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Table 3 Proteins present in glycogen pellet following specific elution with malto-oligosaccharides

From: The 3T3-L1 adipocyte glycogen proteome

Name

ID

Score

Total

#

%

E-value

EmPAI

Glycogen synthase 1, muscle

Q8VEB0_MOUSE

7920

254

29

41.7

8.20E-10

7.67

Glycogen phosphorylase, brain form

PYGB_MOUSE

4197

122

23

33.8

2.70E-09

1.76

Glycogenin-1

GLYG_MOUSE

1360

39

7

21.7

1.40E-08

1.17

Splicing factor, arginine/serine-rich 3

SFRS3_MOUSE

1197

43

4

36.3

9.00E-06

3.31

Cisplatin resistance-associated overexpressed protein

CROP_MOUSE

985

19

5

28.8

1.10E-08

0.93

Cleavage and polyadenylation specificity factor subunit 6

CPSF6_MOUSE

900

13

3

8.8

1.20E-10

0.26

Glyceraldehyde-3-phosphate dehydrogenase

G3P_MOUSE

753

19

5

23.4

2.90E-07

0.65

Splicing factor U2AF 65 kDa subunit

U2AF2_MOUSE

727

34

5

19.6

1.50E-06

0.60

Major vault protein

MVP_MOUSE

726

25

11

16.6

2.50E-05

0.52

Putative RNA-binding protein Luc7-like 2

LC7L2_MOUSE

623

23

6

17

1.60E-06

0.61

ATP synthase subunit beta

ATPB_MOUSE

620

16

6

17.7

1.90E-07

0.55

ATP-dependent RNA helicase DDX3X

DDX3X_MOUSE

552

13

5

10.7

1.00E-07

0.35

ATP synthase subunit alpha

ATPA_MOUSE

530

14

7

18.8

1.90E-06

0.53

Cleavage and polyadenylation specificity factor subunit 5

CPSF5_MOUSE

412

14

5

27.8

3.90E-08

1.58

Splicing factor, arginine/serine-rich 7

SFRS7_MOUSE

409

11

3(2)

22.3

1.30E-06

1.19

Histone H2A type 1-F †

H2A1F_MOUSE

403

13

2

21.5

1.60E-07

1.09

Elongation factor 1-alpha 1

EF1A1_MOUSE

368

12

3

6.3

1.70E-07

0.24

Putative RNA-binding protein Luc7-like 1

LUC7L_MOUSE

355

16

3(1)

10.2

1.40E-02

0.32

Pre-mRNA-splicing factor 38B

PR38B_MOUSE

348

14

3

6.8

3.80E-07

0.18

60 kDa heat shock protein

CH60_MOUSE

323

8

3

8.3

3.90E-07

0.28

Histone H2B type 1-F/J/L †

H2B1F_MOUSE

260

4

2

19.2

1.70E-09

0.66

Splicing factor U2AF 35 kDa subunit

U2AF1_MOUSE

253

7

2

13

4.30E-05

0.29

Heterogeneous nuclear ribonucleoprotein H2

HNRH2_MOUSE

247

7

3(1)

9.6

6.40E-05

0.24

Stress-70 protein

GRP75_MOUSE

242

6

3

6.3

2.80E-06

0.16

Heterogeneous nuclear ribonucleoprotein M

HNRPM_MOUSE

234

7

35

8

1.20E-05

0.21

Trifunctional enzyme subunit alpha

ECHA_MOUSE

226

7

4

8.7

2.50E-05

0.19

Histone H1t †

H1T_MOUSE

213

6

2

10.5

1.90E-06

0.38

Vimentin

VIME_MOUSE

163

3

2

5.2

1.10E-07

0.14

Probable ATP-dependent RNA helicase DDX5

DDX5_MOUSE

148

4

3(2)

4.3

6.70E-05

0.15

Probable ATP-dependent RNA helicase DDX17

DDX17_MOUSE

145

4

2(1)

3.5

9.90E-05

0.10

40S ribosomal protein S7

RS7_MOUSE

126

4

2

10.3

9.90E-06

0.38

60S ribosomal protein L23a

RL23A_MOUSE

115

4

3

19.9

2.40E-04

0.81

Tubulin beta-2B chain †

TBB2B_MOUSE

109

5

2

5.4

1.60E-02

0.24

Pyruvate carboxylase

PYC_MOUSE

104

4

3

3.8

2.40E-04

0.09

Glycogen debranching enzyme *

GDE_HUMAN

104

3

2

2

3.50E-04

0.04

Glycogen debranching enzyme *

Q8CE68_MOUSE

103

3

2(1)

1.9

2.90E-04

0.04

Ubiquitin

UBIQ_MOUSE

87

3

3

44.7

1.60E-04

2.23

60S ribosomal protein L11

RL11_HUMAN

81

2

2

13.8

5.00E-05

0.45

ATP synthase subunit O

ATPO_MOUSE

68

2

2

14.1

3.40E-03

0.35

Histone H4 †

H4_MOUSE

64

2

2

19.4

3.40E-03

0.83

  1. Proteins that were still present in the glycogen pellet after specific treatment with malto-oligosaccharides are listed (name and UNIPROT identifier (ID)) in order of likelihood of identification by Mowse score (score). This population represents proteins whose physical interaction with the glycogen molecule is not disrupted by malto-oligosaccharide treatment either because of non-specific interaction with the particle or because the specific interaction is not adequately competed with by the elution conditions used, 50 mg malto-oligosaccharide / ml. Other parameters included in the table are: the total number of unique non-redundant peptide sequences identified (#), per cent coverage of identified proteins (%), and minimum expectation value for a unique non-redundant peptide from within the identified gene product (E-value). Exponentially modified Protein Abundance Index (emPAI) values are also included [35]. Peptides with expectation scores above 0.05 were included in the analysis. All proteins listed have a minimum of two unique non-redundant peptides identified. †Insufficient data was obtained to conclusively match the identified peptides with a unique gene product.
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Proteome Science

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