The 3T3-L1 adipocyte glycogen proteome

Stapleton, David; Nelson, Chad; Parsawar, Krishna; Flores-Opazo, Marcelo; McClain, Donald; Parker, Glendon

doi:10.1186/1477-5956-11-11

Proteome Science

Table 1 The adipocyte glycogen proteome

From: The 3T3-L1 adipocyte glycogen proteome

Name	ID	Score	Total	#	%	E-value	EmPAI:
Glycogen
Glycogen phosphorylase, brain form	PYGB_MOUSE	20722	599	55	56.5	3.70E-10	17.06
Glycogen synthase, muscle	Q8VEB0_MOUSE	7954	283	39	57.2	8.50E-09	7.67
Glycogen branching enzyme	GLGB_MOUSE	4302	141	28	37.0	2.20E-08	4.30
Glycogen phosphorylase, muscle form	PYGM_MOUSE	3687	138	16(1)	18.3	5.30E-02	1.11
Glycogen debranching enzyme*	GDE_RABIT	3387	115	20	14.9	9.10E-09	0.67
Glycogenin-1	GLYG_MOUSE	1394	49	9	22.3	1.40E-06	2.17
Protein phosphatase 1, regulatory subunit 3D (or R6)	A2AJW4_MOUSE	701	17	4	15.1	4.80E-08	0.55
Lysosomal alpha-glucosidase	LYAG_MOUSE	102	2	2	2.9	5.30E-06	0.07
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	PP1A_MOUSE	76	3	2	8.8	6.50E-04	0.24
Metabolism
Glyceraldehyde-3-phosphate dehydrogenase	G3P_MOUSE	1311	42	10	42.6	1.20E-07	2.01
Pyruvate carboxylase	PYC_MOUSE	1182	31	11	12.3	1.60E-08	0.40
Malate dehydrogenase	MDHM_MOUSE	827	16	4	20.4	2.90E-09	0.49
ATP synthase subunit beta	ATPB_MOUSE	619	16	9	24.5	3.90E-08	0.94
Aldehyde dehydrogenase	ALDH2_MOUSE	513	15	3	7.5	4.00E-07	0.22
ATP synthase subunit alpha	ATPA_MOUSE	441	17	7	17.5	2.30E-05	0.62
L-lactate dehydrogenase A chain	LDHA_MOUSE	438	7	3	14.5	4.20E-10	0.34
Alpha-enolase	ENOA_MOUSE	424	10	4	14.1	2.10E-07	0.36
Aconitate hydratase	ACON_MOUSE	368	7	3	6.7	1.70E-09	0.14
Acetyl-CoA acetyltransferase	THIL_MOUSE	343	12	2	14.1	1.00E-09	0.17
(14 other proteins)
RNA
Cleavage and polyadenylation specificity factor subunit 6	CPSF6_MOUSE	928	16	6	15.8	9.80E-09	0.41
Putative RNA-binding protein Luc7-like 2	LC7L2_MOUSE	633	21	6	18.8	5.10E-07	0.61
Cisplatin resistance-associated overexpressed protein	CROP_MOUSE	529	12	3	17.4	3.40E-08	0.48
Splicing factor, arginine/serine-rich 3	SFRS3_MOUSE	492	16	4	36.3	1.20E-04	2.38
Elongation factor 1-alpha 2	EF1A2_MOUSE	461	15	5	11.5	6.90E-07	0.43
Splicing factor U2AF 65 kDa subunit	U2AF2_MOUSE	460	20	5	19.6	3.20E-05	0.40
Putative RNA-binding protein Luc7-like 1	LUC7L_MOUSE	384	15	3(1)	10.2	3.70E-06	0.32
ATP-dependent RNA helicase DDX3X	DDX3X_MOUSE	361	8	4	8.9	1.10E-07	0.28
Cleavage and polyadenylation specificity factor subunit 5	CPSF5_MOUSE	361	16	6	36.1	6.80E-08	1.57
Pre-mRNA-splicing factor 38B	PR38B_MOUSE	299	9	4	6.8	4.70E-07	0.25
(7 other proteins)
Regulatory proteins
14-3-3 protein gamma	1433G_MOUSE	795	32	9	33.7	3.90E-07	2.55
14-3-3 protein beta/alpha	1433B_MOUSE	554	27	10(4)	40.8	1.30E-05	2.56
14-3-3 protein zeta/delta	1433Z_MOUSE	488	23	6	26.5	7.90E-04	1.16
14-3-3 protein theta	1433T_MOUSE	265	15	4(1)	14.8	5.40E-05	0.70
14-3-3 protein epsilon	1433E_MOUSE	244	14	3(1)	12.9	2.00E-03	0.49
Receptor of activated protein kinase C 1	GBLP_MOUSE	212	7	2	6.3	6.50E-06	0.23
Ribosomes
40S ribosomal protein SA	RSSA_MOUSE	377	8	2	9.5	4.00E-06	0.24
40S ribosomal protein S16	RS16_MOUSE	278	10	4	24.0	1.30E-05	1.34
40S ribosomal protein S18	RS18_MOUSE	265	10	5	25.7	2.20E-05	1.68
40S ribosomal protein S7	RS7_MOUSE	224	9	2	10.3	9.80E-06	0.38
Nucleolin	NUCL_MOUSE	217	5	3	6.1	7.30E-07	0.15
40S ribosomal protein S2	RS2_MOUSE	214	7	3	11.9	2.60E-05	0.41
40S ribosomal protein S4, X isoform	RS4X_MOUSE	186	5	2	9.9	1.10E-05	0.27
40S ribosomal protein S24	RS24_MOUSE	184	6	2	20.3	5.20E-05	0.57
40S ribosomal protein S8	RS8_MOUSE	182	5	2	12.5	9.80E-05	0.34
40S ribosomal protein S13	RS13_MOUSE	150	5	3	24.5	1.30E-04	0.84
(12 other proteins)
Miscellaneous
Major vault protein	MVP_MOUSE	1271	41	13	23.9	1.30E-07	0.69
Histone H2B type 1-B †	H2B1B_MOUSE	881	17	3	27.2	2.00E-09	1.73
Stress-70 protein	GRP75_MOUSE	789	28	7	13.8	3.00E-06	0.41
Histone H2A type 1-F†	H2A1F_MOUSE	556	19	3	43.8	6.80E-07	1.67
60 kDa heat shock protein	CH60_MOUSE	343	12	7	14.1	8.00E-07	0.63
Histone H1.2 †	H12_MOUSE	291	10	4	15.1	3.90E-05	0.91
10 kDa heat shock protein	CH10_MOUSE	238	4	2	19.6	9.50E-09	0.86
Histone H4 †	H4_MOUSE	222	8	5	47.6	9.60E-06	3.51
Actin, alpha skeletal muscle	ACTS_MOUSE	101	3	2	16.5	3.10E-04	0.19
Histone H2A.x †	H2AX_MOUSE	95	6	3(1)	47.3	1.80E-02	1.11
Tubulin beta-2B chain	TBB2B_MOUSE	93	3	3	11.0	1.20E-03	0.24

Proteins isolated from glycogen particles of mouse 3T3-L1 adipocytes were solubilized by malto-oligosaccharide treatment and trypsinized. Peptides were desalted, purified, and analyzed by mass spectrometry (LC/MS/MS) and bioinformatic searches of the “mammalia” MSDB database. Mouse proteins, identified by name and UNIPROT identifier (ID), that meet a significance level of less than 0.05 and with at least two different unique peptide sequences with expectation scores less than 0.05, are listed functionally in order of likelihood by Mowse score (score). Other parameters include: the total number of peptides with expectation scores less than 0.05 (total), number of different unique peptide sequences identified corresponding to the specific gene product (#), percent coverage of the protein (%), and the lowest recorded expectation value (E-value) for a unique non-redundant peptide from the identified protein. In the case of proteins with homology to other glycogen-associated proteins, the number of unique, non-redundant peptides is indicated in parentheses. Exponentially modified Protein Abundance Index (emPAI) values are also included [35]. *The UniProt listing for GDE-MOUSE is not complete therefore the parameters presented correspond to the closet match in the database, GDE_RABIT. †Insufficient data was obtained to conclusively match the identified peptides with a unique gene product. A complete listing of proteins and parameters is located in the Supplemental section (Additional file 1: Table S1).

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ISSN: 1477-5956

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