Table 1.

Protein identities based on peptide matches to Genbank protein databases

				fold enrich.b
spot ID#	func. cat.a	protein identity	Genbank ID	fibre	non-fibre	p-valuec	Mowse score	pep. countd
2	C&E	aconitate hydratase	4586021	1.5		0.14	64	2
3	C&E	aconitate hydratase	4586021	1.5		0.08	68	2
17	C&E	β-amylase	1771782	8.8		< 0.01	46	2
39	C&E	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	168312	1.5		0.25	85	2
40	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	168312		2.0e	0.08	180	4
44	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	1834444		6.1	< 0.01	129	5
45	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	2687483		5.4	< 0.01	130	4
46	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	6983900		2.9	< 0.01	232	6
47	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	1817560		3.3	< 0.01	250	5
48	C&E	enolase	9581744	1.1		0.65	265	7
49	C&E	enolase	8919731		1.1	0.93	158	3
50	C&E	enolase	9581744		3.4	0.02	206	6
51	C&E	ribulose-1,5-bisphosphate carboxylase, large subunit	4098530	2.8		0.04	103	4
57	C&E	fumarate hydratase	108708038	2.5		0.01	83	2
58	C&E	fumarate hydratase	15226618	1.6		0.33	100	4
59	C&E	6-phosphogluconate dehydrogenase	2529229	1.5		0.19	100	3
63	C&E	citrate synthase	11066954	3.7		< 0.01	123	4
68	C&E	phosphoglycerate kinase	1161600	1.2		0.56	257	4
71	C&E	phosphoglycerate kinase	92872324	1.7		0.06	426	7
72	C&E	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	66735801				96	3
73	C&E	rubisco activase	13430332		6.1	< 0.01	70	3
74	C&E	rubisco activase	170129		5.2	< 0.01	61	3
75	C&E	phosphoglycerate kinase	3328122		2.9	0.02	250	6
77	C&E	fructose-bisphosphate aldolase	15227981	1.1		0.82	155	3
78	C&E	fructose-bisphosphate aldolase	20204	2.4		0.03	102	2
79	C&E	fructose-bisphosphate aldolase	15227981	1.1		0.6	116	2
80	C&E	fructose-bisphosphate aldolase	20204	1.3		0.04	177	3
81	C&E	rubisco activase	4261547		2.2	0.03	60	2
82	C&E	succinate-CoA ligase	15225353	2.3		0.02	253	5
83	C&E	glyceraldehyde-3-phosphate dehydrogenase	120666	2.6		0.01	76	2
86	C&E	glyceraldehyde-3-phosphate dehydrogenase	3023813	1.1		0.49	71	3
87	C&E	glyceraldehyde-3-phosphate dehydrogenase	74419004	3.8		< 0.01	215	6
90	C&E	malate dehydrogenase	18297	1.6		0.17	241	4
91	C&E	malate dehydrogenase	18297	1.4		0.26	138	4
92	C&E	malate dehydrogenase	10334493	3.3		< 0.01	296	7
93	C&E	fructokinase	31652274	6.7		< 0.01	142	5
94	C&E	fructokinase	31652274	2.2		< 0.01	154	3
96	C&E	kinase/ribokinase, potential fructokinase	15224669	2		0.01	208	8
1	ATP	AAA-ATPase	86212372	1.6		0.24	322	10
7	ATP	ATPase, transitional endoplasmic reticulum	7378614	1.2e		0.65	101	4
24	ATP	vacuolar proton-ATPase	50251203	2.6		0.02	585	13
31	ATP	ATP binding	15221770		1	0.87	100	4
35	ATP	F1 ATPase	12986	1.6		0.05	143	6
40	ATP	ATP synthase β subunit	21684923		2.0e	0.08	192	4
42	ATP	ATP synthase β subunit	19685	1		0.99	675	12
43	ATP	ATP synthase β subunit	56784991		1.8	0.06	307	7
99	ATP	F1-ATPase gammma subunit	303626	1		0.66	84	3
105	ATP	vacuolar V-H+ATPase subunit E	5733660	1.8		0.01	53	2
106	ATP	vacuolar V-H+ATPase subunit E	5733660		1.1	0.82	100	4
12	CWP	β-galactosidase	115437888	8.4		< 0.01	43	3
13	CWP	β-galactosidase	3641863	8.9		< 0.01	42	2
14	CWP	β-galactosidase	3641863	5.4		< 0.01	105	5
15	CWP	β-galactosidase	3641863	8.8		< 0.01	96	5
16	CWP	β-galactosidase	34913072	9.3		< 0.01	72	4
18	CWP	MUCILAGE-MODIFIED 4	42562732	4.1		< 0.01	57	2
19	CWP	rhamnose biosynthetic enzyme	108707484	6.6		< 0.01	100	6
27	CWP	phosphoglucomutase	12585309	1.8		0.15	170	4
28	CWP	phosphoglucomutase	6272281	3.7		0.02	122	5
36	CWP	UDP-glucose pyrophosphorylase	6136112		1.4	0.37	82	3
38	CWP	UDP-glucose pyrophosphorylase	82659609		3.5	0.01	166	6
41	CWP	UDP-glucose pyrophosphorylase	9280626	1.6e		0.1	129	6
64	CWP	β-galactosidase	3641863	1.2		0.51	72	2
76	CWP	NAD-dependent epimerase/dehydratase (UXS6)	15226950	6.1		< 0.01	109	4
88	CWP	UDP-glucose 4-epimerase	12643850		1.1	0.84	60	2
101	CWP	GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase	12324315	2.3		< 0.01	155	3
104	CWP	dTDP-D-glucose 4,6-dehydratase-like	50253123	3		< 0.01	56	2
9	1C	Met synthase	77556633	2		< 0.01	222	6
10	1C	Met synthase	8439545	2.2		< 0.01	105	3
41	1C	S-adenosyl-L-homocysteine hydrolase	1710838	1.6e		0.1	174	5
53	1C	serine hydroxymethyltransferase	11762130	2.2		0.02	129	4
60	1C	Met adenosyltransferase	37051117	2.1		0.02	94	4
55	MemT	GDP dissociation inhibitor	8439465	2		0.13	212	5
56	MemT	GDP dissociation inhibitor	8439465	1.9		0.08	158	4
95	MemT	K+ channel β-subunit	15219795	8.6		0.01	132	4
102	MemT	34 kDa outer mitochondrial membrane porin-like protein	83283993	1.7			55	2
103	MemT	36kDa porin I	515358	3.9		< 0.01	104	4
5	C&S	myosin heavy chain	108710464	2.5		0.05	46	2
6	C&S	myosin heavy chain	T00727	3.6		0.01	48	2
22	C&S	dynamin central region	92891191	3.1		0.09	83	3
25	C&S	dynamin-like	21593776		1	0.77	143	4
37	C&S	β-tubulin	295851	1.8		0.06	161	6
52	C&S	tubulin/FtsZ family, GTPase domain	62734655	1.7		0.06	367	12
69	C&S	actin	32186910	3.1		0.01	281	8
70	C&S	actin	15242516	1.5		0.21	459	12
4	P&AA	elongation factor EF-2	6056373	2.5		0.02	40	3
7	P&AA	ClpC protease	4105131	1.2e			81	4
8	P&AA	ClpC protease	18423214		1.7	0.06	286	11
11	P&AA	HSP 90	1708314	1.7		0.01	312	10
20	P&AA	HSP 70-3	38325815	1.9		0.08	404	11
21	P&AA	HSP 70	62733235	1.7		0.11	612	13
23	P&AA	HSP 70	22636	2		0.04	100	3
29	P&AA	chaperonin CPN60-1	108706134	2.7		0.04	139	6
30	P&AA	chaperonin CPN60-1	108706134	1.5		0.04	327	7
32	P&AA	HSP 60	16221	2.1		0.02	140	4
54	P&AA	eukaryotic elongation factor 1A	24371059		2.3	0.02	227	7
61	P&AA	26S protease regulatory subunit	1709798	2.1		< 0.01	85	3
62	P&AA	translation initiation factor eIF-4A	475221	1.6		0.09	262	9
65	P&AA	26S proteasome subunit P45	92870338	1.9		0.11	90	3
66	P&AA	aminomethyltransferase	3334196		3.7	< 0.01	67	2
67	P&AA	elongation factor-1 alpha	396134	1.2		0.5	54	3
72	P&AA	glutamine synthetase	121341		1.7e	0.26	119	4
84	P&AA	P0 ribosomal protein	1143507		2.5	< 0.01	155	3
89	P&AA	glutamate-ammonia ligase	99698	1.2e		0.5	65	3
114	P&AA	eukaryotic translation initiation factor 5A	8778393	2		0.04	91	2
26	misc	nucleolar protein NOP5	108708132	1.4		0.37	47	2
33	misc	ferric leghemoglobin reductase	5823556	1.6		0.2	124	4
34	misc	calreticulin	3288109		1	0.9	78	3
85	misc	peroxidase	1389835	2.4		0.03	214	7
89	misc	type IIIa membrane protein cp-wap13	2218152				58	3
97	misc	annexin	1429207	2.2		0.01	146	4
98	misc	annexin	1429207	4.1		0.03	71	2
100	misc	enoyl-ACP reductase	2204236	2.1		0.01	44	2
107	misc	protein kinase C inhibitor	20062	2.8		< 0.01	97	5
108	misc	14-3-3 protein	695767	2.7		0.01	44	3
109	misc	guanine nucleotide regulatory protein	395072	1.5		0.31	64	2
110	misc	NAD(P)H dependent 6'-deoxychalcone synthase	18728		1.1	0.82	56	3
111	misc	inorganic pyrophosphatase	48927683	2.8		0.02	148	3
112	misc	maturase K	33332553	3.4		0.01	55	2
113	misc	CBS (cystathionine β-synthase) domain-containing	15238284	1.6		0.1	92	2

a) Functional category: ATPases (ATP); Cell wall polysaccharide metabolism (CWP); Cytoskeleton and secretion (C&S); Membrane transport (MemT); Miscellaneous (misc); One-carbon metabolism (1C); Primary carbon and energy metabolism (C&E); Protein and amino acid metabolism (P&AA). Only the highest scoring protein for each spot is categorized.

b) Fold enrichment in fibre tissues or non-fibre tissues as compared to the other tissue type, expressed as linear ratio of mean signal intensities.

c) P-value for a t-test of significant differences in mean signal intensities between fibre and non-fibre tissues.

d) Peptide count, i.e. the number of peptides per spot that match the Genbank ID shown.

e) Spots in which multiple proteins were identified. The intensity ratios shown may be due to differences in abundance of more than one protein.

Protein identities are sorted by functional category, in the order in which each category is presented in the text, and then alphabetically within each functional category. Additional data (including peptide sequences) is provided in Additional File 1.