Table 3 Detailed information regarding protein identification and expression pattern in striatum, midbrain and cortex tissues of the PINK1-KO (KO) mice in respect to wildtype control mice (WT):

NCBI access number

Gene symbol

Number of isoforms

Protein name

Expression ratio

(KO vs. wt)

T test (p-value)

Mowse score

Sequence coverage (%)

Number of matched peptides

Molecular weight (Da)

Theoretical pI

Functional annotation (KEGG pathway)

gi|6753428

Ckmt1

1

creatine kinase, mitochondrial 1, ubiquitous

1.37

0.0002

235

12

5

46974

8.39

Metabolic pathways; Arginine and proline metabolism

gi|6755929

Uchl1

7

ubiquitin carboxy-terminal hydrolase L1

1.45

0.0008

67

47

9

24822

5.33

Parkinson's disease

gi|3766201

Sucla2

4

ATP-specific succinyl-CoA synthetase beta subunit

1.42

0.001

299

21

6

46215

5.65

Metabolic pathways; Citrate cycle (TCA cycle); Propanoate metabolism;

gi|6678674

Ldhb

5

lactate dehydrogenase 2, B chain

1.37

0.0012

136

51

2

36549

5.7

Metabolic pathways; Propanoate metabolism; Glycolysis/Gluconeogenesis; Pyruvate metabolism;

gi|31980844

Dhrs1

2

dehydrogenase/reductase (SDR family) member 1

1.54

0.0016

395

21

7

33983

8.66

gi|10946574

Ckb

5

creatine kinase, brain

1.42

0.0018

465

25

8

42686

5.4

Metabolic pathways; Arginine and proline metabolism

gi|112363107

Nefm

7

Neurofilament triplet M protein

0.43

0.0025

56

12

2

95984

4.76

Amyotrophic lateral sclerosis (ALS)

gi|6680117

Gss

3

glutathione synthetase

1.42

0.0035

436

16

8

52214

5.56

Metabolic pathways; Glutathione metabolism;

gi|15277976

Ndrg2

3

N-myc downstream regulated gene 2

1.4

0.0046

93

6

2

40763

5.23

gi|809561

Actg1

4

gamma-actin

1.32

0.0048

84

5

2

40992

5.56

Regulation of actin cytoskeleton

gi|387422

Mdh2

8

malate dehydrogenase

1.37

0.0079

222

12

4

35588

8.93

Metabolic pathways; Citrate cycle (TCA cycle); Pyruvate metabolism;

gi|14198249

Aldoc

4

Fructose-bisphosphate aldolase C

1.34

0.0097

144

9

3

39307

6.47

Metabolic pathways; Glycolysis/Gluconeogenesis; Pentose phosphate pathway; Fructose and mannose metabolism

gi|13097102

Ddah2

2

dimethylarginine dimethylaminohydrolase 2

1.32

0.0098

183

18

4

29627

5.66

gi|33859640

Taldo1

3

transaldolase 1

1.34

0.0109

163

12

4

37363

6.57

Metabolic pathways; Pentose phosphate pathway;

gi|6681195

Dlg4

4

postsynaptic density protein 95

0.64

0.0133

38

4

2

80423

5.56

Huntington's disease

gi|6753476

Cnp

1

cyclic nucleotide phosphodiesterase 1

1.42

0.0142

371

21

8

47094

9.08

gi|27370516

Idh2

6

isocitrate dehydrogenase 2 (NADP+), mitochondrial

1.37

0.0151

221

10

4

50902

8.88

Metabolic pathways; Citrate cycle (TCA cycle); Glutathione metabolism;

gi|54855

Tpi1

25

triosephosphate isomerase

1.36

0.0214

770

42

12

26679

6.9

Metabolic pathways; Glycolysis/Gluconeogenesis; Fructose and mannose metabolism;

gi|12805413

Echs1

2

Echs1 protein

1.31

0.0245

428

26

8

31237

8.76

Metabolic pathways; Propanoate metabolism;

gi|7305485

Sh3gl1

4

SH3-domain GRB2-like 1

1.28

0.0307

136

7

3

41492

5.53

Endocytosis

Midbrain:

NCBI access number

Gene symbol

Number of isoforms

Protein name

Expression ratio (KO vs. wt)

T test (p-value)

Mowse score

Sequence coverage (%)

Number of matched peptides

Molecular weight (Da)

Theoretical pI

Functional annotation (KEGG pathway)

gi|13384652

Mecr

1

trans-2-enoyl-CoA reductase, mitochondrial precursor

0.53

0.001

88

4

2

40316

9.34

Metabolic pathways;

gi|6679937

Gapdh

3

similar to glyceraldehyde-3-phosphate dehydrogenase

0.55

0.002

340

19

5

35787

8.44

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|12849397

Glod4

1

Glyoxalase domain-containing protein 4

0.69

0.003

545

46

11

33296

5.28

gi|6753428

Ckmt1

2

creatine kinase, mitochondrial 1, ubiquitous

0.77

0.003

123

14

2

46974

8.39

Metabolic pathways;

gi|18017596

Snx4

1

sorting nexin 4

0.39

0.007

140

6

2

51745

5.58

gi|27369581

Slc25a12

1

solute carrier family 25 (mitochondrial carrier, Aralar), member 12

0.46

0.007

318

9

5

74523

8.43

gi|21410877

Rap1gap

1

Rap1gap protein

0.72

0.007

62

9

2

45618

5.47

gi|387129

Mdh1

3

cytosolic malate dehydrogenase

0.74

0.01

145

11

3

36454

6.16

Metabolic pathways; Citrate cycle (TCA cycle); Pyruvate metabolism;

gi|33440467

Pafah1b2

2

Platelet-activating factor acetylhydrolase, isoform 1b, alpha2 subunit

0.72

0.015

91

8

2

25476

5.57

Metabolic pathways;

gi|21759113

Etfa

2

Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)

0.61

0.016

455

29

6

35018

8.42

gi|1915915

Ulip3

1

Ulip3 protein

0.73

0.016

177

12

3

62142

6.39

gi|31981086

Efhd2

3

EF hand domain containing 2

0.66

0.018

602

45

9

25084

5.07

gi|18606238

Gsn

1

gelsolin

0.7

0.018

328

9

5

80712

5.83

Regulation of actin cytoskeleton

gi|6671539

Aldoa

4

aldolase 1, A isoform

0.79

0.019

1158

59

17

39331

8.31

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|6678483

Uba1

1

ubiquitin-activating enzyme E1, Chr X

0.76

0.021

669

13

10

117734

5.43

Parkinson's disease

gi|18152793

Pdhb

1

pyruvate dehydrogenase (lipoamide) beta

0.78

0.021

497

32

11

38912

6.41

Metabolic pathways; Glycolysis/Gluconeogenesis; Citrate cycle (TCA cycle); Pyruvate metabolism;

gi|6755963

Vdac1

3

voltage-dependent anion channel 1

0.66

0.0217

855

51

10

30737

8.62

Parkinson's disease; Huntington's disease; Calcium signaling pathway

gi|6755967

Vdac3

1

voltage-dependent anion channel 3

0.66

0.025

224

20

4

30733

8.96

Parkinson's disease; Huntington's disease; Calcium signaling pathway

gi|2690302

Got2

2

aspartate aminotransferase precursor

0.77

0.027

533

23

8

47382

9.05

Metabolic pathways; Alanine, aspartate and glutamate metabolism

gi|11141704

Sir2L2

1

sirtuin 2

0.48

0.029

51

4

2

43244

8.22

gi|22902419

Gpd1l

2

glycerol-3-phosphate dehydrogenase 1-like

0.48

0.029

61

4

2

42517

8.22

Glycerophospholipid metabolism

gi|7106301

Mapre1

1

microtubule-associated protein, RP/EB family, member 1

0.56

0.031

193

18

3

29997

5.12

gi|8567410

Syn2

1

synapsin II

0.61

0.034

70

3

2

52418

7.62

gi|6671569

Arbp

2

acidic ribosomal phosphoprotein P0

1.41

0.037

196

19

4

34195

5.91

gi|9845299

Suclg1

1

succinate-CoA ligase, GDP-forming, alpha subunit

1.21

0.039

88

9

2

34953

9.45

Metabolic pathways; Citrate cycle (TCA cycle); Propanoate metabolism

gi|61098212

Uchl1

1

ubiquitin carboxy-terminal hydrolase L1

0.65

0.04

157

16

3

24822

5.14

Parkinson's disease

gi|6754524

Ldha

6

lactate dehydrogenase 1, A chain

0.61

0.046

151

14

3

36475

7.62

Metabolic pathways; Glycolysis/Gluconeogenesis; Pyruvate metabolism; Propanoate metabolism

gi|29789104

Napb

1

N-ethylmaleimide sensitive fusion protein attachment protein beta

0.76

0.046

708

42

10

33536

6.41

gi|7305027

Eno2

4

enolase 2, gamma neuronal

0.69

0.047

861

43

13

47267

4.99

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|55931021

Gdi2

3

1.64

0.049

158

13

3

50506

5.93

Cortex:

NCBI access number

Gene symbol

Number of Isoforms

Protein name

Expression ratio (KO vs. wt)

T test (p-value)

Mowse score

Sequence coverage (%)

Number of matched peptides

Molecular weight (Da)

Theoretical pI

Functional annotation (KEGG pathway)

gi|4760600

Ak3

1

adenylate kinase isozyme 3

0.66

0.0004

124

47

11

24625

8.57

gi|13385942

Cs

5

citrate synthase

0.74

0.0057

130

28

16

51703

8.72

Metabolic pathways;

gi|37700232

Nme1

4

nucleoside-diphosphate kinase 1

1.22

0.0006

91

48

9

17197

6.84

Metabolic pathways;

gi|19547889

Gss

3

glutathione synthetase

1.24

0.0386

107

26

12

51913

6.52

Metabolic pathways;

gi|42542422

Hspa8

5

Heat shock protein 8

1.24

0.0019

180

35

23

68074

5.32

gi|123230136

Prdx1

1

peroxiredoxin 1

1.24

0.0228

64

23

5

18915

6.82

gi|37202121

Abat

3

4-aminobutyrate aminotransferase

1.25

0.0005

227

37

24

56416

8.35

Metabolic pathways; Alanine, aspartate and glutamate metabolism; Propanoate metabolism; Valine, leucine and isoleucine degradation

gi|113680348

Fscn1

2

fascin homolog 1, actin bundling protein

1.26

0.0017

168

42

17

54474

6.44

gi|34784434

Eno1

4

Eno1 protein

1.26

0.0062

139

43

16

39757

5.86

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|56789289

Ldhb

4

Ldhb protein

1.27

0.0011

86

42

7

11317

5.73

Metabolic pathways; Glycolysis/Gluconeogenesis; Propanoate metabolism; Cysteine and methionine metabolism

gi|6679439

Ppia

4

peptidylprolyl isomerase A

1.3

0.0006

99

53

12

17960

7.74

gi|6755040

Pfn1

3

profilin 1

1.31

0.0022

176

73

14

14948

8.46

Regulation of actin cytoskeleton

gi|6678469

Tuba1c

2

tubulin, alpha 1C

1.32

0.0000088

98

35

13

49877

4.96

gi|809561

3

1

gamma-actin

1.32

0.0028

230

56

24

41724

5.3

Regulation of actin cytoskeleton

gi|6679937

Gapdh

6

glyceraldehyde-3-phosphate dehydrogenase

1.33

0.0005

211

60

23

35787

8.44

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|49868

Actb

2

beta-actin (aa 27-375)

1.35

0.0019

237

54

27

39161

5.79

Regulation of actin cytoskeleton

gi|148686116

Taldo1

2

transaldolase 1, isoform CRA_e

1.39

0.0008

156

51

18

31514

7.66

Metabolic pathways; Pentose phosphate pathway

gi|6678413

Tpi1

1

triosephosphate isomerase 1

1.39

0.0006

147

42

9

26696

6.9

Metabolic pathways; Glycolysis/Gluconeogenesis; Fructose and mannose metabolism

gi|123210063

---

1

novel protein

1.44

0.0009

38

20

4

24445

8.76

gi|6755963

Vdac1

1

voltage-dependent anion channel 1

1.47

0.0019

161

62

15

30737

8.62

gi|6671539

Aldoa

4

aldolase 1, A isoform

1.52

0.005

179

43

17

39331

8.31

Metabolic pathways; Glycolysis/Gluconeogenesis; Pentose phosphate pathway; Fructose and mannose metabolism

gi|1915915

Dpysl1

2

Ulip3 protein

1.56

0.0058

225

40

24

62142

6.39

gi|20072952

Auh

2

Auh protein

1.62

0.000068

114

32

13

32621

9.57

Metabolic pathways; Valine, leucine and isoleucine degradation

gi|11066098

Tkt

1

transketolase

1.89

0.0058

65

26

11

60545

6.54

Metabolic pathways; Pentose phosphate pathway;

gi|21311871

Nebl

1

nebulette

2.2

0.0007

74

40

13

31093

8.54

gi|163838648

Atp5c1

1

ATP synthase, H+ transporting, mitochondrial F1 complex, gamma subunit isoform b

2.2

0.0007

126

42

15

30237

8.86

Metabolic pathways;

gi|202423

Pgk1

2 (with divergent regulation)

phosphoglycerate kinase

1.54; 0.77

5.00E-03; 1.22E-02

265

58

28

44522

8.02

Metabolic pathways; Glycolysis/Gluconeogenesis;

gi|160298209

Got1

2 (with divergent regulation)

glutamate oxaloacetate transaminase 1, soluble

1.62; 0.78

1.12E-02; 2.60E-03

130

30

12

46219

6.68

Metabolic pathways; Alanine, aspartate and glutamate metabolism