Table 1 Comparison of identification of 2D gel separated spots of rat liver protein by chip-based nanoESI/MS/MS and nanoHPLC-MS/MS

1

HPLC

Protein disulfide-isomerase

211

7

12

57.1

0

0

gi129729

Multistep

280

15

26

0

0

HPLC

Iodothyronine 5' monodeiodinase

211

7

13

54.0

gi202549

Multistep

280

15

25

HPLC

Prolyl 4-hydroxylase, beta polypeptide, isoform CRA_a

211

7

11

59.0

gi148702818

Multistep

280

15

25

HPLC

Prolyl 4-hydroxylase, beta polypeptide, isoform CRA_b

211

7

11

61.5

gi148702819

Multistep

280

15

24

2

HPLC

Methionine adenosyltrans-ferase I, alpha

304

7

21

43.5

0

0

gi19526790

Multistep

378

6

28

0

0

3

HPLC

Regucalcin

230

5

18

33.4

0

0

gi6677739

Multistep

211

4

14

0

0

4

HPLC

Carbamoyl-phosphate synthetase 1

1286

28

18

164.5

4

17.39

gi124248512

Multistep

697

23

14

0

0

5

HPLC

Carbamoyl-phosphate synthetase 1

1221

27

18

164.5

3

17.65

gi124248512

Multistep

1112

31

20

0

0

6

HPLC

Glutamate de-hydrogenase 1

416

9

17

61.3

1

9.09

gi6680027

Multistep

364

10

17

0

0

7

HPLC

Arginase 1

284

5

16

34.8

1

12.5

gi7106255

Multistep

290

8

26

0

0

HPLC

Short-chain specific acyl-CoA dehydrogenase, mitochondrial

134

4

10

44.9

gi584714

Multistep

192

6

19

8

HPLC

Sorbitol dehydrogenase precursor

176

4

11

40.7

0

0

gi1009706

Multistep

207

6

17

0

0

HPLC

Sorbitol dehydrogenase

176

4

12

38.2

gi22128627

Multistep

207

6

18

HPLC

L-iditol 2-dehydrogenase

176

4

11

42.8

gi397357

Multistep

Sorbitol dehydrogenase, isoform CRA_a

176

4

14

32.0

gi149023127

9

HPLC

Fumaryl-acetoacetase

191

4

10

46.2

0

0

gi50973

Multistep

290

6

15

0

0

HPLC

4-hydroxy-phenyl-pyruvate dioxygenase

197

4

10

45.1

gi849053

Multistep

F1 protein

197

4

10

43.6

gi1841443

HPLC

Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase Complexed W/4-(Hydroxymethylphosphinoyl)-3-Oxo-Butanoic Acid

191

4

10

46.2

gi13399972

Multistep

Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase

191

4

10

45.9

gi8569272

HPLC

Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase Complexed With Fumarate And Acetoacetate

191

4

10

46.4

gi8569274

Multistep

Glutamate-ammonia ligase

187

5

15

42.0

gi2144563

HPLC

Glutamine synthetase

187

5

15

42.1

gi31982332

Multistep

Long-chain acyl-CoA dehydrog-enase

122

3

6

48.0

gi726095

10

HPLC

Arginase 1

232

4

13

34.8

0

0

gi7106255

Multistep

314

6

23

0

0

HPLC

Aldo-keto reductase family 1, member D1

120

3

7

37.4

gi20302063

Multistep

69

4

9

HPLC

rCG27878

120

3

7

37.4

gi149065268

Multistep

69

4

9

11

HPLC

Ornithine transcarbamyl-ase, isoform CRA_f

298

5

14

42.0

1

14.29

gi148703731

Multistep

285

7

19

0

0

HPLC

Ornithine transcarbamyl-ase

297

5

14

39.8

gi762985

Multistep

284

7

20

HPLC

Otc protein

297

5

14

39.3

gi19353187

Multistep

284

7

20

12

HPLC

Alcohol dehydrogenase 1 (class I)

156

3

9

39.7

0

0

gi6724311

Multistep

102

3

9

0

0

HPLC

Alcohol dehydrogenase 1 (class I), isoform CRA_b

156

3

11

35.3

gi148680154

Multistep

102

3

11

HPLC

Electron transferring flavoprotein, alpha polypeptide

155

3

7

35.0

gi13097375

Multistep

429

9

31

HPLC

MAWD binding protein homolog 1

139

5

21

32.0

gi31560132

13

Multistep

Chain A, Methyl-transferase

284

5

18

32.4

1

12.5

gi1942407

HPLC

236

4

19

0

0

Multistep

Glycine N-methyl-transferase

284

5

18

32.4

gi6754026

HPLC

236

4

19

Multistep

Electron transferring flavoprotein, alpha polypeptide

121

2

7

35.0

gi13097375

14

HPLC

Glutathione S-transferase

mu 1

193

5

19

26.0

1

25

gi6754084

Multistep

237

6

24

0

0

HPLC

mCG131602, isoform CRA_a

193

5

17

29.1

gi148669989

Multistep

237

5

21

HPLC

mCG131602, isoform CRA_b

193

5

19

26.6

gi148669990

Multistep

237

5

24

HPLC

mCG131602, isoform CRA_c

193

5

19

26.7

gi148669991

Multistep

237

5

24

15

HPLC

Hemoglobin beta

378

6

47

15.7

0

0

gi229301

Multistep

403

7

52

0

0

HPLC

Hemoglobin, beta adult major chain

378

6

47

15.7

gi31982300

Multistep

403

7

52

HPLC

Delta-globin

219

4

29

16.0

gi122717

Multistep

208

5

35

16

HPLC

Fatty acid binding protein 1, liver

149

3

22

14.2

0

0

gi8393343

Multistep

115

3

22

0

0