Table 3 Significantly regulated proteins in both TMT-labeling and label-free.

From: Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis

Accession

Protein

TMT-labeling

Label-free

P

S

CPZ-42d

EAE-16d

EAE-32d

 

CPZ-42d

EAE-16d

EAE-32d

  

FC

q

FC

q

FC

q

P

FC

q

FC

q

FC

q

hCSF

hP

(A) Upregulated in CPZ-42d

P14106

C1QB

5

19

5.3

***

0.8

 

0.8

 

2

19.4

*’

1.5

 

1.3

 

Y

Y

Q02105

C1QC

6

14

5.3

***

0.8

 

0.8

 

3

9.1

*’

1.2

 

1.3

 

Y

Y

O89017

LGMN

6

11

4.0

***

0.7

 

0.7

 

1

64.9

*

1.9

 

1.3

 

Y

 

P98086

C1QA

6

20

3.8

***

0.9

 

0.9

 

4

6.8

*’

1.1

 

1.1

 

Y

Y

P16110

LEG3

5

5

3.7

***

1.1

 

0.8

 

2

338.7

*’

2.3

 

1.1

 

Y

 

Q99L04

DHRS1

15

42

3.7

***

0.8

 

0.8

 

3

4.0

*’

0.9

 

0.9

   

P24452

CAPG

6

9

3.4

***

0.9

 

0.9

 

1

4.7

*’

1.2

 

1.0

 

Y

 

P20152

VIME

30

540

3.1

***

1.2

 

1.1

 

22

7.7

*’

1.6

 

1.2

 

Y

Y

P20060

HEXB

18

48

2.9

***

1.0

 

1.0

 

6

5.0

*’

1.6

 

1.2

 

Y

Y

P03995

GFAP

38

658

2.6

***

1.3

 

1.1

 

18

7.2

*’

1.5

 

1.0

 

Y

 

P11835

ITB2

5

5

2.6

***

0.8

 

0.8

 

1

8.2

*’

0.5

 

0.7

 

Y

 

Q9Z127

LAT1

3

7

2.4

***

0.5

***

0.6

***

1

4.5

*’

0.5

 

0.6

   

P26041

MOES

20

46

2.3

***

1.1

 

1.0

 

4

2.6

*’

0.9

 

0.9

 

Y

Y

O35639

ANXA3

15

25

2.2

***

1.0

 

1.0

 

1

5.9

*’

1.4

 

1.3

 

Y

 

P18242

CATD

16

119

2.2

***

1.0

 

0.9

 

10

2.8

*’

1.3

 

1.0

 

Y

Y

Q9DAW9

CNN3

8

22

2.1

***

1.0

 

1.0

 

4

4.0

*’

1.2

 

1.0

   

Q9D379

HYEP

8

11

2.0

***

0.8

 

0.8

 

2

2.9

*’

0.6

 

0.7

   

P10605

CATB

9

57

1.9

***

0.9

 

1.0

 

7

3.4

*’

1.0

 

0.9

 

Y

Y

Q8BTM8

FLNA

30

40

1.9

***

0.8

 

0.9

 

2

1.5

*’

1.4

 

1.0

 

Y

Y

P60824

CIRBP

4

17

1.9

***

1.0

 

1.0

 

1

4.8

*’

1.2

 

1.1

   

Q9DCJ9

NPL

7

11

1.8

***

1.0

 

1.0

 

1

19.8

*’

1.4

 

0.7

   

Q9WVA4

TAGL2

11

38

1.8

***

1.1

 

1.0

 

3

2.9

*’

1.2

 

0.9

 

Y

Y

P09055

ITB1

4

5

1.7

***

0.9

 

0.8

 

1

2.8

*

0.4

 

0.6

 

Y

Y

P10852

4F2

20

107

1.6

**

0.8

 

0.8

 

12

1.9

*’

0.8

 

0.8

 

Y

Y

Q80WG5

LRC8A

4

4

1.6

**

0.8

 

0.8

 

1

2.1

*’

0.8

 

0.7

§

  

P16045

LEG1

6

25

1.6

**

0.9

 

0.9

 

2

3.1

*’

1.0

 

1.0

 

Y

 

P61620

S61A1

2

4

1.6

**

0.8

 

0.8

 

1

2.5

*

0.4

*

0.6

   

Q9CQI6

COTL1

13

138

1.5

*’

1.0

 

1.0

 

5

2.1

*’

0.9

 

0.9

 

Y

 

P16675

PPGB

3

4

1.5

*’

0.9

 

1.0

 

1

3.2

*’

0.9

 

1.0

 

Y

Y

P07356

ANXA2

11

20

1.5

*

1.0

 

1.0

 

3

2.7

*’

0.7

 

0.7

 

Y

Y

Q9DCD0

6PGD

15

27

1.5

*

0.9

 

0.9

 

5

1.7

*

0.8

 

0.8

 

Y

Y

Q9Z110

P5CS

14

22

1.5

*

0.9

 

1.0

 

2

2.9

*’

0.8

 

0.9

   

O89086

RBM3

5

19

1.5

*

1.0

 

1.0

 

1

5.0

*’

1.3

 

1.1

   

P51880

FABP7

4

20

1.5

*

0.9

 

1.4

***

6

2.9

*’

1.1

 

1.9

 

Y

 

Q8CGC7

SYEP

29

34

1.4

*

0.8

 

0.8

 

3

2.1

*’

0.6

 

0.7

   

P08030

APT

6

11

1.4

*

1.1

 

1.0

 

1

2.2

*

1.1

 

1.0

   

Q8VDD5

MYH9

47

94

1.4

*

0.9

 

0.9

 

8

1.8

*’

0.8

 

0.8

 

Y

Y

(B) Downregulated in CPZ-42d

Q5EBJ4

ERMIN

7

21

0.5

***

1.3

 

1.1

 

3

0.5

*’

0.9

 

0.8

 

Y

 

P47911

RL6

13

25

0.5

***

1.3

 

1.0

 

1

0.5

*’

0.9

 

0.8

   

P23927

CRYAB

6

67

0.6

***

1.2

 

1.0

 

4

0.5

*

1.2

 

1.0

   

Q9D8E6

RL4

13

29

0.7

*’

1.1

 

1.0

 

1

0.5

*

0.6

 

0.8

   

Q61699

HS105

36

78

0.7

*

1.0

 

1.0

 

12

0.6

*’

0.9

 

0.9

  

Y

Q920E5

FPPS

9

14

0.7

*

1.0

 

1.0

 

2

0.6

*

0.7

 

0.8

 

Y

 

P14148

RL7

6

10

0.7

*

0.9

 

0.9

 

1

0.6

*

0.7

 

0.8

   

(C) Upregulated in EAE-16d

Q91X72

HEMO

15

28

0.9

 

1.8

***

1.2

 

3

0.9

 

3.3

*

1.5

 

Y

Y

P07758

A1AT1

4

8

1.0

 

1.7

***

1.2

 

1

0.9

 

4.4

*

1.8

 

Y

Y

Q9QXV0

PCSK1

8

102

1.2

 

1.5

**

1.1

 

4

2.1

 

2.2

*

1.1

 

Y

Y

Q8K019

BCLF1

7

7

1.1

 

1.4

*’

1.4

***

1

1.3

 

1.4

*

1.2

   

Q03517

SCG2

28

160

1.1

 

1.4

*

1.1

 

10

1.5

 

2.6

*

1.5

 

Y

 

P22005

PENK

7

35

1.1

 

1.4

*

1.2

 

1

0.7

 

6.0

*

2.6

 

Y

Y

Q9JJF0

NP1L5

5

10

0.9

 

1.4

*

1.1

 

1

1.4

 

2.2

*

1.0

   

Mouse

(D) Downregulated in EAE-32d

P97772

GRM1

4

4

1.1

 

0.7

 

0.7

*

2.0

1.8

 

0.5

 

0.5

§

Y

 
  1. (A) Proteins upregulated in CPZ-42d in both TMT and label-free. (B) Proteins downregulated in CPZ-42d in both TMT and label-free. (C) Proteins upregulated in EAE-16d in both TMT and label-free. (D) Protein downregulated in EAE-32d in both TMT and label-free. For all tables: quantified proteins, number of unique peptides (P) and spectra (S) with fold change relative to respective controls (FC) are shown for CPZ-42d, EAE-16d and EAE-32d. The p-values for the regulated proteins were corrected for multiple hypothesis testing to control false discovery rates, resulting in adjusted p-values (q-values). The q-values are denoted in the table as follows: §, q < 0.1; *, q < 0.05; *’ q < 0.01; **, q < 0.005, *** q < 0.0005. For the TMT-data, the z-scores for all the protein ratios in each condition were calculated using a Gaussian probability function, and the p-values corrected using Benjamini–Hochberg (q-values), as previously described11. For the label-free data Progenesis LC–MS was used to calculate statistically up- and downregulated proteins based on ANOVA (p-value) with correction for multiple hypotheses testing based on FDR (q-value). Consistent regulation in all individuals in CPZ-42d allowed a stringent limit for the corrected p-value from multiple hypothesis testing (q < 0.05), a moderate in in EAE-16d (q < 0.051) and a higher limit in EAE-32d (q ≤ 0.1). Human orthologues present in human cerebrospinal fluid (hCSF) and plasma (hP) according to the CSF-PR database21 are indicated with yes (Y = yes).
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