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Table 1 Amaranth proteins identified in differentially accumulated bands by nLC-MS/MS

From: Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species

Banda No.

Protein

Acc. No.b

Mrc Exp.

Mrd Theor.

Mascot Scoree

PM/SCf (%)

emPAIg

1

Elongation factor 2

001926

97.28

94.87

116

8/11

0.30

Ribonuclease TUDOR 1

004841

109.14

58

18/20

0.38

Low-temperature-induced-like

018897

87.08

51

13/20

0.22

Phosphoenolpyruvate carboxylase 3

004468

108.39

46

5/6

0.08

2

Alpha-xylosidase 1

020003

87.98

93.92

233

9/11

0.30

Poly [ADP-ribose] polymerase 3

003773

82.76

166

12/23

0.29

Starch branching enzyme I

000673

100.56

160

16/20

0.41

Elongation factor 2

001926

94.87

132

10/17

0.34

Chaperone 1

008070

100.77

81

9/12

0.19

Aminopeptidase M1

006828

95.06

58

5/7

0.12

3

Methionine synthase

017360

78.85

78.493

529

18/30

0.39

Late embryogenesis abundant protein

013747

72.37

304

13/23

0.47

Methionine synthase

022179

89.82

219

9/16

0.17

Sucrose synthase

021141

69.92

124

8/17

0.28

Alpha-xylosidase 1

010666

100.26

111

7/9

0.19

Disulfide isomerase

015532

56.01

51

5/14

0.13

4

Vicilin-like

018839

72.74

61.21

191

8/18

0.25

Embryonic protein DC-8-like

000638

65.20

61

6/10

0.23

5

11S globulin

021282

57.85

78.10

186

16/32

0.31

Vicilin-like

018839

61.21

163

8/18

0.50

Catalase

007232

52.51

112

6/12

0.31

Glucose-6-phosphate isomerase

013135

57.20

80

5/12

0.28

6

Vicilin-like

018839

52.81

61.21

409

14/31

1.07

11S globulin

021282

78.10

356

18/34

0.69

Late embryogenesis abundant protein

001171

45.86

265

8/24

0.95

UTP-glucose-1-phosphate uridylyltransferase

008585

48.70

176

9/25

0.63

Enolase 1

001183

45.11

156

9/29

1.13

ATP synthase subunit mitochondrial-like

001716

59.31

145

7/15

0.50

Adenosylhomocysteinase 1

009349

53.89

119

8/16

0.56

Leucine aminopeptidase 1-like

014952

63.04

43

5/10

0.18

7

Vicilin-like

018839

47.21

61.21

96

3/5

0.37

Eukaryotic initiation factor 4A-9

003448

47.07

45

3/9

0.15

8

Phosphoglycerate kinase

006883

43.28

87.94

573

19/27

0.51

Phosphoglycerate kinase

019107

42.55

379

14/38

1.13

11S globulin

021282

78.10

140

14/25

0.15

Vicilin-like

018839

61.21

133

6/13

0.19

Actin-7

019031

41.93

104

7/19

0.40

9

Glyceraldehyde-3-phosphate dehydrogenase

011043

38.41

31.58

410

9/37

0.44

Vicilin-like

018839

61.21

403

10/22

0.46

Aldose 1-epimerase-like

015176

32.27

132

6/24

0.27

Dehydrin Rab18-like

003168

26.47

58

5/27

0.33

11S globulin

021282

78.10

37

5/10

0.10

10

Vicilin-like

018839

37.42

61.21

437

13/25

0.37

Lactoylglutathione lyase

011906

30.92

143

4/14

0.28

Malate dehydrogenase

021284

36.13

124

6/29

0.19

11

Vicilin-like

006304

31.21

62.07

534

15/34

0.47

Late embryogenesis abundant protein (SMP)

006906

28.70

190

6/33

0.60

Late embryogenesis abundant protein (SMP)

016810

22.64

167

5/34

1.10

11S globulin

001411

55.75

130

4/10

0.13

11S globulin

021282

78.10

108

7/16

0.09

60S ribosomal protein L6–3

005418

25.60

94

5/29

0.70

Agglutinin

007409

30.40

80

4/18

0.56

12

Oil body-associated protein 1A

009953

29.19

26.80

255

11/35

1.22

Vicilin-like

006304

62.07

186

3/9

0.12

60S ribosomal protein L7–4

008528

28.35

180

5/18

0.65

Elongation factor 1-beta 1

002577

24.87

170

3/20

0.53

Oil body-associated protein 2A

004342

25.76

98

7/29

0.99

Protein synthesis inhibitor PD-S2-like

011528

30.52

94

4/19

0.42

13

Protein synthesis inhibitor PD-S2-like

011528

27.81

30.52

362

13/42

1.39

Oil body-associated protein 2A

004342

25.76

193

6/25

0.80

14

Cysteine proteinase inhibitor 6

021786

26.87

27.78

270

11/52

1.44

Vicilin-like

018839

61.21

76

5/11

0.26

11S globulin

021282

78.10

46

5/10

0.15

15

11S globulin

001411

22.98

55.75

377

8/19

0.47

16

11S globulin

021282

21.73

78.10

290

10/16

0.51

11S globulin

001411

55.75

242

5/12

0.38

17

17.6 kDa class I heat shock protein 3

013876

17.93

17.92

182

7/46

1.18

Oleosin 5

013707

20.73

72

5/28

0.96

Oleosin 5

015343

20.46

69

4/21

0.67

18

Cyclophilin

002428

17.43

17.21

85

2/13

0.26

17.4 kDa class I heat shock protein 3

012223

17.36

34

6/33

0.25

19

Late embryogenesis abundant protein (LEA_5)

008005

15.82

9.66

152

5/59

2.50

20

Vicilin-like

018839

14.82

61.21

84

4/8

0.30

23

Histone H4

005348

11.74

11.40

62

5/41

1.51

24

Late embryogenesis abundant protein (LEA_5)

019862

10.73

8.53

49

3/49

0.47

27

Granule-bound starch synthase chloroplastic amyloplastic

011500

63.25

63.00

1112

27/58

3.08

11S globulin

021282

78.10

287

14/26

0.42

Vicilin-like

018839

61.21

231

10/23

0.48

Indole-3-aceticacid-amido synthetase

011444

70.17

65

4/6

0.21

28

Granule-bound starch synthase chloroplastic amyloplastic

011500

56.53

63.00

837

19/43

2.36

11S globulin

021282

78.10

475

17/38

1.04

Vicilin-like

018839

61.21

38

3/6

0.12

29

11S globulin

021282

52.41

78.10

412

20/43

1.22

Granule-bound starch synthase chloroplastic amyloplastic

011500

63.00

122

8/13

0.47

Vicilin-like

018839

61.21

119

10/23

0.66

ATP synthase subunit mitochondrial-like

001716

59.31

116

9/21

0.59

Late embryogenesis abundant protein

001171

45.86

114

5/13

0.35

Elongation factor 1-alpha 1

001308

50.96

66

7/17

0.50

Serine hydroxymethyltransferase 4

009350

59.74

66

4/12

0.12

30

Vicilin-like

018839

37.95

61.21

333

9/23

0.50

11S globulin

021282

78.10

210

13/23

0.50

Aldose 1-epimerase-like

015176

32.27

140

5/21

0.38

11-beta-hydroxysteroid dehydrogenase 1B

004692

74.56

109

9/18

0.21

Glyceraldehyde-3-phosphate dehydrogenase

013553

31.71

83

6/28

0.73

31

Vicilin-like

006304

19.47

62.10

90

7/17

0.20

Oil body-associated protein 1A

009953

26.79

89

7/35

1.60

32

Vicilin-like

006304

27.11

62.10

90

3/5

0.06

Protein synthesis inhibitor PD-S2-like

011528

30.52

82

8/30

0.81

Oil body-associated protein 2A

004342

25.76

45

4/20

0.32

33

Vicilin-like

018839

14.75

61.21

137

4/9

0.27

Vicilin-like

006202

59.16

109

5/7

0.28

Nucleoside diphosphate-kinase1

014404

16.19

45

3/17

0.22

11S globulin

001411

55.75

42

3/6

0.55

34

11S globulin

001411

10.72

55.75

109

6/15

0.22

Vicilin-like

006202

59.16

54

5/7

0.28

  1. aBand numbers according Fig. 5. bAccession number according to the database reported by Clouse et al. [9]. cExperimental molecular weight (kDa). dTheoretical molecular weight (kDa). eMASCOT Score, individual ion scores > 33 are statistically significant (P < 0.01), only identifications with peptide matches above identity threshold when FDR ≤5% were considered true. fPeptides Matched/Sequence Coverage. gExponentially Modified Protein Abundance Index. Protein names in bold letters are discussed in the text