Spot No. Protein Identity (Accession. No.) Organism Mr/pI Fold Changes Relative abundanceb
      Theoreticala Observed    
1 Nucleoside diphosphate kinase (gi|12230332) Capsicum annum 16.3 / 6.3 13.0 / 6.6 13.47
2 Thioredoxin H-type 1 (gi|267124) Nicotiana tabacum 13.9 / 5.6 13.0 / 5.9 8.12
3 Constitutive plastid-lipid associated protein (gi|75266239) Solanum lycopersicum 19.7 / 8.8 15.0 / 5.7 16.02
4 Hypothetical protein (gi|302836253) Volvox carteri 13.6 / 9.1 14.0 / 5.5 4.07
5 Predicted protein (gi|168009197) Physcomitrella patens 14.1 / 4.6 12.0 / 4.9 18.47
6 Glycine-rich RNA-binding protein RGP-1c (gi|45533923) Nicotiana sylvestris 13.2 / 9.0 15.0 / 5.2 5.21
7 Constitutive plastid-lipid associated protein (gi|75266239) Solanum lycopersicum 19.7 / 8.8 18.0 / 5.3 6.35
8 Glycine-rich RNA-binding protein RGP-1c (gi|45533923) Nicotiana sylvestris 13.2 / 9.0 18.0 / 5.5 11.78
9 Superoxide dismutase [Cu-Zn], chloroplastic (gi|134682) Solanum lycopersicum 22.2 / 5.7 18.0 / 5.7 5.82
10 Unknown (gi|118482257) Populus trichocarpa 15.2 / 5.4 20.0 / 5.9 2.27
11 Eukaryotic translation initiation factor 5A-2 (gi|20138707) Solanum lycopersicum 17.5 / 5.7 21.0 / 6.0 13.92
12 DH putative beta-hydroxyacyl-ACP dehydratase (gi|193290688) Capsicum annuum 23.9 / 9.3 23.0 / 6.2 9.54
13 Putative pathogenesis related protein (gi|58531054) Capsicum chinense 17.1 / 5.2 22.0 / 5.5 ∞↑ 0.54
14 Putative pathogenesis related protein (gi|58531054) Capsicum chinense 17.1 / 5.2 22.0 / 5.3 23.25
15 Putative Cu/Zn superoxide dismutase (gi|171854653) Capsicum chinense 15.2 / 5.1 23.0 / 5.4 11.88
16 Transposon protein, putative, CACTA, En/Spm sub-class (gi|77553508) Oryza sativa Japonica 91.0 / 6.4 19.0 / 5.0 ∞↑ 40.13
17 Unknown (gi|118481397) Populus trichocarpa 23.0 / 7.6 19.0 / 4.9 12.31
18 P23 protein (gi|587546) Solanum tuberosum 18.7 / 4.5 25.0 / 4.7 5.64
19 Copper chaperone (gi|15228869) Arabidopsis thaliana 12.9 / 4.9 23.0 / 4.8 10.07
20 Conserved hypothetical protein (gi|255542318) Ricinus communis 19.6 / 4.9 25.0 / 4.9 2.88
21 Pathogenesis-related protein 10 (gi|60542787) Capsicum chinense 17.2 / 4.8 25.0 / 5.0 4.99
22 Thioredoxin peroxidase (gi|18654477) Capsicum annum 17.3 / 6.0 24.0 / 6.5 13.62
23 Putative transcription factor Btf3 (gi|121551087) Capsicum annuum 17.6 / 6.3 24.0 / 6.6 9.7
24 Phospholipid hydroperoxide glutathione peroxidase (gi|31872080) Solanum lycopersicum 18.9 / 6.3 26.0 / 5.6 4.32
25 Pathogenesis-related protein 10 (gi|85700977) Capsicum baccatum 17.2 / 5.2 25.0 / 5.5 ∞↑ 100
26 Pathogenesis-related protein 10 (gi|85700977) Capsicum baccatum 17.2 / 5.2 25.0 / 5.3 12.34 ↑ 38.40
27 ATP synthase subunit delta', mitochondrial (gi|2493046) Ipomoea batatas 21.3 / 5.9 27.0 / 5.0 8.71
28 Pathogenesis-related protein R major form (gi|131015) Nicotiana tabacum 24.6 / 5.3 29.0 / 4.7 13.84
29 NACA3 (gi|240256288) Arabidopsis thaliana 22.0 / 4.4 31.0 / 4.6 ∞↑ 12.49
30 Acidic 27 kDa endochitinase (gi|544010) Solanum lycopersicum 26.5 / 4.6 32.0 / 4.6 10.21
31 Unknown (gi|255641541) Glycine max 25.9 / 4.7 31.0 / 4.8 7.16
32 23kDa polypeptide of the oxygen evolving complex of photosystem II (gi|146454486) Sonneratia alba 25.1 / 5.9 27.0 / 5.6 8.57
33 Proteasome subunit beta type, putative (gi|255558626) Ricinus communis 22.8 / 5.1 27.0 / 5.9 3.74
34 Protein P21 (gi|129320  ) Glycine max 21.4 / 4.84 27.0 / 6.7 14.43
35 Proteasome subunit beta type-1 (gi|17380185 ) Petuniax hybrida 24.6 / 6.3 28.0 / 6.5 7.87
36 Dehydroascorbate reductase (gi|160347100) Nicotiana tabacum 23.4 / 6.0 28.0 / 6.3 ∞↑ 10.35
37 Triose phosphate isomerase cytosolic isoform (gi|38112662) Solanum chacoense 27.0 / 5.7 29.0 / 6.2 6.96
38 Triose phosphate isomerase cytosolic isoform-like (gi|38112662) Solanum tuberosum 27.0 / 5.7 30.0 / 5.9 ∞↑ 11.58
39 Chaperonin 10 (gi|3057150) Arabidopsis thaliana 26.9 / 8.8 32.0 / 5.3 13.02
40 Replication factor A 1, rfa1, putative (gi|255546005) Ricinus communis 75.3 / 8.1 33.0 / 4.9 32.11
41 Cysteine protease Cp1(gi|146215994) Actinidia deliciosa 39.1 / 6.1 33.0 / 4.8 8.98
42 GSTL2 (gi|15233164) Arabidopsis thaliana 33.0 / 6.7 30.0 / 5.3 7.85
43 Unknown (gi|255645535) Glycine max 33 1 / 6.8 32.0 / 5.5 12.21
44 Chaperonin 21 precursor (gi|7331143) Solanum lycopersicum 26.5 / 6.8 31.0 / 5.5 3.41
45 Unknown (gi|77416969) Solanum tuberosum 25.6 / 5.3 30.0 / 5.6 12.70
46 Proteasome-like protein alpha subunit (gi|77999303) Solanum tuberosum 27.1 / 5.6 30.0 / 5.7 10.66
47 Unknown (gi|255645535) Glycine max 33.1 / 6.8 32.0 / 5.7 17.65↑ 18.79
48  L-ascorbate peroxidase (gi|804973) Capsicum annuum 27.3 / 5.3 33.0 / 5.8 4.82
49 Tropinone reductase 1 (gi|1717752) Datura stramonium 29.5 / 6.1 32.0 / 6.3 6.97
50 Cytosolic ascorbate peroxidase (gi|62910196) Capsicum annuum 27.4 / 5.7 31.0 / 6.5 7.85
51 Fibrillin (gi|460761) Capsicum annum 35.2 / 5.0 37.0 / 4.8 23.51
52 Unknown (gi|255638262) Glycine max 34.7 / 5.5 35.0 / 5.2 7.49
53 Chloroplast managanese stabilizing protein (gi|283049930) Capsicum annuum 29.9 / 8.1 35.0 / 5.3 12.02
54 Predicted protein (gi|224103823) Populus trichocarpa 33.5 / 6.8 35.0 / 5.3 3.84
55 Harpin binding protein 1 (gi|38679329) Solanum tuberosum 30.0 / 8.3 34.0 / 5.3 3.49
56 Hypothetical protein VITISV_014475 (gi|147856362) Vitis vinifera 30.7 / 5.0 37.0 / 5.4 6.41
57 Phenylcoumaran benzylic ether reductase (gi|213385143) Nicotiana tabacum 33.9 / 5.9 37.0 / 5.9 8.82
58  Predicted protein (gi|224063293) Populus trichocarpa 31.5 / 5.8 39.0 / 6.7 3.36
59 Malate dehydrogenase (gi|68299213) Capsicum chinense 19.9 / 5.3 42.0 / 6.5 ∞↑ 14.18
60 Malate dehydrogenase (gi|68299213) Capsicum chinense 19.9 / 5.3 41.0 / 6.3 5.69
61 Malate dehydrogenase (gi|68299213) Capsicum chinense 19.9 / 5.3 42.0 / 6.3 36.07
62 Malate dehydrogenase (gi|68299213) Capsicum chinense 19.9 / 5.3 41.0 / 6.0 12.37
63 Glutamine synthetase GS1 (gi|209529862) Solanum tuberosum 38.5 / 5.2 44.0 / 6.0 4.49
64  Putative pyruvate dehydrogenase E1 beta subunit (gi|193290724) Capsicum annuum 44.2 / 6.0 42 0 / 5.9 6.25
65 Caffeic acid 3-O-methyltransferase (gi|30315948) Capsicum annum 39.4 / 5.6 46.0 / 5.9 11.31
66 Putative enoyl-acyl-carrier-protein reductase (gi|193290684) Capsicum annuum 41.6 / 8.8 41.0 / 5.7 8.18
67 Alpha-galactosidase (gi|34765755) Petunia x hybrida 31.3 / 4.8 43.0 / 5.7 6.18
68 DegP protease precursor (gi|2565436  ) Arabidopsis thaliana 46.1 / 6.0 41.0 / 5.6 4.42
69 Putative stress related chitinase (gi|62719021) Nicotiana tabacum 9.0 / 3.9 42.0 / 4.7 8.03
70 Fructokinase 3 (gi|38604456) Solanum lycopersicum 41.4 / 5.5 42.0 / 5.1 3.78
71 Cysteine synthase, chloroplastic/ chromoplastic (gi|11131628) Solanum tuberosum 41.0 / 5.4 42.0 / 5.3 5.58
72 Hypothetical protein SELMODRAFT_111224 (gi|302795987) Selaginella moellendorffii 35.5 / 5.1 43.0 / 5.4 3.77
73 Predicted protein (gi|224053535) Populus trichocarpa 38.5 / 5.8 45.0 / 5.6 8.48
74 Caffeic acid O-methyltransferase (gi|12003964) Capsicum annuum 39.3 / 5.5 44.0 / 5.7 5.32
75 Glutamine synthetase GS58  (gi|40457328) Nicotiana attenuata 47.4 / 6.7 47.0 / 5.7 4.35
76 3-oxoacyl-[acyl-carrier-protein] synthase (gi|3599489) Capsicum chinense 52.4 / 8.0 47.0 / 6.2 11.65
77 3-oxoacyl-[acyl-carrier-protein] synthase (gi|3599489) Capsicum chinense 52.4 / 8.0 48.0 / 6.4 ∞↑ 6.05
78 Leucine aminopeptidase 2, chloroplastic (gi|2492530) Solanum lycopersicum 59.5 / 8.1 53.0 / 6.3 6.26
79 Enolase-like (gi|82623425) Solanum tuberosum 48.0 / 7.5 56.0 / 6.2 ∞↑ 13.51
80 UTP--glucose-1-phosphate uridylyltransferase (gi|136739) Solanum tuberosum 51.8 / 5.7 52.0 / 6.0 5.74
81 Enolase-like (gi|82623425) Solanum tuberosum 48.0 / 7.5   5.20
82 UTP--glucose-1-phosphate uridylyltransferase (gi|136739 ) Solanum tuberosum 51.8 / 5.7 51.0 / 5.9 9.42
83 Enolase (gi|119354) Solanum lycopersicum 47.7 / 5.6 60.0 / 5.8 3.13
84 Endopolygalacturonase (gi|78482998) Capsicum annuum 33.9 / 6.8 54.0 / 5.9 3.09
85 Ankyrin-repeat protein HBP1 (gi|13310811) Nicotiana tabacum 37.2 / 4.4 46.0 / 4.6 8.7 ↑ 10.14
86 Adenosine kinase isoform 1T (gi|51949796) Nicotiana tabacum 37.4 / 5.1 45.0 / 5.2 5.26
87 Actin-51 (gi|3219772) Solanum lycopersicum 37.1 / 5.2 47.0 / 5.4 3.81
88 Actin (gi|158529884) Glycyrrhiza uralensis 41.5 / 5.3 46.0 / 5.6 13.74
89 Malate dehydrogenase (gi|56562183) Solanum lycopersicum 48.4 / 6.2 45.0 / 5.6 4.19
90 LEXYL2 (gi|37359708) Solanum lycopersicum 68.8 / 8.0 71.0 / 6.3 15.68 ↑ 4.67
91 Putative branched-chain alpha-keto acid dehydrogenase E2 subuni (gi|193290668) Capsicum annuum 55.0 / 6.7 51.0 / 5.6 2.09
92 Hypothetical protein OsI_31140 (gi|125563499) Oryza sativa Indica 50.7 / 5.7 52.0 / 5.6 2.98
93 RAD23-like (gi|77745475) Solanum tuberosum 40.6 / 4.7 50.0 / 4.9 3.42
94 Calreticulin (gi|11131769) Nicotiana plumbaginifolia 47.4 / 4.4 57.0 / 4.7 ∞  ↑ 23.46
95 RAD23 protein (gi|5640111) Solanum lycopersicum 41.4 / 4.6 50.0 / 4.9 1.80
96 Serine carboxypeptidase III (gi|148469859) Nicotiana tabacum 56.4 / 4.9 51.0 / 5.3 0.288↓ 5.70
97 ATP synthase subunit beta, mitochondrial
(gi|114421)
Nicotiana plumbaginifolia 59.8 / 5.9 57.0 / 5.5 ∞↑ 9.43
98 ATP synthase subunit beta, mitochondrial (gi|114421) Nicotiana plumbaginifolia 59.8 / 5.9 60.0 / 5.4 5.02
99 ATP synthase subunit beta, mitochondrial precursor (gi|162462751) Zea mays 59.0 / 6.0 56.0 / 5.4 ∞↑ 5.91
100 ATP synthase subunit beta, mitochondrial precursor (gi|114421) Zea mays 59.8 / 5.9 60.0 / 5.3 5.20
101 Protein disulfide isomerase-like protein (gi|49257109) Glycine max 58.6 / 5.0 58.0 / 5.1 ∞↑ 4.25
102 RuBisCO large subunit-binding protein subunit alpha, chloroplastic (gi|1351030) Brassica napus 57.6 / 4.8 70.0 / 5.1 5.19
103 Abscisic stress ripening protein (gi|607905) Solanum chacoense 29.0 / 4.9 67.0 / 5.2 ∞  ↑ 4.32
104 Abscisic stress ripening protein (gi|607905) Solanum chacoense 29.0 / 4.9 67.0 / 5.3 11.14
105 Unknown (  gi|116787373) Picea sitchensis 65.5 / 5.6 59.0 / 5.4 4.21
106 RuBisCO large subunit-binding protein subunit beta, chloroplastic (gi|2506277) Pisum sativum 62.9 / 5.8 70.0 / 5.3 2.93
107 Stromal 70 kDa heat shock-related protein, chloroplastic (gi|1708311) Spinacia oleracea 64.8 / 4.8 90.0 / 5.0 12.28 ↑ 1.93
aTheoretical values were obtained with the help of an online tool at http://expasy.org/sprot/.
bRelative to most abundant protein on the gel. Spot volume was estimated as average OD x mm2 in replicate gels using spot density determination tool in PD Quest software.
Table 2: Protein spots identified from fruit lysate of ‘Bhut Jolokia’ along with differentially expressed proteins.