Classifier training

FDR analysis

Predictor discoveryin training set

4

Training setSJIA (12 F, 12 Q)

1

DIGEraw gel images

Matched samplesSJIA (10 F, 10 Q)POLY (5 F, 5 Q)

Spot findingspot alignment

feature extraction

Classifier training

ClassifySJIA F vs Q

DIGE analysis Prediction analysis (LDA)

Predictor testin testing set

5

Testing setSJIA (10 F, 10 Q)

2

Cluster analysis

2d hierarchicalclustering

heatmap plotting

Normalizationmanual review

Manual review

MSMS Protein ID

3

15 protein2d clustering

12 ELISA Assay development

Feature selection

7

DiscriminateSJIA F

KDFI

Supplementary Figure 1

ClusteringBox-and-Whisker Analysis

DiscriminateSJIA FSJIA QPOLY FPOLY Q

ELISA assays

7 ELISA assay

ELISA assayFI (27 )KD (10)

9

ELISA assayQ->F (5)Q->Q (10)

Test to anticipate SJIA F in Q

LDAFisher exact test

randomization

Blind testing

ClassifySJIA F vs Q

Fisher exact test

SJIA F(12) FI (15)

ClassifySJIA F vs FI

Fisher exact test

     

number spot label Protein biomarker 

1 1 (a,b) APO-AI2 2 GSN3 3 TTR4 4 FGB5 5 FGG6 6 APO-D7 7 APO-E8 8 (a,b) ATIII9 9 (a,b) A2M10 10 (a,b) CFH11 11 VDB12 12 KLKB113 13 (a,b) AMBP14 14 APO-AIV15 15 APO-L16 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     

Supplementary Figure 2

pH

MW

/100

0

1 anti-trypsin

2 albumin

3 serrotransferrin

4 Ig heavy chain

5 Haptoglobin

6 Ig light chain

Removed proteins:

Patient 1 and Patient 2 whole plasma

Patient 1 and Patient 2 after protein depletion

213

45

6

A B

Hemoglobin

213

45

6

S100A8/S100A9

Rela

tive

DIGE

MEA

SURE

MEN

TS

F KD FISJIA

APOA1 SAPCRP HP S100A9 SAAS100A8A2M

Q

Supplementary Figure 3

F KD FISJIA

APOA1 SAPCRP HP SAAA2M

Q

Rela

tive

ELIS

A M

EASU

REM

ENTS