supplementary figure 1 ph mw/1000 numberspot label protein biomarker 11 (a,b)apo1 22gsn 33ttr 44fgb...

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Supplementary Figure pH MW/1000 number spot label Protein biomarker 1 1 (a,b) APO1 2 2 GSN 3 3 TTR 4 4 FGB 5 5 FGG 6 6 APOD 7 7 APOE 8 8 (a,b) ATIII 9 9 (a,b) A2M 10 10 (a,b) CFH 11 11 VDB 12 12 KLKB1 13 13 (a,b) AMBP 14 14 APOIV 15 15 APOL 16 16 (a,b,c) C4 17 17 (a,b) C9 18 18 CRP 19 19 (a,b,c) HP 20 20 S100A9 21 21 S100A8 22 22 (a,b) SAA 23 23 SAP 24 24 ACT 25 25 AGP1 26 26 C3

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Page 1: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

Supplementary Figure 1

pH

MW

/100

0

number spot labelProtein biomarker

1 1 (a,b) APO12 2 GSN3 3 TTR4 4 FGB5 5 FGG6 6 APOD7 7 APOE8 8 (a,b) ATIII9 9 (a,b) A2M10 10 (a,b) CFH11 11 VDB12 12 KLKB113 13 (a,b) AMBP14 14 APOIV15 15 APOL16 16 (a,b,c) C417 17 (a,b) C918 18 CRP19 19 (a,b,c) HP20 20 S100A921 21 S100A822 22 (a,b) SAA23 23 SAP24 24 ACT25 25 AGP126 26 C3

Page 2: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

F Q

SJIA

APOA1

GSN

APO-D APO-EATIII

A2M

ATIIICFH

TTR

VDBKLKB1AMBP

APO-L1 APO-IVC4

C9

CRP

HP

S100A9S100A8

SAA

SAPAGP1 C3

ACT

FGGFGB

F Q

POLY

FI KD

Others

Figure 1

Page 3: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

Supplementary Figure 2

UCSDF

UCSFF

StanfordF

UCSFQ

StanfordQ

CRP HP SAA S100A8/S1009

0

2

4

6

8

10

12

Sca

le (

no

rmal

ized

pro

tein

co

nce

ntr

atio

n (

ug

/ml)

/mg

)

Page 4: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

Figure 2

F QSJIA

ATIII C4 C9 SAA A2MPI MW

4.6 55K

4.7 55K

5.3 55K

5.0 60K

4.9 60K

4.8 60K

4.7 60K

PI MW

8.2 35K

8.5 35K

6.3 44K

4.0 17K

PI MW

5.9 75K

5.0 60K

5.1 60K

5.2 60K

5.6 60K

5.3 60K

5.4 60K

PI MW

7.1 11K

5.5 14K

5.5 11K

6.0 11K

6.7 11K

PI MW

5.3 160K

5.8 65K

4.9 160K

5.4 160K

5.3 160K

Page 5: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

SAAS100A9S100A8

CRPHP

SAPAPO IV

ACTAGP1

C4GSNA2M

APO A1CFHTTR

Figure 3

0.00

1 2 5 10 20

Number of features called significant

Fal

se d

isco

very

rat

e (F

DR

)

0.05

0.10

0.15

0.20

0.25

0.30F QSJIA

F QPOLY

KDSJIAF FI

SJIAF

P value: 1.1 E -4 P value: 0.5 P value: 0.19 P value: 1.4 E -4

APO A1

KDSJIAF

AGP1

SAP

SAA

GSN

APOIV

HP

A2M

ATIII

P value: 2.9 E -4

A B C

Page 6: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

Go

od

nes

s o

f cl

ass

sep

arat

ion

– D

pro

bab

ilit

y

SJIA Training SJIA Testing

127654Feature# 8 9 127654 8 9

Figure 3D

Page 7: Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010

Supplementary Figure 3

S100A12

SJIA F

SJIA Q

Poly F

Poly Q

Normal

s0.00

0.05

0.10

0.15

S100A12

ug

/ml

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