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