Table S1. CRC case Pool Control Pool Name UniProt No. FC b VIP value d Spectral Counts Spectral Counts

Transcription

1 Table S1. page 1/4 Phase 1 Exploratory Study, List of proteins identified by LC-ESI-MS/MS after 1DE separation and their relative quantitation by spectral count UniProt Entry SwissProt- CRC case Pool Control Pool Name UniProt No. FC b VIP value d Actin, cytoplasmic 1 ACTB_HUMAN P ± 2 6 ± Afamin AFAM_HUMAN P ± 1 30 ± Alpha-1-acid glycoprotein A1AG1_HUMAN P ± 1 3 ± Alpha-1-acid glycoprotein 2 A1AG2_HUMAN P ± 2 3 ± Alpha-1-antichymotrypsin AACT_HUMAN P ± 8 43 ± Alpha-1B-glycoprotein A1BG_HUMAN P ± 5 20 ± Alpha-2-antiplasmin A2AP_HUMAN P ± 3 12 ± Alpha-2-HS-glycoprotein FETUA_HUMAN P ± 6 27 ± Alpha-2-macroglobulin A2MG_HUMAN P ± ± Angiotensinogen ANGT_HUMAN P ± 1 14 ± Antithrombin-III ANT3_HUMAN P ± ± Apolipoprotein A-I APOA1_HUMAN P ± ± Apolipoprotein A-II APOA2_HUMAN P ± 1 18 ± Apolipoprotein A-IV APOA4_HUMAN P ± 7 47 ± Apolipoprotein B-100 APOB_HUMAN P ± ± Apolipoprotein D APOD_HUMAN P ± 9 25 ± Apolipoprotein E APOE_HUMAN P ± 5 34 ± Apolipoprotein L1 APOL1_HUMAN O ± 1 10 ± Apolipoprotein M APOM_HUMAN O ± 2 6 ± Beta-2-glycoprotein 1 APOH_HUMAN P ± 7 26 ± C-reactive protein CRP_HUMAN P ± 1 1 ± C4b-binding protein alpha chain C4BPA_HUMAN P ± 6 35 ± Carbonic anhydrase 1 CAH1_HUMAN P ± 1 8 ± Carboxypeptidase N catalytic chain CBPN_HUMAN P ± 1 6 ± Carboxypeptidase N subunit 2 CPN2_HUMAN P ± 2 5 ± CD5 antigen-like CD5L_HUMAN O ± 1 5 ± Ceruloplasmin CERU_HUMAN P ± ± Clusterin CLUS_HUMAN P ± 3 33 ±

2 continued Table S1. UniProt Entry Name page 2/4 SwissProt- CRC case Pool Control Pool UniProt No. FC b VIP value d Coagulation factor X FA10_HUMAN P ± 2 4 ± Coagulation factor XII FA12_HUMAN P ± 1 3 ± Complement C1q subcomponent subunit B C1QB_HUMAN P ± 4 9 ± Complement C1q subcomponent subunit C C1QC_HUMAN P ± 4 9 ± Complement C1r subcomponent C1R_HUMAN P ± 4 8 ± Complement C1s subcomponent C1S_HUMAN P ± 1 19 ± Complement C2 CO2_HUMAN P ± 5 12 ± Complement C3 CO3_HUMAN P ± ± Complement C4-B CO4B_HUMAN P0C0L5 218 ± ± Complement C5 CO5_HUMAN P ± 2 41 ± Complement component C6 CO6_HUMAN P ± 3 13 ± Complement component C7 CO7_HUMAN P ± 2 12 ± Complement component C8 alpha chain CO8A_HUMAN P ± 1 4 ± Complement component C8 beta chain CO8B_HUMAN P ± 1 4 ± Complement component C8 gamma chain CO8G_HUMAN P ± 2 10 ± Complement component C9 CO9_HUMAN P ± 5 11 ± Complement factor B CFAB_HUMAN P ± ± Complement factor H CFAH_HUMAN P ± ± Complement factor H-related protein 1 FHR1_HUMAN Q ± 2 11 ± Complement factor I CFAI_HUMAN P ± 1 10 ± Corticosteroid-binding globulin CBG_HUMAN P ± 1 6 ± Fibrinogen alpha chain FIBA_HUMAN P ± ± Fibrinogen beta chain FIBB_HUMAN P ± ± Fibrinogen gamma chain FIBG_HUMAN P ± ± Fibronectin FINC_HUMAN P ± ± Fibulin-1 FBLN1_HUMAN P ± 1 4 ± Ficolin-3 FCN3_HUMAN O ± 1 4 ± Galectin-3-binding protein LG3BP_HUMAN Q ± 2 9 ± Gelsolin GELS_HUMAN P ± 6 39 ±

3 continued Table S1. UniProt Entry Name page 3/4 SwissProt- CRC case Pool Control Pool UniProt No. FC b VIP value d Glutathione peroxidase 3 GPX3_HUMAN P ± ± Hemopexin HEMO_HUMAN P ± ± Heparin cofactor 2 HEP2_HUMAN P ± 3 15 ± Histidine-rich glycoprotein HRG_HUMAN P ± 1 19 ± Ig kappa chain C region IGKC_HUMAN P ± 1 8 ± Ig lambda-2 chain C regions LAC2_HUMAN P0CG05 13 ± 2 12 ± Ig mu chain C region IGHM_HUMAN P ± 0 22 ± Insulin-like growth factor-binding protein complex acid ALS_HUMAN P ± 3 7 ± labile subunit Inter-alpha-trypsin inhibitor heavy chain H1 ITIH1_HUMAN P ± 6 55 ± Inter-alpha-trypsin inhibitor heavy chain H2 ITIH2_HUMAN P ± ± Inter-alpha-trypsin inhibitor heavy chain H3 ITIH3_HUMAN Q ± 0 4 ± Inter-alpha-trypsin inhibitor heavy chain H4 ITIH4_HUMAN Q ± 5 63 ± Kallistatin KAIN_HUMAN P ± 1 7 ± Kininogen-1 KNG1_HUMAN P ± 1 34 ± Leucine-rich alpha-2-glycoprotein A2GL_HUMAN P ± 6 7 ± Mannose-binding protein C MBL2_HUMAN P ± 1 2 ± N-acetylmuramoyl-L-alanine amidase PGRP2_HUMAN Q96PD5 4 ± ± Peroxiredoxin-2 PRDX2_HUMAN P ± 1 5 ± Pigment epithelium-derived factor PEDF_HUMAN P ± 4 16 ± Plasma kallikrein KLKB1_HUMAN P ± 2 22 ± Plasma protease C1 inhibitor IC1_HUMAN P ± 8 36 ± Plasminogen PLMN_HUMAN P ± 6 34 ± Protein AMBP AMBP_HUMAN P ± 3 22 ± Prothrombin THRB_HUMAN P ± 9 31 ± Retinol-binding protein 4 RET4_HUMAN P ± 6 27 ± Serum amyloid A protein SAA_HUMAN P0DJI8 8 ± 0.3 nd c nd c Serum amyloid A-4 protein SAA4_HUMAN P ± 1 14 ± Serum amyloid P-component SAMP_HUMAN P ± 1 15 ±

4 continued Table S1. page4/4 page 4/4 UniProt Entry SwissProt- CRC case Pool Control Pool Name UniProt No. FC b VIP value d Serum paraoxonase/arylesterase 1 PON1_HUMAN P ± 4 22 ± Sex hormone-binding globulin SHBG_HUMAN P ± 1 3 ± Tetranectin TETN_HUMAN P ± 3 6 ± Thyroxine-binding globulin THBG_HUMAN P ± 2 7 ± Transthyretin TTHY_HUMAN P ± 7 57 ± Vitamin D-binding protein VTDB_HUMAN P ± 4 57 ± Vitamin K-dependent protein S PROS_HUMAN P ± 1 4 ± Vitronectin VTNC_HUMAN P ± 4 17 ± Zinc-alpha-2-glycoprotein ZA2G_HUMAN P ± 2 10 ± a Mean ± SD of three technical replicates b FC, Fold Change, Spectral counts of CRC cases/controls; bold, FC 1.5; bold-italic, FC -1.5 c nd, not detectable d VIP, Variable Importance in the Projection (PLS-DA analysis); bold, VIP>1

5 Table S2. page 1/5 Phase 2 EPIC Study, Proteins identified by LC-ESI-MS/MS after 1DE separation and their relative quantitation by spectral count UniProt Entry SwissProt- EPIC-CRC case Name UniProt No. Pool EPIC-Control Pool FC b VIP value c Actin, cytoplasmic 1 ACTB_HUMAN P ± 8 8 ± Adiponectin ADIPO_HUMAN Q ± 3 6 ± Afamin AFAM_HUMAN P ± 9 46 ± Alpha-1-acid glycoprotein 1 A1AG1_HUMAN P ± ± Alpha-1-acid glycoprotein 2 A1AG2_HUMAN P ± ± Alpha-1-antichymotrypsin AACT_HUMAN P ± ± Alpha-1B-glycoprotein A1BG_HUMAN P ± ± Alpha-2-antiplasmin A2AP_HUMAN P ± ± Alpha-2-HS-glycoprotein FETUA_HUMAN P ± ± Alpha-2-macroglobulin A2MG_HUMAN P ± ± Angiotensinogen ANGT_HUMAN P ± 8 42 ± Antithrombin-III ANT3_HUMAN P ± ± Apolipoprotein A-I APOA1_HUMAN P ± ± Apolipoprotein A-II APOA2_HUMAN P ± ± Apolipoprotein A-IV APOA4_HUMAN P ± ± Apolipoprotein B-100 APOB_HUMAN P ± ± Apolipoprotein C-II APOC2_HUMAN P ± 2 3 ± Apolipoprotein D APOD_HUMAN P ± 8 50 ± Apolipoprotein E APOE_HUMAN P ± ± Apolipoprotein L1 APOL1_HUMAN O ± 5 23 ± Apolipoprotein M APOM_HUMAN O ± 2 13 ± Apolipoprotein(a) APOA_HUMAN P ± 3 7 ± Attractin ATRN_HUMAN O ± 1 9 ±

6 continued Table S2. page 2/5 UniProt Entry SwissProt- EPIC-CRC case Name UniProt No. Pool EPIC-Control Pool FC b VIP value c Beta-2-glycoprotein 1 APOH_HUMAN P ± 8 45 ± Beta-Ala-His dipeptidase CNDP1_HUMAN Q96KN2 6 ± 2 3 ± C4b-binding protein alpha chain C4BPA_HUMAN P ± 5 12 ± Carbonic anhydrase 1 CAH1_HUMAN P ± 1 1 ± Carboxypeptidase B2 CBPB2_HUMAN Q96IY4 4 ± 2 6 ± Carboxypeptidase N catalytic chain CBPN_HUMAN P ± 3 11 ± Carboxypeptidase N subunit 2 CPN2_HUMAN P ± 5 9 ± CD5 antigen-like CD5L_HUMAN O ± 2 6 ± Ceruloplasmin CERU_HUMAN P ± ± Clusterin CLUS_HUMAN P ± ± Coagulation factor X FA10_HUMAN P ± 2 8 ± Coagulation factor XII FA12_HUMAN P ± 2 6 ± Coagulation factor XIII A chain F13A_HUMAN P ± 0 6 ± Coagulation factor XIII B chain F13B_HUMAN P ± 2 2 ± Complement C1q subcomponent subunit A C1QA_HUMAN P ± 4 32 ± Complement C1q subcomponent subunit B C1QB_HUMAN P ± 4 23 ± Complement C1q subcomponent subunit C C1QC_HUMAN P ± 1 25 ± Complement C1r subcomponent C1R_HUMAN P ± 5 19 ± Complement C1s subcomponent C1S_HUMAN P ± ± Complement C2 CO2_HUMAN P ± 8 15 ± Complement C3 CO3_HUMAN P ± ± Complement C4-B CO4B_HUMAN P0C0L5 445 ± ± Complement C5 CO5_HUMAN P ± 6 92 ± Complement component C6 CO6_HUMAN P ± 4 27 ± Complement component C7 CO7_HUMAN P ± 5 16 ± Complement component C8 alpha chain CO8A_HUMAN P ± 2 14 ± Complement component C8 beta chain CO8B_HUMAN P ± 3 17 ±

7 continued Table S2. page 3/5 UniProt Entry SwissProt- EPIC-CRC case Name UniProt No. Pool EPIC-Control Pool FC b VIP value c Complement component C8 gamma chain CO8G_HUMAN P ± 7 13 ± Complement component C9 CO9_HUMAN P ± 5 42 ± Complement factor B CFAB_HUMAN P ± ± Complement factor H CFAH_HUMAN P ± ± Complement factor H-related protein 1 FHR1_HUMAN Q ± 3 29 ± Complement factor H-related protein 2 FHR2_HUMAN P ± 1 17 ± Complement factor I CFAI_HUMAN P ± 7 39 ± Corticosteroid-binding globulin CBG_HUMAN P ± 5 20 ± Fetuin-B FETUB_HUMAN Q9UGM5 5 ± 3 5 ± Fibronectin FINC_HUMAN P ± ± Ficolin-2 FCN2_HUMAN Q ± 1 3 ± Ficolin-3 FCN3_HUMAN O ± 7 6 ± Gelsolin GELS_HUMAN P ± ± Glutathione peroxidase 3 GPX3_HUMAN P ± 2 5 ± Hemopexin HEMO_HUMAN P ± ± Heparin cofactor 2 HEP2_HUMAN P ± 5 36 ± Histidine-rich glycoprotein HRG_HUMAN P ± ± Hyaluronan-binding protein 2 HABP2_HUMAN Q ± 1 3 ± Insulin-like growth factor-binding protein ALS_HUMAN P ± 1 16 ± complex acid labile subunit Inter-alpha-trypsin inhibitor heavy chain H1 ITIH1_HUMAN P ± ± Inter-alpha-trypsin inhibitor heavy chain H2 ITIH2_HUMAN P ± ± Inter-alpha-trypsin inhibitor heavy chain H3 ITIH3_HUMAN Q ± 8 15 ± Inter-alpha-trypsin inhibitor heavy chain H4 ITIH4_HUMAN Q ± ± Kallistatin KAIN_HUMAN P ± 3 17 ± Kininogen-1 KNG1_HUMAN P ± ± Leucine-rich alpha-2-glycoprotein A2GL_HUMAN P ± 4 15 ±

8 continued Table S2. page 4/5 UniProt Entry SwissProt- EPIC-CRC case Name UniProt No. Pool EPIC-Control Pool FC b VIP value c Lumican LUM_HUMAN P ± 5 8 ± Mannan-binding lectin serine protease 2 MASP2_HUMAN O ± 1 2 ± Mannose-binding protein C MBL2_HUMAN P ± 2 1 ± Monocyte differentiation antigen CD14 CD14_HUMAN P ± 2 3 ± N-acetylmuramoyl-L-alanine amidase PGRP2_HUMAN Q96PD5 15 ± 1 9 ± Pigment epithelium-derived factor PEDF_HUMAN P ± 5 36 ± Plasma kallikrein KLKB1_HUMAN P ± 2 30 ± Plasma protease C1 inhibitor IC1_HUMAN P ± ± Plasma serine protease inhibitor IPSP_HUMAN P ± 2 14 ± Plasminogen PLMN_HUMAN P ± ± Pregnancy zone protein PZP_HUMAN P ± ± Protein AMBP AMBP_HUMAN P ± 3 42 ± Protein Z-dependent protease inhibitor ZPI_HUMAN Q9UK55 3 ± 2 3 ± Proteoglycan 4 PRG4_HUMAN Q ± 0 4 ± Prothrombin THRB_HUMAN P ± ± Retinol-binding protein 4 RET4_HUMAN P ± ± Serum amyloid A-4 protein SAA4_HUMAN P ± 8 34 ± Serum amyloid P-component SAMP_HUMAN P ± 4 31 ± Serum paraoxonase/arylesterase 1 PON1_HUMAN P ± 6 64 ± Sex hormone-binding globulin SHBG_HUMAN P ± 4 7 ± Tetranectin TETN_HUMAN P ± 2 7 ± Thyroxine-binding globulin THBG_HUMAN P ± 3 12 ± Transthyretin TTHY_HUMAN P ± ± Vitamin D-binding protein VTDB_HUMAN P ± ± Vitamin K-dependent protein C PROC_HUMAN P ± 3 4 ±

9 continued Table S2. page 5/5 UniProt Entry SwissProt- EPIC-CRC case Name UniProt No. Pool EPIC-Control Pool FC b VIP value c Vitamin K-dependent protein S PROS_HUMAN P ± 2 10 ± Vitronectin VTNC_HUMAN P ± 7 42 ± Zinc-alpha-2-glycoprotein ZA2G_HUMAN P ± 5 28 ± a Mean ± SD of three technical replicates b FC, Fold Change, Spectral counts of CRC cases/controls; bold, FC 1.5; bold-italic, FC<-1.5 c VIP, Variable Importance in the Projection (PLS-DA analysis); bold, VIP>1

10 Table S3. Page1/1 Relative amounts of proteins analysed by targeted proteomics (LC-SRM-MS) in the EPIC population not including Phase 2 samples (the number of subjects is given in parenthesis) Candidate Biomarker Relative amount a Mean ± SD P-value b Relative amount a Mean + SD P-value b Relative amount a Mean + SD P-value b Controls CRC Cases Female Controls Female CRC Cases Male Controls Male CRC Cases (38) (38) (22) (22) (16) (16) APOC ± ± ± ± ± ± CLU 7.07 ± ± ± ± ± ± CO4-B ± ± ± ± ± ± CO ± ± ± ± ± ± FETUA 2.6 ± ± ± ± ± ± MASP ± ± ± ± ± ± MBL ± ± ± ± ± ± PGRP ± ± ± ± ± ± a Analyte peak area/internal standard peak area b Mann-Whitney U, two tailed

11 Table S4. ROC analysis: AUC of various combinations of protein biomarkers in males a Biomarker combination AUC 95% CI P-value Sensitivity % 1-Specificity % CLU + APOC2 + CO4-B CLU + APOC2 + MASP a Only the combinations with P-value <0.05 are shown