Table 1 Identification of 53 differentially expressed protein spots in the apple proteome during ripening and senescence as determined by 2-DE analysis, MALDI-TOF-TOF, and MASCOT analysis

From: Dynamic changes in proteins during apple (Malus x domestica) fruit ripening and storage

Spot no. ^a	Protein name ^b	GDR accession no. ^c	Mascot score ^d	Matched % Cov. ^e	Matched peptides ^f	Theo Mr(kDa)/pI ^g	Obse Mr(kDa)/pI	Subcellular location ^h
Energy and Metabolism
Energy (gluconeogenesis, photosynthesis)
Gluconeogenesis
36	NADP-dependent malic enzyme(NADP-ME)	MDP0000268037	49	1	1	83.34/5.81	80.00/6.00	Cytoplasm
40	Triosephosphate isomerase (TIM)	MDP0000694943	431	32	7	27.49/5.76	29.97/6.30	Cytoplasm
Photosynthesis
8	Oxygen-evolving enhancer protein1 (OEE1)	MDP0000248920	444	38	8	35.29/6.09	34.19/5.51	Chloroplast
Metabolism (carbohydrate, amino acid, nucleotide, thiamine, lipid and secondary)
Carbohydrate metabolism
10	Probable 6-phosphogluconolactonase 2 (6PGL 2)	MDP0000223309	109	7	5	34.08/5.12	31.73/5.43	Chloroplast
19	Soluble inorganic pyrophosphatase(PPase)	MDP0000281233	407	11	6	64.36/5.35	29.79/5.62	Cytoplasm
43	Putative uncharacterized protein	MDP0000127723	328	19	4	40.73/5.71	49.93/6.31	Nuclear
35	Beta-galactosidase	MDP0000416548	425	14	10	81.52/5.69	79.87/6.07	Apoplast
46	Beta-galactosidase 3	MDP0000030527	66	1	1	95.63/8.34	79.73/6.15	Apoplast
Amino acid metabolism
20	L-asparaginase 1	MDP0000658649	334	17	5	34.63/5.21	27.93/5.79	Endoplasmic reticulum
27	Cysteine synthase	MDP0000325786	340	22	7	41.19/7.60	41.35/5.66	Chloroplast stroma Chromoplast
34	Probable sarcosine oxidase	MDP0000686885	577	23	7	44.10/5.59	44.26/6.09	Cytoplasm
44	Isovaleryl-CoA dehydrogenase 2 (IVD 2)	MDP0000225981	408	25	8	58.20/6.11	42.73/6.24	Mitochondrion
Nucleotide metabolism
2	Adenine phosphoribosyltransferase 1 (APRT 1)	MDP0000121897	625	76	7	13.00/5.03	27.84/5.17	Chloroplast Cytoplasm
6	UMP/CMP kinase (UMP/CMPK)	MDP0000240174	320	21	7	28.49/5.69	28.59/5.32	Cytoplasm
7	Adenine phosphoribosyltransferase 1 (APRT 1)	MDP0000137185	616	42	8	27.00/8.40	28.00/5.48	Chloroplast Cytoplasm
Thiamine metabolism
24	Thiazole biosynthetic enzyme (THI1)	MDP0000206098	714	27	9	39.30/5.68	34.48/5.67	Chloroplast
Lipid metabolism
25	Epoxide hydrolase 2 (EH 2)	MDP0000161121	349	16	8	35.34/5.20	40.38/5.61	Cytoplasm Peroxisome
Secondary metabolism
45	Chavicol O-methyltransferase (CVOMT 1)	MDP0000219062	314	21	5	42.82/5.89	43.53/6.17	Cytoplasm
Stress response and defense
1	Ferritin-3	MDP0000189389	296	14	4	35.46/5.69	28.93/5.18	Chloroplast
3	Thioredoxin H-type (Trx-H)	MDP0000415439	435	43	7	13.88/5.39	16.30/5.51	Cytoplasm
5	MLP-like protein 328	MDP0000132530	132	22	4	17.83/5.13	21.60/5.45	Cytoplasm
16	Superoxide dismutase [Cu-Zn]	MDP0000258717	380	23	3	22.80/6.09	18.01/5.60	Chloroplast
17	Glycine-rich RNA-binding protein (GRP1A)	MDP0000797759	412	52	8	16.88/5.61	17.17/5.68	Nucleus
21	26.5 kDa heat shock protein	MDP0000435717	364	16	6	37.21/9.34	28.17/5.76	Mitochondrion
22	L-ascorbate peroxidase 2	MDP0000210077	625	20	8	37.95/5.71	31.71/5.73	Cytoplasm
23	Putative lactoylglutathione lyase	MDP0000319112	401	29	8	39.97/6.40	35.32/5.60	Cytoplasm
28	Superoxide dismutase [Cu-Zn]	MDP0000250286	517	29	4	22.28/6.28	18.30/5.83	Chloroplast
33	Abscisic acid stress ripening protein homolog	MDP0000253074	211	11	1	25.72/6.01	30.64/6.05	Nuclear
37	Superoxide dismutase [Cu-Zn] 1	MDP0000201158	173	42	2	80.44/7.88	18.62/6.11	Cytoplasm
39	17.8 kDa class I heat shock protein	MDP0000791550	261	31	5	17.52/5.99	21.42/6.27	Cytoplasm
41	Abscisic acid response protein	MDP0000868045	414	31	4	19.86/8.61	33.55/6.29	Nuclear
47	Outer membrane lipoprotein blc (temperature-induced lipocalin)	MDP0000148808	145	20	6	21.47/6.18	24.96/6.40	Cell outer membrane
49	Abscisic acid response protein	MDP0000868045	257	17	3	19.86/8.62	32.46/6.43	Nuclear
50	Superoxide dismutase [Mn]	MDP0000187714	444	13	7	60.57/8.51	27.00/6.60	Mitochondrion matrix
51	Glutathione S-transferase	MDP0000096349	632	57	9	24.03/6.17	28.13/6.58	Cytoplasm
52	Abscisic acid response protein	MDP0000868045	397	31	4	19.86/8.68	31.09/6.65	Nuclear
53	universal stress protein (USP) family protein	MDP0000639609	130	10	1	19.81/6.30	23.34/6.68	Cytoplasm
55	Peroxiredoxin-2F, mitochondrial (PRXIIF)	MDP0000258515	161	15	2	21.61/8.77	23.90/6.85	Mitochondrion matrix
4	Major allergen Pru ar 1	MDP0000288293	340	33	5	17.61/5.10	19.28/5.35	Cytoplasm
15	Major allergen Mal d 1	MDP0000216907	444	38	5	17.52/5.54	18.47/5.53	Cytoplasm
18	MLP-like protein 329	MDP0000277802	383	31	4	17.83/5.41	23.27/5.68	Cytoplasm
31	Major allergen Mal d 1	MDP0000942516	566	28	6	17.53/5.62	20.27/5.82	Cytoplasm
38	Major allergen Mal d 1	MDP0000942516	592	52	9	17.53/5.62	20.68/6.10	Cytoplasm
54	Thaumatin-like protein 1a	MDP0000223025	85	1	2	12.26/5.71	22.79/6.68	Extracellular
Ripening and senescence
12	1-aminocyclopropane-1-carboxylate oxidase 1 (ACC oxidase 1)	MDP0000195885	617	39	9	35.56/5.24	38.74/5.53	Cytoplasm
13	1-aminocyclopropane-1-carboxylate oxidase 1 (ACC oxidase 1)	MDP0000195885	547	42	9	35.56/5.24	39.08/5.44	Cytoplasm
14	1-aminocyclopropane-1-carboxylate oxidase 1 (ACC oxidase 1)	MDP0000195885	593	42	9	35.56/5.25	39.72/5.76	Cytoplasm
Signal transduction
9	14-3-3 protein 7	MDP0000270640	207	13	4	30.54/5.31	32.77/5.42	Cytoplasm
48	GTP-binding nuclear protein Ran-3	MDP0000130864	66	8	2	28.54/6.14	31.30/6.53	Cytoplasm
Cell structure
11	Pollen-specific leucine-rich repeat extensin-like protein 3 (AtPEX3/Pollen-specific LRR)	MDP0000158152	45	2	1	60.12/6.37	31.19/5.47	Cell wall
30	Actin-depolymerizing factor 2 (ADF 2)	MDP0000245712	277	27	4	23.07/6.84	21.90/5.99	Extracellular
Protein synthesis
29	Eukaryotic translation initiation factor 5A-2	MDP0000201872	308	42	6	17.76/5.46	21.48/5.81	Cytoplasm
32	Proteasome subunit beta type-1	MDP0000193666	55	4	1	34.19/8.07	28.22/6.02	Cytoplasm Nucleus

^aNumbering corresponds to the 2-DE gel in Fig.1.
^bNames of the proteins obtained via the MASCOT software v2.1 against the apple EST database from Genome Database for Rosaceae (GDR) (http://www.rosaceae.org/species/malus/malus_x_domestica/genome_v1.0)
^cAccession number from the apple EST database from GDR.
^dTotal ion score for the entire protein and for ions complemented by 100% of the confidence index (C.I).
^ePercent sequence coverage.
^fNumbers of matchedr peptides.
^gTheoretical molecular mass (Mr) and isoelectric point (pI) of the homologous protein available at the apple EST database, observed molecular mass (Mr) and isoelectric point (pI) estimated in comparison to the 2-DE gel with marker proteins.
^hSubcellular location of each spot is based on the Uniprot Database.

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Table 1 Identification of 53 differentially expressed protein spots in the apple proteome during ripening and senescence as determined by 2-DE analysis, MALDI-TOF-TOF, and MASCOT analysis

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