Online-only Table 1 Studies selected for meta-analysis.

1

Haytural et al. Mol Cell Proteomics, 2020¹⁴

Outer 2/3 of the molecular layer (Dentate gyrus)^#

TMT

SDS-based

5 AD

91 ± 4.3

5.17 ± 1.3

4 F / 1 M

2/5

IV

7458

5 C

81.8 ± 9.2

6.8 ± 1

4 F / 1 M

1/5

0-II

2

Schedin-Weiss et al. (manuscript in preparation)

Frontal cortex^‡

¹⁸O

Urea-based

5 AD

81 ± 5

6.3 ± 1.1

3 F / 2 M

n/a

III – VI

2298

5 C

79 ± 6

6.8 ± 2

3 F / 2 M

0-II

3

Hippocampus^#

5 AD

81 ± 5

6.3 ± 1.1

3 F / 2 M

n/a

III – VI

2251

5 C

79 ± 6

6.8 ± 2

3 F / 2 M

0-II

4

Bereczki et al. Brain, 2018⁸

Dorsolateral prefrontal cortex (BA9)^‡

TMT

SDS-based

9 AD

85.6 ± 6.5

23.7 ± 10

6 F / 3 M

n/a

-

7097

8 C

83 ± 3.8

35.2 ± 18.4

4 F / 4 M

5

Mendonça et al. Neurobiol Dis, 2019¹⁹

Entorhinal cortex^#

Label-free

Urea-based

6 AD

82.8 ± 5.19

4.58 ± 1.5

4 F / 2 M

n/a

IV – VI

2014

7 C

65 ± 10.2

4.36 ± 2.43

1 F / 6 M

n/a

6

Frontal cortex^‡

10 AD

82.5 ± 6.06

5.25 ± 0.89

8 F / 2 M

n/a

IV – VI

2230

7 C

58.3 ± 12.7

5.29 ± 3.4

2 F / 5 M

n/a

7

Parahippocampal cortex^#

5 AD

80.2 ± 9.42

4.9 ± 0.74

5 F

n/a

V – IV

2204

11 C

64.1 ± 14.1

4.77 ± 2.79

4 F / 7 M

n/a

8

Temporal cortex^#

11 AD

81.2 ± 8.05

5 ± 1.28

9 F / 2 M

n/a

IV – VI

2101

7 C

58.3 ± 12.7

5.29 ± 3.4

2 F / 5 M

n/a

9

Ping et al. Sci Data, 2018¹²

BA9^‡

TMT

Urea-based

10 AD

65.1 ± 7.43

5.4 ± 1.5

5 F / 5 M

7/10

V – VI

7129

10 C

63.7 ± 10.2

9.3 ± 7.09

5 F / 5 M

2/10

0 - II

10

Johnson et al. Mol Neurodegener, 2018¹⁰

BA9^‡

TMT

Urea-based

20 AD

86.3 ± 8.7

14.2 ± 4.9

10 F / 10 M

7/20

IV – VI

5888

13 C

81.3 ± 10.9

17.4 ± 5.8

3 F / 10 M

1/13

I-III

11

Johnson et al. Nat Med, 2020⁶

BA9^‡

Label-free

Urea-based

252 AD

-

5.8 ± 4.6

141 F / 111 M

n/a

III – VI

2793

94 C

-

8.2 ± 6.6

44 F / 50 M

0 - III

12

Temporal cortex^#

83 AD

82.3 ± 7.7

7.6 ± 4.8

47 F / 36 M

43/83

IV – VI

3286

28 C

89 ± 1.4

11.3 ± 8.7

17 F / 11 M

3/28

0 - III

13

BA9^‡

49 AD

78.1 ± 10.7

12.7 ± 5.4

27 F / 22 M

n/a

?

2249

46 C

65.2 ± 8.9

14.7 ± 4. 9

19 F / 27 M

?

14

Bai et al. Neuron, 2020⁹

Frontal gyrus^‡

TMT

Urea-based

15 AD

78 ± 8.5

3.1 ± 0.92

9 F / 6 M

n/a

V – VI

12521

18 C

84.9 ± 5.9

2.6 ± 0.7

8 F / 10 M

I - IV

15

Frontal gyrus^‡

39 AD

84 ± 10.1

6.4 ± 4.4

27 F / 12 M

22/39

II – VI

12147

23 C

80.8 ± 10.4

9.5 ± 6.3

11 F / 12 M

2/23

0 - III

16

Zhang et al. Acta Neuropathol Commun., 2018⁷

Frontal cortex^‡

Label-free

SDS-based

8 AD

70.8 ± 5.84

7.2 ± 4.06

2 F / 6 M

4/8

V – VI

1968

8 C

70.8 ± 11.8

7.5 ± 2.6

4 F / 4 M

1/8

0 - II

17

Xu et al. Commun Biol., 2019¹¹

Hippocampus^#

iTRAQ

SDS-based

6 AD

70.6 ± 7.8

6.5 ± 1.3

3 F / 3 M

n/a

V – VI

2910

6 C

69.1 ± 7.3

10.2 ± 3.1

3 F / 3 M

n/a

18

Entorhinal cortex^#

9 AD

70.3 ± 7

6.8 ± 2.3

4 F / 5 M

n/a

IV – VI

2585

9 C

70.1 ± 6.6

9.6 ± 2.6

4 F / 5 M

n/a

Sample size

Number of proteins

123 AD

17296

102 C

424 AD

4292

208 C