Table I.

Functional classification of tomato proteins whose level varied significantly during fruit development and ripening

List of identified proteins from pericarp tissues of Cervil. Data were classified according to the FunCat scheme. For each spot, the computed and theoretical pIs and M_r and the mean normalized volume at the six stages of development were indicated.

Spot No.a	MSb	Database	Accession No.c	Coveraged	Peptides Identifiede	UniProt Accession No.	Assignment	Species	Computed		Observed		Mean % Volumef
									pI	Mr	pI	Mr	7 DPA	14 DPA	21 DPA	30 DPA	Breaker	RR
				%
C compounds and carbohydrate metabolism
108	M	MSDB	Q42896	61	21/33	Q42896	Fructokinase Frk2	Lycopersicon esculentum	5.76	34.8	6.15	36	50.75	36.31	26.64	15.02	8.43	6.79
100	M	MSDB	Q9AV98	21	16/53	Q6IVK5	UDP-glucuronate decarboxylase 1	Tobacco	7.10	38.7	6.6	45	8.21	19.73	13.44	12.18	8.02	8.11
10	E	TIGR	BF050929	na	5	Q8W147	Putative kunitz- type tuber invertase inhibitor precursor	Potato	8.22	24.5	5.98	27	43.23	22.82	12.66	16.51	15.05	19.37
118	E	TIGR	TC162820	na	14	Q9LQ04	3,5-Epimerase/ 4-reductase	Arabidopsis	5.73	33.6	6.49	32	6.64	6.22	5.35	3.94	2.29	1.29
57	M	TIGR	TC153775	na	8/27	Q94CE4	Similar to carbonic anhydrase	Arabidopsis	6.66	30.8	6.07	29	2.30	1.76	6.08	3.11	9.16	11.31
6	M	MSDB	S31157	34	14/23	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.31	70.1	5.87	30	4.86	6.17	12.35	15.02	22.81	43.96
73	E	TIGR	TC161907	na	6	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.31	70.1	5.74	21	0.00	4.69	2.86	4.44	6.29	33.20
74	M	TIGR	AAL75449	21	8/11	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.54	70.1	5.69	20	0.00	4.40	6.69	4.92	9.31	31.21
75	M	TIGR	AAL75449	22	9/18	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.54	70.1	5.7	20	7.68	3.23	3.75	5.40	7.43	15.34
115	M	MSDB	S31157	18	14/21	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.54	70.1	5.67	27	2.93	4.92	3.62	5.07	8.52	8.41
144	M	TIGR	AAL75449	16	7/14	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.54	70.1	5.82	49	20.74	27.29	36.02	35.72	55.10	62.32
145	M	TIGR	AAL75449	34	17/31	P29000	Acid β-fructo furanosidase precursor	L. esculentum	5.54	70.1	5.9	49	14.41	16.40	21.40	23.72	44.49	47.79
26	M	MSDB	S44364	60	13/30	Q43778	Glucan endo- 1,3-β-d- glucosidase	L. esculentum	5.38	37.9	5.73	33	0.00	0.00	1.44	3.89	12.72	12.34
20	E	TIGR	TC154654	na	5	Q76MS4	Xylosidase LEXYL2 protein	L. esculentum	8.04	68.9	6.47	60	3.94	5.88	2.37	7.10	7.35	7.79
133	M	MSDB	Q9FUR8	30	10/21	Q9SP05	α-Galactosidase	L. esculentum	5.3	44.9	5.7	37	4.01	4.63	6.89	6.57	14.67	19.39
Photosynthesis/respiration
37	M	MSDB	RKTOS2	33	6/20	P07179	Rubisco small chain 2A	L. esculentum	6.58	20.3	5.84	7	10.17	20.60	35.40	40.55	17.58	14.33
72	M	MSDB	S16586	40	13/23	P26320	PSII oxygen- evolving complex protein 1	Potato	5.84	35.4	5.72	31	26.67	29.17	35.47	26.45	18.83	6.61
138	M	MSDB	T06368	49	13/23	P26320	PSII oxygen- evolving complex protein 1	Potato	5.84	35.4	5.76	31	30.34	31.47	34.32	32.92	26.38	10.89
76	M	MSDB	F2TOX2	43	9/21	P29795	PSII oxygen- evolving complex protein 2	L. esculentum	8.27	27.8	5.75	22	50.28	77.00	69.70	69.31	51.31	27.77
32	E	TIGR	TC158143	na	8	Q6NQE2	At4g27270, similar to 1,4-benzoquinone reductase	Arabidopsis	6.08	21.8	6.12	25	2.42	3.46	5.91	5.83	7.04	8.06
Amino acid metabolism
97	M	TIGR	TC154906	na	11/16	O04130	d-3-Phos phoglycerate dehydro genase (3-PGDH)	Arabidopsis	5.81	66.5	6.13	60	6.80	4.75	3.63	3.43	1.22	0.00
99	M	TIGR	TC154906	na	14/19	O04130	d-3-Phos phoglycerate dehydro genase (3-PGDH)	Arabidopsis	5.81	66.5	6.22	60	6.88	3.37	3.88	3.81	0.00	0.00
23	M	MSDB	S46540	30	8/16	P43282	S-adenosyl methionine synthetase 3	L. esculentum	5.76	42.7	6.26	46	19.60	9.96	4.71	3.02	1.77	1.22
109	M	MSDB	S46540	34	11/34	P43282	S-adenosyl methionine synthetase 3	L. esculentum	5.76	42.7	6.2	45	19.99	12.44	8.96	6.65	2.88	2.38
147	M	MSDB	S46540	37	12/14	P43282	S-adenosyl methionine synthetase 3	L. esculentum	5.76	42.7	6.34	45	10.18	7.00	2.82	2.27	1.28	1.02
105	E	TIGR	TC164711	na	3	Q9FFW8	Trp synthase β-chain	Arabidopsis	6.79	55.7	6.53	50	3.61	5.85	3.99	6.41	4.02	2.64
22	M	MSDB	Q9XGI9	46	9/35	Q9XGI9	β-Alanine synthase	L. esculentum	5.87	33.4	6.25	33	0.00	1.32	3.52	3.26	3.58	3.34
102	E	TIGR	TC162607	na	12	P50217	Homolog to NADP+-specific isocitrate dehydrogenase	Potato	6.54	46.8	6.61	37	2.00	2.12	2.56	1.57	2.70	4.71
103	M	MSDB	S47013	37	15/40	P50217	Homolog to NADP+-specific isocitrate dehydrogenase	Potato	6.54	46.8	6.6	45	1.47	1.94	1.93	1.65	6.37	9.05
Protein synthesis/storage
16	E	TIGR	TC162231	na	5	Q9AXQ5	eIF-5A 2	L. esculentum	5.78	17.6	6.12	18	15.34	11.05	1.05	4.30	10.70	5.93
112	E	TIGR	TC155242	na	8	P19954	Plastid-specific 30S ribosomal protein 1	Spinacia oleracea	6.68	33.7	5.89	33	15.63	13.58	13.98	9.52	5.59	4.30
15	E	TIGR	TC162122	na	10	Q9AXQ3	eIF-5A 4	L. esculentum	5.6	17.5	5.99	18	17.18	23.44	6.06	7.47	11.85	19.73
Protein fate, modification, degradation
91	M	TIGR	TC162419	na	11/12	Q9XF61	Similar to protein disulfide- isomerase precursor	Datisca glomerata	4.84	57.1	5.5	58	11.14	8.05	8.31	5.28	5.20	3.25
58	M	MSDB	JQ0988	34	5/11	P54153	Peptide methionine sulfoxide reductase, protein E4	L. esculentum	6.1	21.9	6.19	23	0.00	0.00	0.00	0.00	29.48	46.78
60	M	MSDB	JQ0988	34	7/15	P54153	Peptide methionine sulfoxide reductase, protein E4	L. esculentum	6.1	21.9	6.39	23	0.00	0.00	0.00	0.99	35.71	51.62
5	M	MSDB	S66348	30	6/20	Q40143	Cysteine proteinase 3 precursor	L. esculentum	8.59	38.9	5.89	29	4.21	11.35	14.27	23.53	24.44	28.44
7	E	TIGR	TC153677	na	8	Q9FRW8	Similar to aspartic proteinase 2	Nepenthes alata	5.28	55.4	6.03	31	0.00	1.33	5.87	9.08	6.74	10.14
Secondary metabolism
3	E	TIGR	TC162337	na	14	Q9FES7	Homolog to sulfur (Mg chelatase)	Tobacco	6	46.3	5.72	40	7.06	4.09	4.20	2.32	2.03	0.00
51	E	TIGR	TC162337	na	17	Q9FES7	Homolog to sulfur (Mg chelatase)	Tobacco	6	46.3	5.65	40	6.14	7.28	5.98	4.75	2.72	0.00
2	E	TIGR	TC166223	na	9	Q9LHN8	Weakly similar to leucoantho cyanidin dioxygenase- like	Arabidopsis	5.26	40.7	5.75	41	11.81	9.98	7.19	4.68	1.93	1.66
67	E	TIGR	TC156069	na	14	Q9FGT8	Similar to outer membrane lipoprotein-like (lipocalin)	Arabidopsis	5.98	21.4	6.34	20	5.02	7.95	8.37	8.43	41.39	45.32
68	E	TIGR	TC156069	na	5	Q9FGT8	Similar to outer membrane lipoprotein-like (lipocalin)	Arabidopsis	5.98	21.4	6.41	20	0.00	0.00	0.00	0.00	25.95	41.78
Vitamin biosynthesis
53	M	MSDB	Q9SLR7	22	6/11	Q9SLR7	Thiamin biosynthetic enzyme	Glycine max	5.8	37.0	5.59	34	1.72	7.83	11.76	15.60	0.00	0.00
Lipid metabolism
148	M	MSDB	T06339	29	21/43	P38416	Lipoxygenase loxB	L. esculentum	5.56	97.1	6.32	59	2.95	3.58	2.27	4.16	5.28	8.35
DNA processing
134	M	TIGR	TC155302	na	10/30	Q94KA9	Homolog to importin α 2	Pepper	5.32	58.5	5.76	56	4.79	10.27	9.05	9.44	8.42	9.66
Stress response
126	E	TIGR	TC153554	na	9	P93570	Chaperonin- 60 β-subunit	Potato	5.72	63.0	5.88	57	3.70	1.64	1.00	1.07	1.65	1.29
123	E	TIGR	TC162423	na	4	Q8LEG8	Weakly similar to dehydration stress-induced protein	Arabidopsis	5.12	20.0	5.66	16	10.39	26.50	23.18	27.51	18.76	14.92
11	M	MSDB	T04316	58	13/27	O80432	Mitochondrial small HSP	L. esculentum	6.47	23.8	5.61	21	6.69	16.32	9.18	5.66	11.07	18.44
34	M	MSDB	O82010	62	11/18	O82010	HSP 20.1	L. peruvianum	5.83	17.7	5.92	18	9.70	34.36	37.15	71.12	82.64	111.60
120	M	MSDB	O82545	28	5/26	O82013	HSP 20.2	L. peruvianum	6.32	17.3	6.64	17	3.79	18.51	21.88	23.03	38.14	54.40
140	M	TIGR	TC162823	na	14/26	Q39641	Homolog to HSP 70	Cucumis sativus	5.15	75.4	5.46	69	0.00	1.94	3.13	3.45	5.28	5.22
141	M	TIGR	TC162823	na	17/27	Q39641	Homolog to HSP 70	C. sativus	5.15	75.4	5.49	69	1.87	4.14	7.03	6.88	11.48	11.19
146	M	MSDB	JC4786	43	23/44	Q40151	Hsc 70 protein	L. esculentum	5.18	71.5	5.7	67	0.00	6.38	7.18	8.56	12.77	17.20
94	M	MSDB	S53498	18	9/19	Q40980	HSP 70	Pea	5.17	71.2	5.77	68	9.02	5.78	6.90	5.10	20.19	22.93
65	M	TIGR	TC155466	na	8/25	Q6WHC0	Similar to chloroplast small HSP class I	Capsicum frutescens	6.2	18.2	6.61	18	0.00	7.78	10.28	11.64	24.49	33.31
64	E	TIGR	TC162458	na	5	Q84JS5	Similar to At3g58450: universal stress protein family	Arabidopsis	6.09	22.4	6.63	20	0.00	5.89	13.69	18.40	46.17	37.24
18	M	TIGR	TC154685	na	7/20	Q8H0L9	Similar to DS2 protein	Solanum chacoense	4.99	29.1	5.49	62	0.00	1.49	2.84	6.73	5.50	3.08
85	M	TIGR	TC154685	na	13/20	Q8H0L9	Similar to DS2 protein	S. chacoense	4.99	29.1	5.52	62	0.78	3.77	6.93	12.36	11.93	6.37
58c	M	MSDB	T06324	40	9/15	Q95661	Small HSP, chloroplast HSP21 TOM111	L. esculentum	7.84	26.2	6.2	22	0.00	0.00	0.00	0.00	3.66	6.34
63	E	TIGR	TC160055	na	3	Q9LS37	Small HSP	L. esculentum	5.89	21.5	6.49	20	0.00	4.58	8.21	4.37	28.85	42.80
66	M	MSDB	Q9LS37	37	8/45	Q9LS37	Small HSP	L. esculentum	5.89	21.5	6.23	20	5.28	11.61	11.51	6.18	39.07	57.11
55	E	TIGR	TC165474	na	8	Q9SSQ8	Weakly similar to 26.5-kD class I small HSP-like	Arabidopsis	6.86	26.5	5.97	25	0.00	3.41	4.78	6.12	23.33	39.65
59	E	TIGR	TC165474	na	5	Q9SSQ8	Weakly similar to 26.5-kD class I small HSP-like	Arabidopsis	6.86	26.5	6.17	25	3.77	7.32	5.81	5.13	19.18	20.79
121	M	MSDB	Q9SYU8	75	15/29	Q9SYU8	17.7-kD class I small HSP	L. esculentum	5.84	17.7	6.09	19	10.10	29.77	27.31	40.69	89.14	94.40
Disease/defense
4	M	TIGR	AW040299	na	8/21	P49248	Similar to In2-1 protein	Maize	4.80	27.0	5.5	29	17.71	5.64	2.81	2.08	0.82	0.00
49	E	TIGR	AW040299	na	8	P49248	Similar to In2-1 protein	Maize	4.80	27.0	5.76	42	8.31	12.62	9.82	9.31	3.01	1.54
78	E	TIGR	TC156701	na	3	Q6RYA0	Similar to salicylic acid- binding protein 2	Tobacco	5.39	29.3	6.16	29	6.42	7.91	5.54	3.45	4.39	14.10
Detoxification
89	M	MSDB	T07747	48	6/28	O24032	Glutathione peroxidase GPXle-2	L. esculentum	5.13	11.2	5.64	20	37.96	14.27	9.89	7.65	8.45	9.04
122	E	TIGR	TC154854	na	6	Q7XAV2	SOD	L. esculentum	6.01	22.3	6.03	15	14.15	16.44	13.91	14.63	9.89	10.28
14	M	TIGR	TC162330	na	5/20	Q7F8S5	Similar to putative thioredoxin peroxidase	Rice	6.15	23.2	5.44	17	10.14	31.24	11.53	10.83	52.36	46.86
149	M	TIGR	TC158002	na	7/10	Q8LSK6	Homolog to ascorbate peroxidase	L. esculentum	8.65	42.2	6.28	30	17.03	15.11	13.47	14.69	16.99	30.11
Electron transport
52	E	TIGR	TC155238	na	5	Q9LZG0	Similar to adenosine kinase 2	Arabidopsis	5.14	37.8	5.52	40	8.04	9.61	8.00	5.90	4.62	3.55
44	M	MSDB	S57814	32	12/17	Q9ZSH4	2-Oxoglutarate- dependent dioxygenase	S. chacoense	5.54	37.9	5.98	39	41.25	17.02	10.64	5.80	4.54	0.00
40	M	MSDB	S01642	33	13/24	P10967	Ripening protein E8	L. esculentum	5.61	41.1	6.1	40	6.77	2.08	5.67	6.72	11.31	11.51
46	M	MSDB	S01642	40	16/40	P10967	Ripening protein E8	L. esculentum	5.61	41.1	6.12	40	7.37	4.56	5.60	8.15	35.92	40.06
61	M	MSDB	S01642	13	6/19	P10967	Ripening protein E8	L. esculentum	5.61	41.1	6.23	24	0.00	0.00	0.00	0.00	5.98	9.20
106	M	MSDB	S01642	36	15/38	P10967	Ripening protein E8	L. esculentum	5.61	41.1	6.09	40	0.00	2.70	6.73	2.01	16.23	19.52
110	M	MSDB	S01642	37	13/36	P10967	Ripening protein E8	L. esculentum	5.61	41.1	6.21	40	3.00	2.91	1.41	1.58	7.12	13.94
47	E	TIGR	TC161768	na	4	Q944Z0	Weakly similar to 2-oxoglutarate- dependent dioxygenase	Arabidopsis halleri	5.27	34.0	5.75	37	1.40	1.49	1.08	2.74	7.79	17.36
Nucleotide metabolism
88	M	MSDB	JQ1599	71	10/19	P32518	dUTP pyrophosphatase	L. esculentum	5.19	17.9	5.67	21	17.32	17.57	14.67	11.11	8.39	8.05
Biogenesis of cellular components
111	M	MSDB	O81536	60	21/36	O81536	Annexin P34	L. esculentum	5.38	35.8	5.91	35	12.32	15.31	17.52	13.60	8.61	5.99
Transport
39	M	MSDB	O24345	18	6/10	O82722	Mitochondrial ATPase β-subunit	Nicotiana sylvestris	5.73	59.6	5.67	54	11.02	10.86	11.71	7.77	5.71	3.69
54	E	TIGR	TC163246	na	6	P32980	Homolog to ATP synthase δ chain	Tobacco	8.96	26.8	5.33	23	5.44	11.99	11.77	14.13	8.85	5.59
93	M	TIGR	TC163028	37	20/28	Q84XW6	Vacuolar H+- ATPase A1	L. esculentum	5.2	68.6	5.68	64	5.37	7.77	7.88	6.45	5.34	4.22
Unclassified
139	E	TIGR	TC155857	na	9	At2g37660.1g	Expressed protein	Arabidopsis	8.37	34.9	6.42	30	15.90	10.67	10.65	8.58	6.62	5.69
125	E	TIGR	BI927338	na	5	At1g24020g	Bet v I allergen family protein	Arabidopsis	5.09	17.1	5.52	17	58.47	59.38	37.32	28.13	19.17	12.83
143	E	TIGR	TC154714	na	16	At3g09350.1g	Similar to armadillo/ β-catenin repeat family protein	Arabidopsis	5.04	40.4	5.61	50	2.88	6.21	4.18	4.86	6.28	8.09
117	M	TIGR	TC154018	na	16/30	Q8S4X0	Similar to embryo-abundant protein EMB	Pea	5.44	29.7	6.03	29	4.19	3.56	2.49	1.69	5.67	7.88
132	E	TIGR	TC156218	na	3	Q8LF25	Similar to DNA- damage inducible protein DDI1-like	Arabidopsis	4.83	45.4	5.69	42	14.36	32.53	43.09	42.72	44.04	44.54
28	E	TIGR	TC154116	na	12	O82062	Homolog to 39-kD EF-hand containing protein	Potato	4.65	38.9	5.12	42	1.60	2.78	1.87	3.04	5.06	10.94

^aSpot number as index in the reference gel.

^bMS method used either MALDI-TOF (M) or LC-MS/MS (E).

^cAccession number of the sequence in the searched database, either MSDB or TIGR EST database.

^dPercent sequence coverage; no available data (na) when EST database was used.

^eRatios indicate number of matching peptides on nonmatching peptides obtained by MALDI-TOF analysis; for MS/MS analysis, the number of identified peptides is given.

^fMean value of the three spot volumes at each analyzed stage.

^gProtein accession number of corresponding sequence in the TAIR database.