Supplementary Figure 1

1. Supplementary Figure 1 MW/1000 pH

2. SJIA POLY Others F FI F KD Q Q C3 AGP1 ACT SAP SAA S100A8 S100A9 HP CRP C9 C4 APO-IV APO-L1 AMBP KLKB1 VDB CFH ATIII A2M ATIII APO-E APO-D FGG FGB TTR GSN APOA1 Figure 1

3. 12 10 8 Scale (normalized protein concentration (ug/ml)/mg) 6 S100A8/S1009 4 CRP HP SAA UCSD F UCSF F Stanford F UCSF Q Stanford Q 2 0 Supplementary Figure 2

4. SJIA F Q ATIII C4 C9 SAA A2M PI MW PI MW PI MW PI MW PI MW 4.6 55K 5.9 75K 7.1 11K 5.3 160K 8.2 35K 4.7 55K 5.0 60K 5.5 14K 5.8 65K 5.3 55K 5.1 60K 8.5 35K 5.0 60K 5.2 60K 5.5 11K 4.9 160K 4.9 60K 6.3 44K 5.6 60K 6.0 11K 5.4 160K 4.8 60K 5.3 60K 4.0 17K 4.7 60K 6.7 11K 5.3 160K 5.4 60K Figure 2

5. SJIA SJIA SJIA SJIA POLY F F Q Q F Q F KD F FI 0.30 0.25 TTR CFH 0.20 APO A1 A2M False discovery rate (FDR) GSN 0.15 C4 AGP1 0.10 ACT APO IV SAP 0.05 HP CRP 0.00 S100A8 S100A9 20 1 2 5 10 SAA Number of features called significant Figure 3A

6. SJIA F KD ATIII A2M HP APOIV GSN APO1 SAA SAP AGP1 Supplementary Figure 3

7. Goodness of class separation – D probability SJIA Training SJIA Testing Feature# 4 5 6 7 8 9 12 4 5 6 7 8 9 12 Figure 3B

8. Supplementary Figure 4