Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry

Dupont, Frances M; Vensel, William H; Tanaka, Charlene K; Hurkman, William J; Altenbach, Susan B

doi:10.1186/1477-5956-9-10

Proteome Science

Table 10 Identification and quantification of enzymes and other factors by 2DE-MS/MS.

From: Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry

Spot #	Predominant protein¹	Total proteins in spot²	Spot Volume³	Std Dev⁴	MS/MS Coverage⁵	Predicted MW⁶	pI⁷
	Beta-amylase (β-Amy-A1, β-Amy-B1, β-Amy-D1)
476	Beta-amylase Bu-1⁸	4	-	-	32	60016	6.9
537	Beta-amylase Bu-1	2	0.04	0.010	18	60016	6.9
94	Beta-amylase Bu2	2	0.04	0.006	47	54481	5.9
462	Beta-amylase Bu2	2	0.11	0.014	60	54481	5.9
64	Beta-amylase Bu3	1	0.05	0.010	13	54319	5.8
92	Beta-amylase Bu3	1	0.18	0.029	34	54319	5.8
93	Beta-amylase Bu3	1	0.09	0.013	55	54319	5.8
	Other enzymes ⁹
89	ADP-glucose PP lg subunit [GenBank:CAD98749]	1	0.03	0.002	10	53030	5.6
128	ADP-glucose PP lg subunit [GenBank:CAD98749]	1	0.10	0.047	11	53030	5.6
108	ADP-glucose PP sm subunit [GenBank:AAF61173]	2	0.09	0.013	60	52061	5.5
110	ADP-glucose PP sm subunit [GenBank:AAF61173]	2	0.06	0.019	24	52061	5.5
118	Alanine amino transferase TC11_282456	1	0.06	0.002	36	52820	6.1
109	ATP-synthase beta-subunit [GenBank:CAA52636]	1	0.02	0.004	32	58562	5.4
232	Chitinase, rye, [GenBank:BAB18520]	1	0.04	0.009	40	26095	8.7
455	Chitinase [GenBank:AAX83262]	1	0.05	0.010	26	26022	8.3
241	Dehydroascorbate reductase TC264934	2	0.09	0.013	83	23358	5.9
123	Enolase TC11_292359	2	0.07	0.014	64	48033	5.4
178	Glyoxalase I TC11_288238	1	0.10	0.020	68	32568	5.4
202	Glucose/ribitol dehydrogenase RS_UWI_14903	1	<0.01	0.000	57	31851	6.3
436	Ketol-acid reducto isomerase TC234371	3	0.05	0.005	21	57486	5.4
175	Malate dehydrogenase [GenBank:AAT64932]	1	0.03	0.007	41	35486	5.8
176	Malate dehydrogenase [GenBank:AAT64932]	1	0.15	0.000	58	35486	5.8
450	Methionine synthase RS_UWI_10957	1	0.02	0.005	11	84552	5.7
371	Orthophosphate dikinase TC11_322894	1	0.03	0.004	19	73501	5.8
299	PDI3 [GenBank:AAK49425]	3	0.14	0.016	53	54094	4.9
475	Sucrose synthase 2 [GenBank:CAA03935]	1	0.08	0.011	19	92608	6.2
189	Thiamine biosynth enzyme TC11_308909	2	0.08	0.007	35	33167	5.7
225	Triose-phosphate isomerase [GenBank:CAC14917]	1	0.05	0.006	38	26803	5.4
239	27 K thiol reductase-like TC11_300123	1	0.16	0.037	54	23642	6.1
479	27 K thiol reductase like TC11_299048	2	0.02	0.005	16	23788	6.1
	Other
311	Elongation factor EF1A [Swiss-Prot: Q03033]	1	0.11	0.005	14	49169	9.2
533	HSP70 (Butte 86) [GenBank:AAB99745]	1	0.08	0.009	18	71031	5.1
413	Initiation factor Eif4A [Swiss-Prot: P41378.1]	1	0.06	0.014	36	46928	5.3
295	LTP Bu-2	1	0.04	0.009	38	9606	8.2
456	Thaumatin-like protein TC11_283136	2	0.05	0.007	39	21408	7.9

Loci are indicated within parentheses if known.
¹ Protein that matched the greatest number of peptides detected in spot by MS/MS. Accession numbers from TaGI Release 10.0 are denoted with the prefix TC and TaGI release 11.0 with the prefix TC11_. Accession numbers from HarvEST 1.14 are denoted with RS_UWI_. Sequences of proteins from Butte 86 are found in Additional file 2.
^2-7 Footnotes as in Table 3.
⁸Although Scaffold identified more peptides for beta-amylase in spot 476, other data indicate that this spot was predominantly omega-gliadin.
⁹The following enzymes or factors were detected as minor components of other spots: alcohol dehydrogenase, aspartic protease, formate dehydrogenase, fructose bisphosphate aldolase, GDP-binding protein, manganese superoxide dismutase, peroxidase, peroxiredoxin, phosphoglycerate kinase.

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ISSN: 1477-5956

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