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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).