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Table 4 Differentially expressed proteins identified by MALDI TOF-TOF MS

From: Metaproteomic analysis of ratoon sugarcane rhizospheric soil

Spot no. a)

GI no. b)

Protein name

Score (PMF) c)

PMF/Coveraged)

MW/ pIe)

Score (MS-MS) f)

Pept g)

Species

Function h)

RS/

CK i)

RS/

NS j)

12

gi|115470493

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

106

20/34%

69494/6.61

185

3

Oryza sativa

TCA

1.9

1.9

13

gi|115467370

Phosphofructokinase

130

18/38%

61907/6.01

251

4

Oryza sativa

EMP

1.7

1.7

16

gi|115459078

Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3

117

14/51%

36921/6.34

122

2

Oryza sativa

EMP

1.6

1.5

18

gi|115480019

Proteasome beta type-1

136

11/50%

24608/6.43

92

2

Oryza sativa

Protein degradation

0.8

1.5

23

gi|51090388

Putative PrMC3

107

16/59%

34540/5.61

296

3

Oryza sativa

Stress/defense response

1.6

1.7

25

gi|115111257

Betaine aldehyde dehydrogenase

86

10/31%

55361/5.29

276

4

Oryza sativa

Amino acid metabolism

2.2

2.2

26

gi|115464537

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

127

20/42%

61003/5.25

361

5

Oryza sativa

EMP

2.0

1.0

27

gi|115448989

Heat shock 70 kDa protein, mitochondrial precursor

96

19/34%

73081/5.49

456

4

Oryza sativa

Stress/defense response

2.3

2.2

28

gi|54606800

NADP dependent malic enzyme

84

24/37%

65824/5.79

193

3

Oryza sativa

Pyruvate metabolism

2.1

2.1

29

gi|115477952

Cyclase family protein

80

11/39%

29792/5.32

115

2

Oryza sativa

Signal transduction

2.4

1.0

31

gi|115440691

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

189

30/50%

60980/5.42

500

4

Oryza sativa

EMP

1.1

1.7

32

gi|108708038

Fumarate hydratase 1, mitochondrial precursor, putative, expressed

124

13/27%

53991/6.93

210

4

Oryza sativa

TCA

1.8

1.6

35

gi|968996

Glyceraldehyde-3-phosphate dehydrogenase

139

14/50%

36641/6.61

379

3

Oryza sativa

EMP

1.7

1.5

37

gi|3024122

S-adenosylmethionine synthase 2

100

18/60%

43330/5.60

405

4

Oryza sativa

Amino acid metabolism

0.4

0.6

1

gi|1203832

Beta-D-glucan exohydrolase, isoenzyme ExoII

  

67835/7.96

153

2

Hordeum vulgare

Glycan metabolism

4.0

1.5

4

gi|3868754

Catalase

  

57052/6.49

147

2

Oryza sativa

Stress/defense response

2.9

1.7

21

gi|115455455

UDP-glucose 6-dehydrogenase

  

53435/5.79

208

3

Oryza sativa

Glycan metabolism

1.5

1.0

33

gi|38605779

NAD-dependent isocitrate dehydrogenase

  

36882/5.77

221

3

Oryza sativa

TCA

1.8

1.0

2

gi|226357624

Putative sugar ABC transporter, periplasmic component

84

10/33%

46676/9.68

  

Deinococcus deserti

Membrane transport

3.0

1.6

3

gi|241957693

Mitochondrial N-glycosylase/DNA lyase

74

11/39%

40573/8.46

  

Candida dubliniensis

Nucleotide metabolism

3.1

1.9

5

gi|254399905

ABC transporter ATP-binding subunit

82

18/31%

66963/5.53

  

Streptomyces sviceus

Membrane transport

2.0

1.5

6

gi|126662203

Oxidoreductase

74

13/20%

76867/8.83

  

Flavobacteria bacterium

Oxidation reduction

2.4

1.7

7

gi|261195979

ORP1

74

10/39%

36747/9.48

  

Ajellomyces dermatitidis

Signal transduction

1.6

1.5

8

gi|238481813

ADP-ribosylglycohydrolase

84

18/28%

49119/6.02

  

Aspergillus flavus

Signal transduction

1.0

0.5

9

gi|261854741

Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

85

9/41%

26805/4.63

  

Halothiobacillus neapolitanus

Amino acid metabolism

0.6

0.6

10

gi|115456914

Elongation factor EF-2

101

23/31%

94939/5.85

  

Oryza sativa

Protein metabolism

4.6

2.3

11

gi|219667596

Radical SAM domain protein

82

11/46%

38272/5.24

  

Desulfitobacterium hafniense

Diverse reaction

2.3

2.5

14

gi|111024023

Acyl-CoA dehydrogenase

87

13/37%

41071/5.40

  

Rhodococcus jostii

Amino acid metabolism

2.8

1.9

15

gi|23009750

Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit

87

7/92%

6114/4.52

  

Magnetospirillum magnetotacticum

TCA

1.9

1.0

17

gi|253988359

Phosphoglycerate kinase

83

9/33%

41652/5.19

  

Photorhabdus asymbiotica

EMP

0.6

1.0

19

gi|94497581

Electron-transferring-flavoprotein dehydrogenase

84

9/25%

61194/5.66

  

Sphingomonas sp.

Energy metabolism

0.5

0.6

20

gi|85110870

Related to kinesin-like protein

74

26/21%

195364/5.31

  

Neurospora crassa

Cytoskeleton protein

2.0

2.0

22

gi|194366013

Nitrate reductase, alpha subunit

71

19/16%

140507/5.98

  

Stenotrophomonas maltophilia

Nitrogen metabolism

1.9

1.1

24

gi|21492793

Conjugal transfer protein A

91

24/19%

171793/6.93

  

Rhizobium etli

Bacterial conjugation

2.1

1.0

30

gi|219664364

Two-component system sensor kinase

87

19/15%

176010/6.50

  

Rhodococcus sp.

Signal transduction

3.0

1.6

34

gi|126135008

Isocitrate dehydrogenase [NADP], mitochondrial precursor

76

14/32%

48355/8.21

  

Pichia stipitis

TCA

1.7

1.7

36

gi|52426030

MrcA protein

90

18/25%

96552/6.40

  

Mannheimia succiniciproducens

Glycan metabolism

1.6

1.0

38

gi|148685933

Tubulin, gamma complex associated protein 2

90

18/29%

89598/6.52

  

Mus musculus

Cytoskeleton protein

0.6

0.9

  1. Note: Protein spots 12, 13, 16, 18, 23, 25-29, 31, 32, 35 and 37 shared equal searching by MS/MS and MS. Protein spots 1, 4, 21 and 33 matched at least two MS/MS peptides. The remainders matched at least three PMFs. a) The numbering corresponds to the 2-DE gel in Additional file 3: Figure S3. b) GI number in NCBI. c) MASCOT score of PMF. d) The number of peptides identified by MS/sequence percentage coverage. e) Theoretical molecular weight and pI. f) MASCOT score of MS/MS. g) Number of peptides identified by MS/MS. h) Functional classification using KEGG database. i) the ratio of ratoon cane soil (RS) to control soil (CK). j) the ratio of ratoon cane soil (RS) to plant cane soil (NS).