Table 4.

Differentially expressed proteins identified by MALDI TOF-TOF MS

Spot no. a)	GI no. b)	Protein name	Score (PMF) c)	PMF/Coveraged)	MW/ pI e)	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

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).