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
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