Classifier training

1. Supplementary Figure 1 DIGE analysis Cluster analysis ELISA assays Prediction analysis (LDA) 1 3 2 Predictor discovery in training set Predictor test in testing set DIGE raw gel images Matched samples SJIA (10 F, 10 Q) POLY (5 F, 5 Q) 2d hierarchical clustering heatmap plotting 12 ELISA Assay development 4 5 7 Test to anticipate SJIA F in Q randomization Training set SJIA (12 F, 12 Q) Testing set SJIA (10 F, 10 Q) ELISA assay FI (27 ) KD (10) SJIA F(12) FI (15) 9 FDR analysis ELISA assay Q->F (5) Q->Q (10) Feature selection Spot finding spot alignment feature extraction 15 protein 2d clustering LDA Fisher exact test Normalization manual review Classifier training Blind testing Classifier training 7 ELISA assay Clustering Box-and-Whisker Analysis Fisher exact test Fisher exact test Manual review Discriminate SJIA F SJIA Q POLY F POLY Q Discriminate SJIA F KD FI Classify SJIA F vs Q Classify SJIA F vs Q Classify SJIA F vs FI MSMS Protein ID

2. Supplementary Figure 2 A B Patient 1 and Patient 2 whole plasma 3 2 4 1 5 Removed proteins: 1 anti-trypsin 2 albumin 3 serrotransferrin 4 Ig heavy chain 5 Haptoglobin 6 Ig light chain 6 MW/1000 Patient 1 and Patient 2 after protein depletion 3 2 4 1 5 Hemoglobin 6 pH

3. SJIA SJIA F Q KD FI F Q KD FI Relative DIGE MEASUREMENTS Relative ELISA MEASUREMENTS A2M APOA1 CRP HP S100A9 S100A8 SAA SAP A2M APOA1 CRP HP S100A8 /S100A9 SAA SAP Supplementary Figure 3