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. 2010 Jun 6;9(9):2019–2033. doi: 10.1074/mcp.M110.000349

Table I. MALDI-TOF MS identification of proteins preferentially accumulated in wild-type or in fl mutant cotton ovules.

Spot no.a Protein name NCBI Accession no. pI/exp.b molecular mass (kDa) pI/theo.c molecular mass (kDa) Score/cov.d (%) Matched/searchede Relative protein content
 Ratio WT/FL
WT-10 FL-10
1 Profilin ABO43717 5.33/13.01 5.38/14.41 72/56 10/60 0.397 ± 0.034 0.205 ± 0.026 1.94
2f Major latex-like protein FJ415202 5.44/14.83 5.46/17.16 86/60 10/86 0.236 ± 0.028 0.121 ± 0.014 1.95
3 Annexin 1 AAR13288 6.31/15.81 6.19/36.15 172/55 20/64 0.103 ± 0.017 0.017 ± 0.009 6.06
6 Annexin AAB67993 6.08/16.10 6.41/36.03 99/35 13/68 0.037 ± 0.005 0 g
18f Annexin FJ415173 6.52/28.49 6.74/35.98 123/38 14/60 0.065 ± 0.021 0.022 ± 0.008 2.95
5 Fiber annexin AAC33305 6.11/16.04 6.34/36.21 99/37 15/81 0.075 ± 0.015 0.038 ± 0.011 1.97
4f Copper,zinc-superoxide dismutase FJ415203 5.83/15.98 5.47/15.36 106/92 10/59 0.162 ± 0.021 0.084 ± 0.025 1.93
7f Copper,zinc-superoxide dismutase FJ415203 5.83/16.35 5.47/15.36 88/92 10/93
8f Peroxiredoxin FJ415174 5.35/17.41 5.58/17.30 140/74 10/44 0.127 ± 0.028 0.048 ± 0.008 2.65
9f Dimethylmenaquinone methyltransferase FJ415179 5.41/18.54 5.60/18.05 104/50 7/42 0.145 ± 0.023 0.080 ± 0.008 1.81
10 Benzoquinone reductase ABN12321 6.09/21.65 6.09/21.65 69/39 5/49 0.295 ± 0.013 0.053 ± 0.007 5.57
13 Benzoquinone reductase ABN12321 6.27/27.60 6.09/21.65 80/39 5/56
14 Benzoquinone reductase ABN12320 6.47/27.83 6.20/21.79 82/31 5/29 0.348 ± 0.039 0.034 ± 0.012 10.24
88f Benzoquinone reductase FJ415183 7.68/24.72 6.97/21.74 94/48 12/53 0.131 ± 0.019 0 g
11 Ascorbate peroxidase ABR18607 5.13/27.49 5.93/27.74 84/52 9/50
12 Ascorbate peroxidase ABR18607 5.43/27.51 5.93/27.74 79/44 7/100
15 Ascorbate peroxidase ABR18607 5.68/27.84 5.93/27.74 90/46 6/77
16 Ascorbate peroxidase ABR18607 5.29/27.87 5.93/27.74 78/47 9/59 0.239 ± 0.025 0.040 ± 0.017 5.98
19 Ascorbate peroxidase ABR18607 5.32/28.70 5.93/27.74 101/49 9/51
20 Ascorbate peroxidase ABR18607 5.64/28.75 5.93/27.74 151/64 15/41
21 Ascorbate peroxidase ABR18607 5.15/29.28 5.62/27.58 112/60 13/67
17f Ascorbate peroxidase FJ415185 4.96/27.89 5.62/27.58 66/38 5/60 0.207 ± 0.032 0.043 ± 0.015 4.81
38f Stromal ascorbate peroxidase FJ415186 6.24/36.78 8.89/41.05 85/35 13/75 0.102 ± 0.014 0.047 ± 0.015 2.17
40f Stromal ascorbate peroxidase FJ415186 6.10/37.04 8.89/41.05 73/28 9/100
22f α-1,4-glucan phosphorylase FJ415211 4.94/30.21 5.32/10.67 108/23 19/94 0.132 ± 0.010 0 g
23f S-Formylglutathione hydrolase FJ415188 6.59/30.65 6.82/32.18 77/47 10/89 0.120 ± 0.036 0.050 ± 0.002 2.40
24f Triose-phosphate isomerase FJ415177 6.53/31.54 6.00/27.47 142/82 15/110 0.253 ± 0.035 0.170 ± 0.019 1.49
25f 20 S proteasome subunit α-1 FJ415181 6.44/31.80 5.91/27.39 112/47 11/49 0.105 ± 0.009 0.035 ± 0.01 3.00
26f Heat shock protein 70 FJ415196 6.27/32.83 5.07/71.57 74/19 9/77 0.146 ± 0.010 0.036 ± 0.025 4.06
68f Heat shock protein 70 FJ415196 4.75/52.95 5.10/71.37 84/26 15/99
63f Heat shock protein 70 FJ415199 4.59/49.92 5.10/71.35 88/27 9/95 0.113 ± 0.007 0.043 ± 0.041 2.63
67f Heat shock protein 70 FJ415194 4.69/52.90 5.14/71.28 89/21 9/37 0.468 ± 0.027 0.134 ± 0.030 3.49
90f Heat shock protein 70 FJ415194 7.52/33.12 5.14/71.28 84/20 9/65
73f Heat shock protein 70 FJ415195 4.75/54.07 5.07/71.57 90/13 8/47 0.059 ± 0.007 0.010 ± 0.011 5.90
27f Catalase FJ415187 6.30/33.59 6.68/57.25 73/30 16/84 0.197 ± 0.032 0.091 ± 0.015 2.16
28f Serine hydroxymethyltransferase FJ415180 5.54/34.18 7.57/52.38 95/26 9/59 0.091 ± 0.008 0.014 ± 0.001 6.50
31f Serine hydroxymethyltransferase FJ415180 5.83/34.82 7.57/52.38 75/36 12/76
29f Lactoylglutathione lyase FJ415204 5.71/34.38 5.69/32.61 69/34 11/69 0.202 ± 0.016 0 g
30f α-Soluble NSFh attachment protein FJ415171 5.08/34.75 5.11/33.05 120/39 9/23 0.110 ± 0.033 0.034 ± 0.012 3.24
32f UER1 FJ415167 5.94/34.94 5.73/33.95 180/62 18/79 0.253 ± 0.030 0.253 ± 0.030 1.78
33f UER1 FJ415167 6.22/34.97 5.73/33.95 215/64 15/31
34f Fructokinase FJ415169 5.05/36.08 5.28/35.20 206/58 16/41 0.080 ± 0.002 0.045 ± 0.009 1.78
35 Enolase ABW21688 5.21/36.28 5.49/47.98 85/29 7/78 0.049 ± 0.003 0 g
36 Actin AAP73454 5.43/36.64 5.23/41.90 90/46 12/63 0.178 ± 0.027 0.027 ± 0.028 6.59
52 Actin AAP73452 5.62/42.35 5.44/41.94 69/29 7/86 0.264 ± 0.017 0.018 ± 0.020 14.67
53 Actin AAP73457 5.56/43.29 5.31/41.91 149/60 28/142 0.244 ± 0.03 0.039 ± 0.036 6.26
71 Actin AAP73460 5.45/53.58 5.37/41.94 163/57 22/91 0.189 ± 0.023 0.120 ± 0.032 1.58
37f Granule-bound starch synthase FJ415189 4.97/36.64 8.79/63.84 80/20 8/55 0.087 ± 0.012 0 g
39f Granule-bound starch synthase FJ415205 4.91/36.78 8.59/67.73 135/35 13/89 0.090 ± 0.016 0.019 ± 0.011 4.76
41f Glutamine synthase FJ415178 5.64/37.12 5.77/39.36 140/43 10/50 0.078 ± 0.006 0 g
42f Malate dehydrogenase FJ415192 6.14/38.50 6.10/36.45 93/27 10/77 0.337 ± 0.004 0.222 ± 0.028 1.52
56f Malate dehydrogenase FJ415192 6.67/46.15 6.10/35.87 88/43 8/100
43 Phenylcoumaran benzylic ether reductase-like protein ABN12322 5.58/38.89 5.76/33.89 92/35 11/48 0.227 ± 0.021 0.102 ± 0.022 2.23
51 Phenylcoumaran benzylic ether reductase-like protein ABN12322 5.87/41.46 5.76/33.89 129/58 18/97
45 β-Tubulin 19 ABY86665 5.75/39.76 4.76/50.65 173/58 26/70 0.073 ± 0.034 0 g
46 α-Tubulin 4 AAN33000 5.57/39.90 5.36/34.41 207/64 19/40 0.145 ± 0.007 0.059 ± 0.018 2.46
49 α-Tubulin 4 AAN33000 5.43/40.90 5.36/34.41 107/44 12/65
48 α-Tubulin ABO47738 5.72/40.45 4.97/50.29 159/43 19/38 0.155 ± 0.029 0 g
50f Glyceraldehyde-3-phosphate dehydrogenase C subunit FJ415206 6.61/41.24 7.70/36.65 73/33 7/87 0.234 ± 0.030 0.115 ± 0.052 2.04
54f 2-Nitropropane dioxygenase FJ415176 5.43/43.73 5.32/36.17 211/68 18/62 0.330 ± 0.009 0.134 ± 0.033 2.46
55f Quinone oxidoreductase FJ415175 5.21/45.90 5.28/34.39 149/67 16/106 0.088 ± 0.014 0 g
57 Gibberellin 20-oxidase 1 ABA01482 5.23/48.01 5.35/41.72 215/64 24/84 0.030 ± 0.007 0 g
58 Flavanone 3-hydroxylase ABM64799 5.33/48.10 5.43/41.75 171/66 26/130 0.485 ± 0.007 0.226 ± 0.023 2.14
59f Mannitol dehydrogenase FJ415191 5.93/49.11 5.85/39.57 100/61 16/90 0.252 ± 0.032 0.144 ± 0.026 1.75
60f Adenosine kinase FJ415170 5.46/49.66 5.47/37.81 200/59 15/38 0.059 ± 0.018 0.145 ± 0.028 1.40
61f Adenosine kinase FJ415170 5.31/49.66 5.47/37.81 128/55 18/64 g
62f Phosphoglycerate dehydrogenase FJ415190 5.20/49.84 7.14/64.06 81/23 7/54 0.111 ± 0.009 0 g
65f Phosphoglycerate dehydrogenase FJ415190 5.13/50.35 7.14/64.06 77/27 8/100
64f Pyruvate dehydrogenase α subunit FJ415197 6.74/50.17 7.16/43.69 79/30 9/100 0.222 ± 0.013 0.157 ± 0.008 1.41
66 Anthocyanidin reductase ABM64802 5.53/51.74 5.54/36.54 138/49 16/86 0.358 ± 0.003 0 g
69f Luminal binding protein FJ415200 4.57/53.09 5.13/73.57 81/31 17/95 0.062 ± 0.016 0.015 ± 0.012 4.13
70f Luminal binding protein FJ415200 4.50/53.55 5.13/73.57 76/23 9/100
72f Luminal binding protein FJ415200 4.55/53.94 5.13/73.57 104/25 10/67
74f Phosphoglycerate kinase FJ415172 6.14/56.40 5.97/42.29 140/44 14/59 0.063 ± 0.008 0.035 ± 0.003 1.80
75 Chloroplast biotin carboxylase ABP98813 6.30/57.92 7.57/59.17 94/34 19/85 0.083 ± 0.011 0.049 ± 0.010 1.69
77 Chloroplast biotin carboxylase ABP98813 6.31/59.64 7.57/59.17 139/61 26/101
76f Dihydrolipoamide dehydrogenase FJ415193 6.62/59.37 6.93/54.13 70/25 8/100 0.118 ± 0.026 0 g
78f UGP2 FJ415165 5.54/60.41 5.62/51.45 155/49 18/100 0.205 ± 0.015 0.145 ± 0.023 1.42
79f UGP1 FJ415164 6.07/61.70 5.81/51.74 132/52 17/61 0.178 ± 0.016 0.092 ± 0.014 1.93
80f UGP1 FJ415164 6.10/61.70 5.81/51.74 216/61 22/63
81f UGD1 FJ415166 6.11/62.84 5.84/53.64 183/59 23/109 0.124 ± 0.016 0.057 ± 0.013 2.18
83f UGD1 FJ415166 6.30/64.12 5.84/53.64 188/53 18/49
82f myo-Inositol-1-phosphate synthase FJ415168 5.69/63.53 5.46/56.54 207/54 24/106 0.090 ± 0.006 0.046 ± 0.010 1.96
84 Acyltransferase-like protein AAL67994 5.67/64.47 5.67/48.29 107/40 22/108 0.100 ± 0.013 0.019 ± 0.008 5.26
85 Acyltransferase-like protein AAL67994 5.56/64.82 5.67/48.29 72/38 15/110
86f Pyruvate decarboxylase FJ415201 6.57/69.52 6.13/60.77 99/30 11/100 0.128 ± 0.033 0.025 ± 0.014 5.00
87f Glycine-rich RNA-binding protein FJ415184 7.82/15.01 7.82/17.08 111/62 13/72 0.116 ± 0.030 0 g
89 Manganese-superoxide dismutase AAC78469 7.49/25.40 8.54/22.14 158/75 16/100 0.089 ± 0.015 0.041 ± 0.008 2.17
91f Glyceraldehyde-3-phosphate dehydrogenase FJ415182 7.74/43.72 7.06/37.04 92/58 15/100 0.167 ± 0.023 0.048 ± 0.015 3.48
92f Isocitrate dehydrogenase FJ415198 7.32/53.15 6.29/46.41 188/63 28/100 0.381 ± 0.030 0.256 ± 0.029 1.49
93f Isocitrate dehydrogenase FJ415198 7.07/53.29 6.29/46.41 140/57 23/100
94f Eukaryotic translation initiation factor 5A GU295062 5.55/18.88 5.61/17.63 96/52 9/61 0.156 ± 0.026 0.293 ± 0.024 0.53
95f Chalcone isomerase GU295063 4.84/29.85 4.85/23.42 95/67 10/66 0.104 ± 0.021 0.177 ± 0.017 0.59
96f Triose-phosphate isomerase GU295064 5.52/30.18 6.66/33.50 101/53 16/138 0.051 ± 0.009 0.122 ± 0.016 0.42
97f Thiazole biosynthetic enzyme GU295068 5.03/36.81 5.64/38.24 170/63 17/49 0.048 ± 0.008 0.155 ± 0.024 0.31
98f Transaldolase GU295065 4.91/45.56 5.78/43.06 129/33 10/18 0.036 ± 0.005 0.089 ± 0.012 0.40
100f Transaldolase GU295065 5.09/46.62 5.78/43.06 123/29 12/32
99f U2 small nuclear ribonucleoprotein A GU295066 5.06/45.90 4.97/32.19 204/68 18/50 0.062 ± 0.003 0.237 ± 0.033 0.26
101 Chalcone synthase ABS52573 6.11/54.17 6.12/42.98 87/35 11/45 0.039 ± 0.010 0.104 ± 0.026 0.38
102 Protein-disulfide isomerase ABO41843 5.01/65.30 5.07/55.89 203/59 24/77 0.051 ± 0.010 0.102 ± 0.003 0.50
103f RNA helicase-like protein GU295067 5.91/69.24 5.65/56.15 201/43 17/32 0.062 ± 0.012 0.121 ± 0.020 0.51
104 Betaine-aldehyde dehydrogenase AAR23816 5.44/69.43 5.60/55.37 100/42 19/103 0.055 ± 0.011 0.114 ± 0.012 0.48

a Protein spots are arranged from lowest to highest molecular mass with spots encoded by the same cotton cDNA quantified as one protein and spots presumably encoded by the same gene family located next to each other. Spots 1–93 were preferentially accumulated in the wild type, and spots 94–104 were preferentially accumulated in the mutant.

b Experimental.

c Theoretical.

d Coverage.

e Number of matched/searched polypeptides.

f Sixty-eight polypeptides encoded by 50 putative full length and one partial (spot 22, FJ415211) cotton cDNAs obtained for the first time in the current work.

g Protein spots only observed in WT-10.

h N-Ethylmaleimide-sensitive factor.