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Table 3 Differentially expressed proteins in stimulated CD4+ T cells

From: Quantitative proteomics reveals protein dysregulation during T cell activation in multiple sclerosis patients compared to healthy controls

Accession

Protein identity

Gene names

p-value

Adjusted p-value

FC MS vsrses HC (log2)

Median intensity MS (log2)

MS SD

Median intensity HC (log2)

HC SD

% seq cov

# pep

PC1

PC2

Q13588

GRB2-related adapter protein

GRAP

1.77E−16

1.01E−12

5.346

31.399

1.303

25.885

0.832

61

10

0.224

− 0.070

Q9H2F5

Enhancer of polycomb homolog 1

EPC1

5.59E−15

1.59E−11

3.473

23.533

0.548

20.114

0.946

1

1

0.213

− 0.095

Q6ICL3

Transport and Golgi organization protein 2 homolog

TANGO2

2.05E−11

3.81E−08

4.479

26.502

0.813

22.015

1.666

23

4

0.156

− 0.257

Q9BV20

Methylthioribose-1-phosphate isomerase

MRI1

2.67E−11

3.81E−08

− 2.355

25.694

0.521

27.987

0.897

36

11

0.198

− 0.122

Q6UW02

Cytochrome P450 20A1

CYP20A1

6.87E−11

7.83E−08

− 1.365

26.049

0.540

27.365

0.355

55

21

0.143

− 0.210

Q8WV92

MIT domain-containing protein 1

MITD1

8.61E−10

8.18E−07

− 3.449

21.702

1.336

25.776

1.359

15

3

0.145

− 0.313

Q9H4A6

Golgi phosphoprotein 3

GOLPH3

1.75E−09

1.43E−06

2.248

26.038

1.023

23.927

0.456

26

7

0.229

− 0.028

Q9NWS0

PIH1 domain-containing protein 1

PIH1D1

3.57E−09

2.55E−06

− 1.367

24.477

0.552

25.772

0.581

38

7

0.148

− 0.299

Q9Y5B6

PAX3- and PAX7-binding protein 1

PAXBP1

9.10E−08

5.77E−05

1.162

26.019

0.335

24.924

0.650

22

16

− 0.137

− 0.013

Q96G46

tRNA-dihydrouridine(47) synthase [NAD(P)( +)]-like

DUS3L

1.14E−07

5.93E−05

− 2.660

22.773

1.476

25.446

0.966

23

10

0.186

− 0.202

Q9BRQ6

MICOS complex subunit MIC25

CHCHD6

1.04E−07

5.93E−05

− 4.215

21.766

0.898

26.389

2.373

20

4

0.174

− 0.091

Q7L8W6

Diphthine–ammonia ligase

DPH6

2.76E−07

1.31E−04

− 1.913

21.418

0.980

23.404

0.962

7

2

− 0.183

− 0.173

Q8WUK0

Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1

PTPMT1

3.13E−07

1.37E−04

− 3.168

20.553

1.865

24.854

1.171

6

1

− 0.142

− 0.184

Q02539

Histone H1.1

H1-1

4.31E−07

1.76E−04

− 3.260

22.786

1.968

26.447

1.160

50

15

0.164

− 0.114

Q2TBE0

CWF19-like protein 2

CWF19L2

2.63E−06

9.98E−04

− 1.787

21.730

1.185

23.318

0.757

6

5

− 0.164

− 0.218

Q5T4S7

E3 ubiquitin-protein ligase UBR4

UBR4

3.57E−06

1.27E−03

0.815

30.188

0.564

29.497

0.298

29

117

− 0.137

− 0.224

P54098

DNA polymerase subunit gamma-1

POLG

4.04E−06

1.28E−03

− 1.351

20.008

0.942

21.367

0.504

2

3

0.162

− 0.307

Q9H2K8

Serine/threonine-protein kinase TAO3

TAOK3

3.93E−06

1.28E−03

0.710

27.728

0.461

27.239

0.358

36

31

− 0.174

− 0.192

P17706

Tyrosine-protein phosphatase nonreceptor type 2

PTPN2

5.97E−06

1.79E−03

0.847

24.107

0.409

23.441

0.578

23

8

− 0.204

0.026

Q5THJ4

Vacuolar protein sorting-associated protein 13D

VPS13D

1.58E−05

4.49E−03

3.492

24.517

2.648

19.778

1.488

1

2

− 0.147

− 0.155

Q8IV53

DENN domain-containing protein 1C

DENND1C

1.88E−05

5.10E−03

− 0.596

25.891

0.445

26.401

0.295

35

20

− 0.143

− 0.044

O94762

ATP-dependent DNA helicase Q5

RECQL5

3.96E−05

1.03E−02

1.558

21.522

0.917

19.793

1.172

1

1

− 0.157

− 0.132

Q2M296

Methenyltetrahydrofolate synthase domain-containing protein

MTHFSD

4.59E−05

1.14E−02

− 3.585

26.603

3.050

31.143

0.892

11

3

− 0.186

− 0.191

Q96SB8

Structural maintenance of chromosomes protein 6

SMC6

8.32E−05

1.98E−02

− 1.074

23.137

0.690

24.224

0.838

11

9

− 0.144

− 0.226

Q8NEM7

Transcription factor SPT20 homolog

SUPT20H

1.00E−04

2.28E−02

− 1.168

20.132

0.830

21.584

0.869

2

2

− 0.168

0.051

Q8WXA9

Splicing regulatory glutamine/lysine-rich protein 1

SREK1

1.14E−04

2.50E−02

0.993

23.502

0.867

22.472

0.505

14

5

− 0.202

− 0.174

Q8IWV7

E3 ubiquitin-protein ligase UBR1

UBR1

1.41E−04

2.92E−02

0.511

26.361

0.313

25.872

0.433

21

31

− 0.196

− 0.009

Q9HC21

Mitochondrial thiamine pyrophosphate carrier

SLC25A19

1.44E−04

2.92E−02

− 1.415

20.523

1.025

22.021

1.090

11

4

0.152

− 0.278

Q5PSV4

Breast cancer metastasis-suppressor 1-like protein

BRMS1L

1.53E−04

3.01E−02

− 1.678

20.204

1.064

21.904

1.415

7

2

− 0.177

− 0.118

Q6WCQ1

Myosin phosphatase Rho-interacting protein

MPRIP

1.92E−04

3.66E−02

1.342

23.142

0.681

21.771

1.234

9

6

− 0.160

− 0.184

Q9BQ69

ADP-ribose glycohydrolase MACROD1

MACROD1

2.08E−04

3.82E−02

− 1.085

23.281

0.651

24.858

0.967

18

4

− 0.182

0.015

Q9H410

Kinetochore-associated protein DSN1 homolog

DSN1

2.26E−04

4.03E−02

− 1.220

21.639

1.149

22.896

0.594

21

6

− 0.176

− 0.154

Q9BYC9

39S ribosomal protein L20, mitochondrial

MRPL20

2.43E−04

4.20E−02

− 0.643

23.390

0.533

24.157

0.468

24

4

− 0.210

− 0.070

  1. The table shows the accession number, protein identity and gene names for each protein, in addition to the unadjusted (p-value) and adjusted p-value, the log2-fold changes in MS versus HC based on normalized values, median log2-transformed protein abundances with standard deviation (SD) for each group, the percentage of sequence coverage (% seq cov), the number of peptides (# pep) identified for each protein, and the loadings for the first (PC1) and the second principal component (PC2). Large loadings (cutoff 0.174) are highlighted in bold
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Clinical Proteomics

ISSN: 1559-0275