. 2013 Mar 19;8(3):e59353. doi: 10.1371/journal.pone.0059353

Table 2. Annotation of differentially expressed proteins identified in the endosperm and embryo of the three maize hybrids during the linear phase of grain filling.

Hybrid	Spot no.^a	Accession no.^b	Protein name [Zea mays]^c	Function^d	M _r gel/M _r predicted^e	pI gel/pI predicted^f	Peptide count^g	Total ion score^h	Total ion score C.I. (%)ⁱ	Score^j	Coverage (%)^k	P-value^l
Zhengdan 958	1	gi\|226503896	elongation factor 1-delta 1	Protein synthesis	40400/24951	4.2/4.4	1	64.54	100	65	4	8.00E−65
	2	gi\|257673482	general regulatory factor1	Protein destination	40100/29757	4.5/4.8	3	91.88	100	92	18	2.20E−133
	3	gi\|254256262	pyruvate, orthophosphate dikinase1	C metabolism	78700/106168	5.3/6.1	3	67.51	100	68	3	0.00E+00
	4	gi\|162459370	glutamine synthetase2	Energy	57200/40462	5.8/5.6	10	108	100	169	38	3.50E−169
	5	gi\|195634941	sarcosine oxidase	Amino acid metabolism	62500/44129	6.0/5.8	4	97.39	100	97	11	6.00E−115
	6	gi\|219895497	IAA-glu synthetase	Secondary compound metabolism	63100/50135	6.1/5.8	3	150.42	100	150	7	1.40E−81
	7	gi\|194701792	cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC2	Glycolysis	52300/36632	6.2/6.4	5	151.97	100	152	21	1.20E−146
	8	gi\|257696234	APx1 - Cytosolic Ascorbate Peroxidase	Defense	31100/33693	5.8/8.9	2	50.64	99.97	51	8	3.30E−114
	9	gi\|257696218	APx1 - Cytosolic Ascorbate Peroxidase	Defense	31100/27509	5.6/5.7	10	169	100	169	59	2.30E−113
	10	gi\|195639126	fructokinase-2	Energy	52600/35954	5.5/5.3	4	158.7	100	159	12	1.30E−121
	11	gi\|227308398	sorbitol dehydrogenase homolog1	Ionic homeostasis	40000/39747	6.0/6.3	4	146.44	100	146	14	1.80E−138
	12	gi\|219906911	glycine-rich RNA binding protein	Protein synthesis	12100/15532	6.0/6.1	2	46.69	99.94	47	15	7.20E−32
	13	gi\|195618512	eukaryotic translation initiation factor 5A	Protein synthesis	18300/17713	5.8/5.6	2	43.39	99.83	43	13	7.30E−71
	14	gi\|195622856	nucleoside diphosphate kinase 1	Energy	13400/16530	6.1/6.3	2	79.84	100	80	16	4.80E−67
	15	gi\|257643482	APx1 - Cytosolic Ascorbate Peroxidase	Defense	32100/39482	5.9/7.1	2	33.38	98.63	33	9	2.30E−113
	16	gi\|238013894	uncharacterized LOC100502283	Cellular communication/signal transduction	34500/25665	6.0/5.9	3	74.98	100	75	19	1.40E−85
	17	gi\|259703147	triosephosphate isomerase	Glycolysis	30900/27236	5.7/5.5	4	128.27	100	128	18	5.30E−100
Nongda 108	18	gi\|195605696	elongation factor 1-delta 1	Protein synthesis	4040/24977	4.2/4.4	2	46.69	99.89	47	6	3.00E−65
	19	gi\|262359935	general regulatory factor1	Protein destination	40100/29757	4.5/4.8	4	75.15	100	75	22	2.20E−133
	20	gi\|37932483	glyoxalase I	Defense	41300/32450	5.8/5.6	3	90.49	100	90	11	1.10E−115
	21	gi\|22190	protein b-32	Protein destination	45500/33467	6.0/6.0	3	147.48	100	147	12	5.90E−02
	22	gi\|194708718	LOC100274593	Defense	19000/17815	5.6/5.7	4	75.3	99.66	75	34	2.10E−43
	23	gi\|195605740	eukaryotic translation initiation factor 5A	Protein synthesis	18300/17713	5.8/5.6	5	51.62	99.98	52	13	7.30E−71
	24	gi\|219888685	glycine-rich RNA binding protein	Protein synthesis	134000/14642	6.1/5.7	2	128	100	128	82	7.40E−32
	25	gi\|194701792	cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC2	Glycolysis	52400/36632	6.5/6.4	7	72.8	100	73	17	1.20E−146
	26	gi\|238013894	uncharacterized LOC100502283	Cellular communication/signal transduction	34500/25665	6.0/5.9	4	69.04	100	69	19	1.40E−85
	27	gi\|195605636	triose-phosphate isomerase, cytosolic	Glycolysis	31000/27278	5.7/5.5	3	140.42	100	140	18	5.20E−100
Pioneer 335	28	gi\|194699380	elongation factor 1-delta 1	Protein synthesis	40400/24951	4.2/4.4	4	77.24	100	77	10	8.00E−65
	29	gi\|257710933	general regulatory factor1	Protein destination	40100/29724	4.5/4.8	2	61.28	100	61	18	2.00E−132
	30	gi\|226496099	hypothetical protein LOC100274355	Cellular communication/signal transduction	62100/47785	6.0/6.0	3	53.37	99.98	53	6	2.90E−122
	31	gi\|226498420	hypothetical protein LOC100273405	Ionic homeostasis	57200/48681	6.0/6.1	2	63.1	100	63	9	2.80E−181
	32	gi\|257645318	malate dehydrogenase5	Tricarboxylic acid cycle	51300/35909	5.9/5.8	3	243	100	243	69	8.70E−157
	33	gi\|257696218	APx1 - Cytosolic Ascorbate Peroxidase	Defense	32100/27509	5.9/5.7	2	204	100	204	63	2.40E−113
	34	gi\|238013894	uncharacterized LOC100502283	Cellular communication/signal transduction	34500/25665	6.1/5.9	2	28.47	96.48	28	13	1.40E−85
	35	gi\|194708718	LOC100274593	Defense	19100/17815	5.4/5.7	5	79.9	99.88	80	34	2.10E−43
	36	gi\|195618512	eukaryotic translation initiation factor 5A	Protein synthesis	18300/17713	5.8/5.6	2	50.26	99.96	50	13	7.30E−71
	37	gi\|195658559	trypsin/factor XIIA inhibitor precursor	Defense	12300/16861	5.9/8.1	2	108.04	100	108	10	1.50E−29
	38	gi\|257743783	elongation factor 1−delta 1	Protein synthesis	13500/15532	6.0/6.1	2	35.6	99.07	36	28	7.20E−32
	39	gi\|259703147	Hb	Glycolysis	30900/27236	5.7/5.5	3	109.28	100	109	13	5.30E−100
Zhengdan 958	40	gi\|226507242	hypothetical protein LOC100274379	Cellular biogenesis	68000/38769	6.8/6.3	8	87.1	97.66	87	22	1.50E−49
	41	gi\|194700850	cytosolic glyceroldehyde-3-phosphate dehydrogenase GAPC2	Glycolysis	22000/32076	6.6/6.4	7	91.52	100	92	9	1.20E−127
	42	gi\|194706410	1-Cys peroxiredoxin antioxidant	Defense	42000/25126	6.9/6.4	10	136.49	100	132	47	5.80E−80
	43	gi\|195607718	hypothetical protein	Defense	23000/47848	6.7/6.7	2	38.24	98.88	38	3	1.40E−09
	44	gi\|1169520\|sp\|P46517.1\|EMB5_MAI	RecName: Full = Late embryogenesis abundant protein EMB564	Development	18000/9677	6.3/6.6	2	42.8	98.91	108	43	1.10E−23
	45	gi\|195642018	stress-inducible membrane pore protein	Transport facilitation	32000/17918	6.5/6.4	3	148.47	100	148	14	8.10E−26
	46	gi\|195638850	glycine-rich protein 2b	Nucleotide metabolism	35000/20576	6.0/5.9	2	104.35	100	104	19	1.40E−35
	47	gi\|195635073	hypothetical protein	Defense	27000/11830	6.1/5.1	3	64.3	95.75	64	55	8.40E−40
	48	gi\|195659143	secreted protein	Transport facilitation	54000/27503	6.1/5.8	7	131.97	100	76	32	1.00E−66
	49	gi\|195658029	lipoprotein	Cellular communication/signal transduction	47000/26539	6.2/5.9	1	63.74	99.85	64	5	2.80E−80
	50	gi\|194707248	thiamine biosynthesis2	Nitrogen metabolism	64000/37454	5.3/5.6	1	42.3	99.81	42	3	2.90E−124
	51	gi\|195658465	late embryogenesis abundant protein D-34	Development	57000/27274	5.5/5.4	3	83.45	100	83	16	4.30E−59
	52	gi\|228310	globulin 2	Defense	43000/50234	5.5/6.2	2	92.08	100	92	6	4.60E−64
	53	gi\|195606798	cupin family protein	Cellular biogenesis	50000/56775	5.6/6.1	2	33.19	98.68	33	5	1.90E−102
	54	gi\|195638870	ATP synthase D chain, mitochondrial	Energy	36000/19914	5.2/5.2	8	128	100	128	61	1.00E−64
	55	gi\|257708811	hypothetical protein(Sorghum bicolor)	Transport facilitation	22000/10891	5.1/5.0	2	90.81	100	91	25	2.40E−42
	56	gi\|195658877	hypothetical protein	Cellular biogenesis	27000/13413	6.0/5.6	2	70.85	100	71	20	6.40E−10
Nongda 108	57	gi\|162460575	1-Cys peroxiredoxin antioxidant	Defense	40000/25060	6.7/6.3	4	174	100	174	26	1.20E−79
	58	gi\|194708200	uncharacterized LOC100274491	Inositol metabolism	81000/42380	6.0/5.2	2	54.92	99.99	55	7	2.30E−204
	59	gi\|194707114	uncharacterized LOC100274264	Tricarboxylic acid cycle	62000/35491	6.1/8.2	2	50.01	99.97	50	11	3.20E−118
	60	gi\|194707256	uncharacterized LOC100274292	Cellular biogenesis	53000/33565	6.1/6.0	4	72.39	100	72	21	4.90E−51
	61	gi\|253786492	LOC100272498	Ionic homeostasis	52000/33151	6.1/5.8	3	126.48	100	126	13	1.00E−98
	62	gi\|195659367	lipoprotein	Lipid metabolism	42000/26549	6.0/5.9	4	147.85	100	148	22	3.90E−81
	63	gi\|195639126	fructokinase-2	Energy	59000/35954	5.4/5.3	5	172.21	100	172	20	1.30E−121
	64	gi\|195658465	late embryogenesis abundant protein D-34	Development	51000/27274	5.2/5.4	4	89.55	100	90	26	4.30E−59
	65	gi\|596078	thiamine biosynthetic enzyme	Nitrogen metabolism	58000/37308	5.1/5.2	2	67.5	100	68	9	2.80E−126
	66	gi\|195653831	6-phosphogluconolactonase	C metabolism	46000/34874	5.0/7.7	3	117.15	100	117	12	9.20E−89
	67	gi\|226502636	hypothetical protein LOC100276943	Lipid metabolism	28000/15621	5.3/12.3	1	65.59	100	66	8	9.30E−09
	68	gi\|195658153	embryonic abundant protein 1	Development	18000/9663	6.1/6.6	2	74.19	100	74	27	8.40E−24
	69	gi\|162464017	embryo specific protein5	Development	21000/11933	5.3/5.6	1	38.3	99.54	38	10	6.90E−29
	70	gi\|257696216	ascorbate peroxidase	Defense	42000/27467	5.8/5.6	3	49.62	99.97	50	18	1.90E−113
Pioneer 335	71	gi\|223973215	inositol-3-phosphate synthase-like	Inositol metabolism	80000/56278	6.3/5.8	2	81.25	100	81	4	3.20E−244
	72	gi\|195607992	succinate semialdehyde dehydrogenase	Secondary compounds metabolism	75000/52875	6.0/5.7	3	46.53	99.93	47	10	2.60E−203
	73	gi\|226533140	hypothetical protein LOC100274292	Cellular biogenesis	53000/33565	6.4/6.0	8	126	100	126	42	4.90E−51
	74	gi\|239985530	thiamine biosynthetic enzyme precursor	Nitrogen metabolism	56000/37308	5.4/5.2	2	64.83	100	65	9	2.80E−126
	75	gi\|195628018	enoyl-[acyl-carrier-protein] reductase [NADH]	Lipid metabolism	53000/39381	5.5/7.6	3	89.49	100	89	9	7.00E−123
	76	gi\|195658465	late embryogenesis abundant protein D-34	Development	50000/27274	5.5/5.4	4	76.59	100	77	24	4.30E−59
	77	gi\|257696218	APx1 - Cytosolic Ascorbate Peroxidase	Defense	43000/27509	6.1/5.7	4	57.78	99.99	58	26	2.40E−113
	78	gi\|195658011	globulin-1 S allele precursor	Defense	38000/50275	5.8/6.2	2	93.61	100	94	6	6.80E−61
	79	gi\|228310	globulin 2	Defense	38000/50234	5.7/6.2	2	90.86	100	91	6	4.60E−64
	80	gi\|195658137	embryonic abundant protein 1	Development	20000/9663	6.4/6.6	2	67.71	100	68	27	8.40E−24
	81	gi\|223945515	uncharacterized LOC100502218	Defense	20000/22859	4.6/5.7	5	69.1	98.59	69	30	3.20E−08
	82	gi\|212722552	hypothetical protein LOC100193701	Cellular biogenesis	43000/26549	6.3/5.9	2	52.39	99.97	52	13	3.90E−81

Number of identified differentially expressed protein spots on each 2-D map. Preferentially accumulated proteins: more than 2-fold changes; t-test or ANOVA: P<0.01 in three independent biological replicates.

Accession number of each protein identified by MS.

Identified proteins obtained from the NCBI Zea mays protein sequence database using the TurboSEQUEST algorithm.

Functional annotation of each protein identified by MS.

Molecular weight of protein on gel/predicted molecular weight of protein.

pI of protein on gel/predicted pI of protein.

Number of peptides matching the corresponding protein.

Calculated by weighting ion score (based on the probability that ion fragmentation matches are non-random) events for all individual peptides matched to the protein. Ion scores for duplicated matches are excluded from the calculation.

ⁱ

Confidence level of the total ion score.

Calculated by Mascot search (−10×LogP) for identified proteins.

Percentage of coverage of the identified proteins.

Probability that the peptide mass matches are non-random events.