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Table 3 Top-hit list of differentially expressed proteins in CD8+ T cells from MS patients compared healthy controls

From: Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

Accession

Protein identity

Gene names

p-value

FC MS versus HC (log2)

Median intesity MS (log2)

MS SD

Median intensity HC (log2)

HC SD

% seq cov

# pep

AUC

P36915

Guanine nucleotide-binding protein-like 1

GNL1

0.000363

0.3823

22.9373

0.13239

22.555

0.19548

22.6

9

0.9

P57764

Gasdermin-D

GSDMD

0.0004

− 0.247

23.0081

0.09966

23.2551

0.13969

27.9

8

0.91

Q15027

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1

ACAP1

0.000818

0.3588

25.3317

0.13259

24.9729

0.21057

44.7

22

0.89

Q14240

Eukaryotic initiation factor 4A-II; eukaryotic initiation factor 4A-II, N-terminally processed

EIF4A2

0.001679

0.2287

25.7838

0.1338

25.5551

0.31408

75.4

23

0.92

Q9GZP4

PITH domain-containing protein 1

PITHD1

0.001791

0.1974

22.8647

0.13746

22.3619

0.14509

47.9

8

0.91

P10155

60 kDa SS-A/Ro ribonucleoprotein

TROVE2

0.001865

0.1765

25.7638

0.08234

25.9917

0.13787

37.4

16

0.87

P14174

Macrophage migration inhibitory factor

MIF

0.002217

0.3238

23.462

0.21611

23.2646

0.28198

36.5

4

0.88

Q96ST3

Paired amphipathic helix protein Sin3a

SIN3A

0.002395

0.2302

25.1124

0.11111

24.9359

0.14227

14.2

13

0.85

P06703

Protein S100-A6

S100A6

0.002446

− 0.7296

26.8304

0.62637

26.5066

0.61209

52.2

4

0.9

P51452

Dual specificity protein phosphatase 3

DUSP3

0.002706

− 0.5138

23.1048

0.19565

22.8746

0.4382

29.2

4

0.88

O75431

Metaxin-2

MTX2

0.002927

0.293

25.2256

0.21249

25.9552

0.11457

33.8

5

0.82

Q8TBC4

NEDD8-activating enzyme E1 catalytic subunit

UBA3

0.002937

0.1439

24.5971

0.10266

24.3764

0.1286

51.6

13

0.85

P30405; Q6BAA4

Peptidyl-prolyl cis–trans isomerase F, mitochondrial

PPIF

0.003314

− 1.0344

21.1705

0.33533

21.6843

0.63539

40.1

8

0.84

P21953

2-oxoisovalerate dehydrogenase subunit beta, mitochondrial

BCKDHB

0.003651

0.2586

22.4515

0.21161

22.1585

0.24451

15.3

4

0.83

Q8TCD5

5(3)-deoxyribonucleotidase, cytosolic type

NT5C

0.003791

0.3211

24.2434

0.14217

24.0995

0.45523

54.2

7

0.86

P57737

Coronin-7

CORO7

0.004431

0.147

23.7522

0.148

23.3999

0.0888

49.4

28

0.86

O94925

Glutaminase kidney isoform, mitochondrial

GLS

0.0047

0.1506

22.33535

0.10161

22.9562

0.13926

45

22

0.85

Q3ZCW2

Galectin-related protein

LGALSL

0.005089

− 2.2604

21.7926

0.93109

22.827

0.91857

61

8

0.86

P63151; Q00005; Q9Y2T4

Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform

PPP2R2A

0.005319

0.243

21.8042

0.15983

21.5456

0.24976

48.1

12

0.84

O94826

Mitochondrial import receptor subunit TOM70

TOMM70A

0.005477

0.235

23.0302

0.0878

22.7091

0.2231

32.1

13

0.89

Q13586; Q9P246

Stromal interaction molecule 1

STIM1

0.005533

− 0.2404

26.1487

0.20417

26.0017

0.23545

32.7

16

0.82

P13224

Platelet glycoprotein Ib beta chain

GP1BB

0.005768

− 1.9102

24.998

0.8499

24.8474

1.00102

23.8

5

0.82

O00186

Syntaxin-binding protein 3

STXBP3

0.005812

0.193

22.9285

0.11405

23.296

0.15529

10.5

5

0.87

P20645

Cation-dependent mannose-6-phosphate receptor

M6PR

0.006115

− 0.1934

22.3302

0.22866

23.6924

0.17682

22

4

0.84

Q96RQ3

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

MCCC1

0.007633

0.5028

21.2898

0.19278

23.5502

0.34081

16.4

7

0.83

P78417

Glutathione S-transferase omega-1

GSTO1

0.007795

− 0.2279

23.6102

0.09562

23.1469

0.19987

59.3

14

0.79

P24666

Low molecular weight phosphotyrosine protein phosphatase

ACP1

0.008395

0.2207

23.6258

0.18286

23.3828

0.19924

72.2

8

0.82

Q9H0R4

Haloacid dehalogenase-like hydrolase domain-containing protein 2

HDHD2

0.008617

0.3523

24.1578

0.21888

23.9228

0.23008

67.2

8

0.84

Q12913

Receptor-type tyrosine-protein phosphatase eta

PTPRJ

0.008808

− 0.62085

24.2463

0.30864

24.4867

0.44153

10.9

11

0.83

P49327

Fatty acid synthase; [acyl-carrier-protein] S-acetyltransferase;[acyl-carrier-protein] S-malonyltransferase; 3-oxoacyl-[acyl-carrier-protein] synthase; 3-oxoacyl-[acyl-carrier-protein] reductase; 3-hydroxyacyl-[acyl-carrier-protein] dehydratase; enoyl-[acyl-carrier-protein] reductase; oleoyl-[acyl-carrier-protein] hydrolase

FASN

0.009384

− 0.3675

23.3745

0.18085

25.2847

0.4045

10.9

18

0.8

P04275

von Willebrand factor; von Willebrand antigen 2

VWF

0.009824

− 1.3622

22.1391

1.21897

21.9461

1.05341

13

25

0.84

P35573

Glycogen debranching enzyme; 4-alpha-glucanotransferase; amylo-alpha-1,6-glucosidase

AGL

0.010066

0.4633

21.956

0.26486

21.7305

0.29541

20.9

22

0.8

Q8TDQ7

Glucosamine-6-phosphate isomerase 2

GNPDA2

0.010164

0.2255

23.3542

0.28146

23.8593

0.21281

59.8

10

0.84

P16615

Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

ATP2A2

0.010248

− 0.5051

24.5083

0.30171

24.3585

0.32708

28.7

21

0.81

Q13555; Q13554

Calcium/calmodulin-dependent protein kinase type II subunit gamma; calcium/calmodulin-dependent protein kinase type II subunit beta

CAMK2G; CAMK2B

0.010445

0.2908

22.9757

0.12761

22.6849

0.25143

24.6

10

0.82

P12931; Q9H3Y6; P42685; P08581; Q04912

Proto-oncogene tyrosine-protein kinase Src

SRC

0.01081

− 1.20015

22.8527

0.73685

24.05285

0.66689

37.5

15

0.81

Q15120

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial

PDK3

0.010829

0.24475

20.7149

0.28722

20.47015

0.26592

12.1

3

0.81

P05556

Integrin beta-1

ITGB1

0.010894

− 0.4327

24.5472

0.41637

24.9799

0.37748

32.8

19

0.81

Q9P0J1

[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial

PDP1

0.011178

0.3474

22.5526

0.14746

22.2052

0.18283

16.9

7

0.82

P01137

Transforming growth factor beta-1; latency-associated peptide

TGFB1

0.012983

− 0.87595

24.8165

0.44917

24.6229

0.65195

29.5

7

0.81

P14770

Platelet glycoprotein IX

GP9

0.013113

− 1.25275

29.9764

0.73326

29.8298

0.84609

30.5

5

0.82

P05386

60S acidic ribosomal protein P1

RPLP1

0.014256

0.2666

22.157

0.16745

22.4676

0.17334

94.7

5

0.81

Q02083

N-acylethanolamine-hydrolyzing acid amidase; N-acylethanolamine-hydrolyzing acid amidase subunit alpha; N-acylethanolamine-hydrolyzing acid amidase subunit beta

NAAA

0.014286

0.43565

23.0686

0.40847

23.6457

0.49594

27.9

8

0.87

P50148; P29992; O95837

Guanine nucleotide-binding protein G(q) subunit alpha

GNAQ

0.014465

− 0.487

24.8592

0.48364

24.5987

0.51884

30.6

8

0.82

O14828

Secretory carrier-associated membrane protein 3

SCAMP3

0.014503

− 0.2404

22.5342

0.16111

22.3259

0.19252

22.8

5

0.8

P67936; Q2TAC2

Tropomyosin alpha-4 chain

TPM4

0.015754

− 0.598

23.0621

0.52458

22.8134

0.46362

70.6

27

0.81

O14561

Acyl carrier protein, mitochondrial

NDUFAB1

0.015958

0.2347

23.5152

0.23866

23.7086

0.12417

21.2

4

0.82

Q00653

Nuclear factor NF-kappa-B p100 subunit; nuclear factor NF-kappa-B p52 subunit

NFKB2

0.016322

0.322

22.11305

0.2449

22.989

0.28366

15.8

9

0.81

P35244

Replication protein A 14 kDa subunit

RPA3

0.016781

0.2976

23.4742

0.16891

24.72695

0.38956

86.8

7

0.8

O95379

Tumor necrosis factor alpha-induced protein 8

TNFAIP8

0.016869

0.2251

22.0409

0.1305

23.8998

0.38972

40.4

5

0.8

Q9NY12

H/ACA ribonucleoprotein complex subunit 1

GAR1

0.01728

0.2208

27.6053

0.18001

28.7912

0.21825

29

5

0.8

P16109

P-selectin

SELP

0.017721

− 2.0401

24.1549

1.03363

23.9684

1.06785

29

14

0.81

Q96RP9

Elongation factor G, mitochondrial

GFM1

0.020163

0.288

24.2375

0.19021

24.3248

0.22518

13.2

7

0.8

Q96F86

Enhancer of mRNA-decapping protein 3

EDC3

0.02024

0.44525

26.7743

0.34422

26.5077

0.41686

12.4

3

0.82

P08134

Rho-related GTP-binding protein RhoC

RHOC

0.022534

0.3601

23.692

0.17871

23.25635

0.48992

65.8

10

0.81

Q15283

Ras GTPase-activating protein 2

RASA2

0.025799

0.2581

25.2002

0.25399

25.0644

0.3012

14.5

9

0.8

O95866

Protein G6b

G6B

0.025824

− 1.4023

21.8137

0.77427

22.3007

0.97969

23.7

5

0.81

O75874

Isocitrate dehydrogenase [NADP] cytoplasmic

IDH1

0.026221

− 0.3508

21.6884

0.25198

21.9288

0.44714

52.4

17

0.81

P09564

T-cell antigen CD7

CD7

0.027969

0.3583

22.542

0.19792

22.6533

0.35246

16.7

4

0.82

O75439

Mitochondrial-processing peptidase subunit beta

PMPCB

0.031524

0.2241

22.4262

0.21703

24.1114

0.27829

22.1

7

0.83

P24158

Myeloblastin

PRTN3

0.049099

− 0.55295

28.221

0.57502

28.819

0.84918

20.7

4

0.81

  1. The table displays proteins (n = 61) that are differentially expressed in CD8+ T cells from MS patients compared to healthy controls (HC). The proteins are extracted from Additional file 2: Table S2 and selected by fulfilling at least two of the three criteria: p-value (p < 0.01), area under the curve (AUC) (AUC > 0.8) and log fold-change (FC) > [0.2] between samples from MS patients and healthy controls. The log2-fold changes in MS versus HC is based on normalized values. Accession number, protein identity and gene names are indicated for each protein, in addition to median log2-transformed protein abundances with standard variation (SD) for each group, the percentage of sequence coverage (% sequence coverage) and number of peptides (# peptides) identified for each protein