1. Supplementary Figure 1 pH MW/1000 numberspot label Protein biomarker 11 (a,b)APO1 22GSN 33TTR 44FGB 55FGG 66APOD 77APOE 88 (a,b)ATIII 99 (a,b)A2M 1010 (a,b)CFH 11 VDB 12 KLKB1 1313 (a,b)AMBP 14 APOIV 15 APOL 1616 (a,b,c)C4 1717 (a,b)C9 18 CRP 1919 (a,b,c)HP 20 S100A9 21 S100A8 2222 (a,b)SAA 23 SAP 24 ACT 25 AGP1 26 C3

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

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

4. Figure 2 FQ SJIA ATIIIC4C9SAAA2M PIMW 4.655K 4.755K 5.355K 5.060K 4.960K 4.860K 4.760K PIMW 8.235K 8.535K 6.344K 4.017K PIMW 5.975K 5.060K 5.160K 5.260K 5.660K 5.360K 5.460K PIMW 7.111K 5.514K 5.511K 6.011K 6.711K PIMW 5.3160K 5.865K 4.9160K 5.4160K 5.3160K

5. FQ SJIA Figure 3A SAA S100A9 S100A8 CRP HP SAP APO IV ACT AGP1 C4 GSN A2M APO A1 CFH TTR 0.00 12510 20 Number of features called significant False discovery rate (FDR) 0.05 0.10 0.15 0.20 0.25 0.30 FQ SJIA FQ POLY KD SJIA FFI SJIA F

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

7. Goodness of class separation –  probability SJIA TrainingSJIA Testing 127654 Feature# 8912765489 Figure 3B

8. Supplementary Figure 4