Supplementary Table S5. List of all the peptides that were included in the peptide biomarker panels for detecting primary UBC Sequence information Peptide- SwissProt Amino acid Sequence‡ Protein name ID† Accession ID 1747 DCGDNSDEEN Low-density lipoprotein receptor-related protein 2 LRP2 1907 SAYQEAMDIS 14-3-3 protein sigma, SFN SFN 1944 PpGPpGpPGPpS Collagen alpha-1(I) chain CO1A1 2032 GGpGSDGKpGPpG Collagen alpha-1(III) chain CO3A1 2200 TPEEKSAVTAL Hemoglobin subunit beta HBA 2451 PTALGVRGASRS Bromodomain-containing protein 1 BRD1 2522 KPLKEPGLGQL Mitogen-activated protein kinase 14 MAPK14 2543 LSALEEYTKK Apolipoprotein A-I APOA1 2592 DDGEAGKpGRpG Collagen alpha-1(I) chain CO1A1 2597 TCGDSCDQCCPG Laminin subunit alpha-2 LAMA2 2794 DGPAGApGTPGpQG Collagen alpha-1(I) chain COL1A1 Basement membrane-specific heparan sulfate 2801 GTCSGCNCNGHAS HSPG2 proteoglycan core protein 2830 VDEVGGEALGRL Hemoglobin subunit beta HBB 2858 EAGGGSNSLQNSP FERM domain-containing protein 4A FRM4A 3183 KPWAAQDGPKPG Leucine-rich repeat-containing protein 25 LRC25 3202 EEYTKKLNTQ Apolipoprotein A-I APOA1 3223 PGYTGNGYGPNGC Cubilin CUBN 3430 KVVAGVANALAHK Hemoglobin subunit delta HBD 3651 MYVSGpPGpPGpP Collagen alpha-1(XVII) chain, COL17A1 COL17A1 3758 VHLTPEEKSAVT Hemoglobin subunit beta HBB 4152 4157 VAGVANALAHKYH Hemoglobin subunit beta HBB 4270 AVADTRDQADGSR Polymeric immunoglobulin receptor PIGR 4532 GSYNLPSLPDIDC Transcription intermediary factor 1-alpha, TRIM24 TRIM24 4535 GPPGpPGPpGPPGPPS Collagen alpha-1(I) chain CO1A1 4759 GpPGEGLPGPpGpPGS Collagen alpha-1(XVII) chain, COL17A1 COL17A1 4957 ALEEYTKKLNTQ Apolipoprotein A-I APOA1 5087 VVAGVANALAHKYH Hemoglobin subunit beta HBB Membrane-associated progesterone receptor 5216 DSDDDEPPPLPRL PGRMC1 component 1, PGRMC1 5423 VGpPGPPGpPGPPGPPS Collagen alpha-1(I) chain CO1A1 5438 PRGDqGqDGAAGPpGP Collagen alpha-1(XXIII) chain, COL23A1 COL23A1 5444 TKVPEPGSIKVPDQ Small proline-rich protein 3 SPRR3 5673 KGDpGpAGLpGKDGpP Collagen alpha-1(V) chain COL5A1 5705 DGQPGAKGEpGDAGAKG Collagen alpha-1(I) chain COL1A1 5781 ADSGEGDFLAEGGGVR Fibrinogen alpha chain FIBA 5998 EDGHPGKPGRpGERG Collagen alpha-2(I) chain COL1A2 6355 DpGPpGQSGRDGYPGp Collagen alpha-1(XXIII) chain CONA1 6373 PpGFGRpGDPGPPGPpG Collagen alpha-1(XV) chain COL15A1 6498 GPpGPPGPPGPPGVSGGGY Collagen alpha-2(I) chain COL1A2 6571 6708 GSSVGTGTNLHSESASF Serine/threonine-protein kinase D1 PRKD1 6924 GPpGPpGTSGHPGSpGSpG Collagen alpha-1(III) chain CO3A1 6985 TGDAGpVGPpGPpGPPGPP Collagen alpha-1(I) chain CO1A1 6998 RINHTVILDDPFDD Peptidyl-prolyl cis-trans isomerase-like 4 PPIL4 7390 PpGEAGKpGEQGVpGDLG Collagen alpha-1(I) chain CO1A1 7502 7648 TGLSMDGGGSPKGDVDPF Sodium/potassium-transporting ATPase subunit gamma ATNG 7711 EpGSpGENGApGQMGPRG Collagen alpha-1(I) chain CO1A1 7772 SDLHAHKLRVDPVNF Hemoglobin subunit alpha HBA1 7778 pGqpGIKGDRGFpGEMG Collagen alpha-1(X) chain COL10A1 8185 EEAPSLRPAPPPISGGGY Fibrinogen beta chain FGB 8222 WGKVNVDEVGGEALGRL Hemoglobin subunit beta, HBB HBB 8225 IGTYCGQPVCENGCQNGG Fibrillin-2, FBN2 FBN2 8322 GpAGSpGSNGApGQRGEpGP Collagen alpha-1(III) chain COL3A1 8371 GEpGSpGENGAPGQmGpRG Collagen alpha-1(I) chain COL1A1 8694 DEPPQSPWDRVKDLAT Apolipoprotein A-I APOA1 8739 NpGPPGpSGSpGKDGPpGPAG Collagen alpha-1(III) chain COL3A1 8755 EGSpGRDGSpGAKGDRGET Collagen alpha-1(I) chain CO1A1 8878 pPGPTGPGGDKGDTGPpGPQG Collagen alpha-1(III) chain, COL3A1 COL3A1 8946 HLPAEFTPAVHASLDKF Hemoglobin subunit alpha HBA1 9003 ADLADGVSGGEGKGGSDGGGSH CD99 antigen, CD99 CD99 9061 GApGApGGKGDAGAPGERGppG Collagen alpha-1(III) chain CO3A1 9121 TQPPEEETLSQAPESEE Rho guanine nucleotide exchange factor 25, ARHGEF25 ARHGEF25 9385 AARLEALKENGGARLAEY Apolipoprotein A-I APOA1 9588 DGVWNGMIGEVFYQRAD Glutamate receptor ionotropic, NMDA1 GRIN2D 10081 AAHLPAEFTPAVHASLDKF Hemoglobin subunit alpha HBA 10200 GppGESGREGApGAEGSPGRDG Collagen alpha-1(I) chain COL1A1 Disintegrin and metalloproteinase domain-containing 10706 KPGDGDSFYSDIPPGVSTNSA ADAM22 protein 22 10745 DEPPQSPWDRVKDLATVY Apolipoprotein A-I APOA1 GpTGpIGPpGpAGQPGDKGEGGA 10838 Collagen alpha-1(III) chain CO3A1 P 11343 EAEDLQVGQVELGGGPGAGSLQP Insulin INS 11348 11407 AAAAQGTAPPQDGEQPAESPEPP Diacylglycerol kinase kappa DGKK NGDDGEAGKPGRpGERGPpGPQ 11536 Collagen alpha-1(I) chain CO1A1 G NGDDGEAGKPGRPGERGppGpQ 11672 Collagen alpha-1(I) chain CO1A1 G Thioredoxin-dependent peroxide reductase, 11802 TFVCPTEIVAFSDKANEFHD PRDX3 mitochondrial QNGEpGGKGERGApGEKGEGGp 11905 Collagen alpha-1(III) chain, COL3A1 COL3A1 pG 11977 EHGPPPPPDERDHSHGPPLPQ Histidine-rich glycoprotein HRG1 12210 GDSMDRIEKDRLqGMAPAAGAD Collagen alpha-1(XVII) chain, COL17A1 COL17A1 TGGPpGENGKPGEpGpKGDAGA 12312 Collagen alpha-1(III) chain COL3A1 pGAP GPIGppGVRGSVGEAGpEGPPGE 12707 Collagen alpha-2(V) chain COL5A2 pGP GPpGKNGDDGEAGKpGRpGERG 13322 Collagen alpha-1(I) chain CO1A1 PPGP 1-phosphatidylinositol 4,5-bisphosphate 13763 ELDCWDGKGEDQEPIITHGKAMC PLCB4 phosphodiesterase beta-4, PLCB4 13845 LAPEPLSAPPGSPPPSAAPTSATSN 13932 Homeobox protein Hox-B3 HOXB3 SSN NRGERGSEGSPGHpGQPGPpGPP 14224 Collagen alpha-1(III) chain CO3A1 GApGP DGKTGPpGpAGQDGRPGPPGpP 14251 Collagen alpha-1(I) chain COL1A1 GARGQAG ERGEAGIpGVpGAKGEDGKDGSp 14253 Collagen alpha-1(III) chain CO3A1 GEpGA DGVSGGEGKGGSDGGGSHRKEG 14255 CD99 antigen, CD99 CD99 EEADAPG GGEGKGGSDGGGSHRKEGEEAD 14316 CD99 antigen CD99 APGVIPG 14586 EVEMKPDSSPSEVPEGVSETEGAL 14737 SH3 and multiple ankyrin repeat domains protein 2 SHANK2 QI GPPGESGREGApGAEGSPGRDGS 14943 Collagen alpha-1(I) chain COL1A1 PGAKGDR TGARGLVGEpGpAGSKGESGNKG 15400 Collagen alpha-2(I) chain COL1A2 EpGSAGPQ SPADKTNVKAAWGKVGAHAGEY 16053 Hemoglobin subunit alpha HBA GAEALER DGLQAAFTTAHELGHVFNMPHD A disintegrin and metalloproteinase with 16219 ADAMTS1 DAKQCA thrombospondin motifs 1, ADAMTS1 LTPEEKSAVTALWGKVNVDEVGG 16283 Hemoglobin subunit beta, HBB HBB EALGRL pGPPGSpGPAGPTGKQGDRGEA 16632 Collagen alpha-1(II) chain COL2A1 GAQGPMGpSGpAG GLPGPKGEKGApGDFGpRGDQG 16811 Collagen alpha-1(XXIII) chain COL23A1 QDGAAGpPGPpG VLSPADKTNVKAAWGKVGAHAG 16970 Hemoglobin subunit alpha HBA EYGAEALER 17307 PAGDRGPRGERGPpGppGRDGE 17317 Collagen alpha-2(I) chain COL1A2 DGPTGPPGPpGP VLSPADKTNVKAAWGKVGAHAG 17614 Hemoglobin subunit alpha HBA EYGAEALERm PpGPSGpRGQPGVMGFpGPKGN 17983 Collagen alpha-1(III) chain COL3A1 DGAPGKNGERGGPGG DGTESSEDSFSFTVTDGTHTDFYVF 18106 FRAS1-related extracellular matrix protein 2, FREM2 FREM2 PDTVFE DGQPGPKGDQGEKGERGTPGIG 18941 Collagen alpha-1(VII) chain COL7A1 GFpGPSGNDGSAGpPGpp RERpQNQQpHRAQRSPQQqPSRL 18981 Collagen alpha-2(XI) chain COL11A2 HRpQNQE 19288 SNGNpGPPGPSGSPGKDGPPGpA 19346 Collagen alpha-1(III) chain COL3A1 GNTGApGSpGVSGPKGDAGQPG GAGPGSGSnVSMNQQNPqAPQA 20775 qSLGGMHVNGAPPLMqASMQG Cleavage stimulation factor subunit 2 CSTF2 GVPAPGQMP DGETGAAGppGPAGPAGERGEq 20853 GAPGPSGFQGLPGPPGPPGEGGK Collagen alpha-1(II) chain, COL2A1 COL2A1 pGDQGVPGEAGAPG 21031 21321 21329 IQRTPKIQVYSRHPAENGKSNFLNc YVSGFHPSDIEVDLLKNGERIEKVE 21470 HSDLSFSKDWSFYLLYYTEFTPTEK Beta-2-microglobulin B2M DEYAcRVNHVTLSQPKIVKWDRD M IQRTPKIQVYSRHPAENGKSNFLNc YVSGFHPSDIEVDLLKNGERIEKVE 21471 HSDLSFSKDWSFYLLYYTEFTPTEK Beta-2-microglobulin B2M DEYAcRVNHVTLSQPKIVKWDRD m * Abbreviations: Amp, amplitude; AUC, Area under the ROC curve; CE-MS, capillary electrophoresis mass spectrometry; Da, Dalton; min, minutes; N/A,not available; N, number of patients; STD, standard deviation; UBC, Urothelial bladder † Peptide identification number. ‡ Lower case p, k and m indicate hydroxyproline, hydroxylysine and oxidized methionine. Supplementary Table S5. List of all the peptides that were included in the peptide biomarker panels for detecting primary UBC PRIMARY BIOMARKER PANEL CE-MS characteristics Distribution in Primary UBC cases Distribution in non-UBC controls (n=341) (n=110) CE migration Peptide-ID† Mass [Da] Frequency Mean Amp ± STD Frequency Mean Amp ± STD time [min] 1747 1096.33 35.81 33.53 89.33±184.65 32.73 110.17±308.29 1907 1113.47 27.24 42.77 160.96±261.95 50.91 206.5±379.02 1944 1116.47 36.90 12.14 18.08±82.78 29.09 77.79±227.39 2032 1126.51 25.59 38.73 96.93±174.92 35.45 76.27±140.51 2200 1144.59 26.51 21.68 376.8±1863.93 5.45 79.55±510.76 2451 1170.64 21.36 30.64 3170.92±17424.53 14.55 2267.26±17324.91 2522 1178.71 19.19 14.45 49.74±178.01 11.82 53.09±211.26 2543 1180.62 21.29 17.63 109.63±396.36 10.91 80.42±409.25 2592 1186.53 22.31 74.57 510.08±686.58 81.82 476.61±491.92 2597 1187.34 36.35 13.87 263.26±886.92 12.73 327.48±1196.92 2794 1209.52 39.52 26.88 56.76±201.05 42.73 84.01±131.73 2801 1210.37 36.45 57.23 559.75±953.72 44.55 574.97±1198.88 2830 1213.62 27.33 20.52 334.58±1878.8 10 270.82±2258.01 2858 1216.54 24.59 77.75 1189.96±1308.9 84.55 1242.82±1452.25 3183 1250.64 20.57 45.95 637.11±3324.82 40.91 224.65±1452.35 3202 1252.64 21.63 17.92 226.45±1245.28 13.64 152.23±587.87 3223 1255.48 35.73 26.59 315.32±1133.54 15.45 214.12±1215.58 3430 1276.71 19.96 24.57 51.48±180.33 27.27 51.34±124.02 3651 1299.58 22.37 65.61 287.8±314.73 57.27 241.79±295.12 3758 1309.70 21.89 37.57 4147.69±17313.78 19.09 1627.88±7028.46 4152 1349.41 36.43 70.23 339.46±400.76 73.64 393.01±405.18 4157 1349.70 20.28 22.54 713.65±4427.13 10.91 764.04±4988.64 4270 1360.62 22.65 21.1 22.87±58.62 34.55 44.03±83.75 4532 1392.63 27.65 8.67 6.91±34.24 21.82 14.94±34.22 4535 1392.67 39.08 16.18 40.12±172.68 23.64 264.03±2199.37 4759 1416.64 28.20 14.74 12.34±40.15 10.91 8.09±25.56 4957 1436.73 23.26 17.63 149.88±1016.4 7.27 138.86±844.5 5087 1448.79 20.38 25.72 1199.97±6759 15.45 1069.5±9877.39 5216 1464.66 31.31 45.09 3467.74±23409.26 41.82 1548.86±6065.55 5423 1491.73 39.89 68.5 614.67±867.63 73.64