.40/7.49	51	24/35	615			1.30
Cell structure
12	alpha-tropomyosin 2	gi|27465053	TPM1	32.85/4.65	40	8/17	164	7.73
15	protein syndesmos	gi|45382147	NUDT16L1	33.98/5.74	48	12/33	277	7.24
28	lamin-A	gi|45384214	LMNA	73.35/6.50	14	1/11	373	-8.00
36	mitochondrial inner membrane protein	gi|57530041	IMMT	79.54/5.72	31	2/31	745	1.24
37	mitochondrial inner membrane protein	gi|57530041	IMMT	79.54/5.72	24	2/28	479	1.02
38	desmin	gi|2959450	DES	51.69/5.30	53	12/35	272	1.46
63	F-actin-capping protein subunit alpha-1	gi|45382905	CAPZA1	33.11/5.43	53	3/15	499		-8.42
66	translationally-controlled tumor protein homolog	gi|45382329	TPT1	19.69/4.90	90	12/23	372		-7.95
67	glia maturation factor beta	gi|71894963	GMFB	16.88/5.19	28	1/4	144		-8.10
71	translationally-controlled tumor protein homolog	gi|45382329	TPT1	19.69/4.90	50	8/24	190		8.19
75	mitochondrial inner membrane protein	gi|57530041	IMMT	79.54/5.72	40	15/36	1360		6.91
79	lamin-A	gi|45384214	LMNA	73.35/6.50	58	24/44	512		7.76
92	alpha-tropomyosin	gi|211109	TPM1	32.81/4.75	15	2/4	177		1.61
109	coronin-1C	gi|86129440	CORO1C	53.74/6.22	39	20/34	244			6.78
Protein folding
49	10 kDa heat shock protein, mitochondrial	gi|45384204	HSPE1	11.13/8.68	82	1/20	438	-1.5892
59	cyclophilin	gi|118089782	PPIA	39.80/5.61	27	4/16	95		-7.12
106	T-complex protein 1 subunit alpha	gi|57530301	TCP1	61.06/5.66	34	9/18	181			8.83
107	T-complex protein 1 subunit alpha	gi|57530301	TCP1	61.06/5.66	43	11/32	1071			9.28
131	hsc70-interacting protein	gi|71896903	ST13	40.36/5.07	36	8/22	646			-6.97
134	peptidylprolyl isomerase A	gi|261490820	PPIA	18.08/8.29	67	9/28	194			-9.24
Transporter
24	heme-binding protein 1	gi|71896913	HEBP1	21.26/5.76	34	3/7	88	7.85
31	chloride intracellular channel protein 2	gi|71895359	CLIC2	28.46/5.39	42	4/19	492	-8.06
119	coatomer subunit epsilon	gi|57530593	COPE	34.52/4.99	35	4/31	371			9.29
129	clathrin light chain A	gi|86129544	CLTA	23.86/4.42	40	6/12	189			-8.33
137	transitional endoplasmic reticulum ATPase	gi|113206112	VCP	89.95/5.14	54	21/60	496			1.04
Unknown function
9	MGC82288 protein	gi|50729534		50.12/6.35	44	14/23	264	10.66
13	protein PRRC1	gi|71894751	PRRC1	45.84/5.52	10	2/4	80	7.89
20	hypothetical protein RCJMB04_5n23	gi|53129586	TPM3	28.80/4.69	47	12/24	305	9.33
25	hypothetical protein	gi|118083300		10.04/4.17	14	2/4	58	9.29
32	ES1 protein homolog, mitochondrial	gi|71895261	C1H21orf33	27.87/8.54	46	17/45	213	-9.54
34	hypothetical protein	gi|118098539		28.31/7.63	42	3/28	647	-8.71
41	hypothetical protein RCJMB04_1j22	gi|53127216		60.28/8.09	51	20/40	412	1.23
60	hypothetical protein	gi|118087385		44.65/5.82	16	4/6	185		-8.23
72	sorcin	gi|124249424	SRI	22.21/5.37	55	9/17	216		8.01
73	sorcin	gi|124249425	SRI	22.21/5.37	24	2/5	51		8.76
91	hypothetical protein RCJMB04_1g3	gi|53126716		33.27/5.60	46	5/19	579		-1.06
96	hypothetical protein	gi|50800573		11.84/4.42	66	8/11	348		1.06
100	LOC495096 protein isoform 3	gi|50734923		28.44/6.45	34	2/13	297		1.26
101	thyroid hormone responsive spot 14 beta 2	gi|45826439	THRSPB	14.52/5.10	20	1/3	98		1.13
113	hypothetical protein	gi|50728520		48.21/6.29	42	15/30	430			10.66
115	LOC495029 protein	gi|118098511		45.06/6.55	63	26/45	716			9.86
117	MGC83663 protein	gi|118093845		51.57/6.30	30	6/18	730			8.70
138	MGC82230 protein	gi|50756617		43.26/5.76	61	11/33	1036			1.03

^a Spot no. corresponds to the number of protein spots in Fig 1. Protein name is given when proteins were identified by LC-Chip ESI-QTOF MS. Accession no. is the unique number given to mark the entry of a protein in the database NCBInr. Theoretical molecular weight (Mr) and isoelectric point (pI) of the identified proteins are retrieved from the protein database of NCBInr (S1 Table). Sequence coverage is the ratio of the number of amino acids in every peptide that matches with the mass spectrum divided by the total number of amino acids in the protein sequence. Matched peptide is the number of paring an experimental fragmentation spectrum to a theoretical segment of protein and searched peptide is the total searched peptide. Mascot scores are derived from ion scores as a non-probabilistic basis for ranking protein hits.