Table 1.

Proteins identified by MALDI TOF/TOF MS from transgenic cotton leaves

Spot no a.	GI no. b	Function category protein name	Plant species	Exper. c pI/Mr	Thero. d pI/Mr	M P e	SC% f	M. S. g	Relative change (WT/BT) h
Posttranslational modification, protein turnover, chaperones (O)
1	255556934	ATPase	R. communis	5.49/90	5.13/90.1	11	21	324
7	147819511	Hypothetical protein	V. vinifera	4.86/72	5.20/61.4	5	10	256
9	225433375	Chaperonin	V. vinifera	5.40/63	5.85/61.7	6	14	204
16	12620883	Rubisco activase	G. hirsutum	4.99/49	5.06/48.6	13	41	822
27	14594915	Proteasome subunit	N. tabacum	5.77/27	6.12/18.2	3	32	113
Carbohydrate transport and metabolism (G)
2	110224784	Transketolase	P. acerifolia	5.73/76	6.25/26.0	2	11	82
3	255541252	Transketolase	R. communis	5.80/76	6.52/81.6	5	8	277
4	255541252	Transketolase	R. communis	5.95/76	6.52/81.6	5	8	262
5	255541252	Transketolase	R. communis	5.89/76	6.52/81.6	6	10	404
6	255541252	Transketolase	R. communis	6.05/76	6.52/81.6	6	11	337
8	3560664	Rubisco	C. ensifolium	5.73/66	6.4/49.7	5	13	211
14	11230404	Rubisco, large subunit	C. Pettersson	5.96/53	5.96/52.9	12	40	998
15	33415263	Enolase	G. hirsutum	5.69/49	6.16/47.9	11	36	502
22	329317332	Rubisco, large subunit	G. barbadense	6.20/35	6.00/53.7	5	16	326
24	449442663	Phosphoglycolate phosphatase	C. sativus	5.58/32	6.47/41.7	8	26	442
26	1881499	Rubisco, large subunit	P. pendula	6.24/30	6.61/52.6	9	22	366
32	548699	Rubisco, large chain	(−)	6.40/19	6.12/52.6	4	9	104
Energy production and conversion (C)
10	40850676	Betaine-aldehyde dehydrogenase	G. hirsutum	5.43/63	5.6/55.4	5	12	124
11	91208909	ATP synthase, beta subunit	G. hirsutum	5.33/59	5.22/53.6	13	42	939
20	225451308	Auxin-induced protein	V. vinifera	6.09/39	5.96/37.9	1	3	55
33	315364830	Ion-sulfur protein	C. lanatus	6.54/19	8.45/24.6	3	18	231
Cytoskeleton (Z)
17	281485191	actin	P. americana	5.34/44	5.31/41.9	12	46	984
Amino acid transport and metabolism (E)
18	211906462	Glutamine synthase	G. hirsutum	5.80/43	5.77/39.4	5	16	160
Coenzyme transport and metabolism (H)
19	449433772	Magnesium-chelatase subunit	C. sativus	4.98/40	5.72/46.0	5	15	150
21	255558669	Porphobilinogen deaminase	R. communis	6.07/38	6.55/40.3	3	10	50
Inorganic ion transport and metabolism (P)
23	225431122	Ferredoxin--NADP reductase	V. vinifera	6.46/34	8.91/40.8	7	22	270
Cell envelope biogenesis, outer membrane (M)
25	292668595	Sanguinarine reductase	E. californica	5.18/29	4.97/29.6	2	6	104
Nucleotide transport and metabolism (F)
34	225457446	Nucleoside diphosphate kinase,	V. vinifera	6.41/18	9.28/26.0	3	13	147
No related to COG (NO)
12	255558986	Hypothetical protein	R. communis	5.39/58	8.23/54.9	2	2	69
13	255558986	Hypothetical protein	R. communis	5.55/59	8.23/54.9	2	2	53
28	226358407	Chlorophyll binding protein	G. hirsutum	5.30/27	5.53/25.6	3	20	166
29	118489712	Unknown	P. trichocarpa	4.73/26	4.77/24.4	3	9	156
30	147767601	Hypothetical protein	V. vinifera	5.23/42	8.46/25.5	2	11	59
31	302595736	Oxygen-evolving enhancer protein	(−)	6.26/22	8.67/28.2	3	9	215
35	211906510	Major latex-like protein	G. hirsutum	5.38/17	5.46/17.2	3	27	116

^aAssigned spot number as indicated in Figure 2.

^bDatabase GI numbers according to NCBInr.

^c,d The experimental (c) and theoretical (d) mass (kDa) and pI of the identified proteins.

^eNumber of the matched peptides (MP).

^fThe amino acid sequence coverage (SC) for the identified proteins.

^gThe Mascot searched score (M. S.) against the database NCBInr.

^hThe relatively changed ratios of protein amount on different 2-D gels.