Supplementary Table S5. List of All the Peptides That Were Included in the Peptide Biomarker Panels for Detecting Primary UBC

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 73.64 995.83±1178.17 5438 1493.63 21.97 36.13 145.17±277.47 40.91 183.89±351.06 5444 1493.80 22.91 35.55 6016.32±29779.35 20.91 4005.45±22464.78 5673 1522.73 22.99 29.77 223.59±826.66 30 99.29±225.56 5705 1526.69 23.89 51.73 91.47±132.28 63.64 118.27±132.6 5781 1535.69 30.14 39.6 4919.76±42431.33 30 4560.69±23676.21 5998 1560.75 19.56 13.29 16.84±61.51 10.91 14.63±64.58 6355 1600.69 29.84 42.49 199.86±326.98 49.09 204.28±291.8 6373 1602.74 29.19 55.49 163.51±198.41 57.27 142.96±181.14 6498 1615.66 40.87 20.52 2897.85±23321.18 17.27 2123.44±9756.73 6571 1622.72 26.99 68.21 227.73±271.73 66.36 190.29±231.61 6708 1636.74 22.52 77.75 11771.88±11540.45 87.27 11503.35±8976.53 6924 1659.76 31.06 8.38 6.67±27.51 12.73 9.31±32.41 6985 1667.79 40.64 45.09 409.97±679.83 37.27 266.34±492.18 6998 1668.81 40.58 44.8 606.03±940.28 57.27 952.47±1156.48 7390 1708.78 31.16 26.3 539.88±1114.85 35.45 785.74±1265.38 7502 1720.69 19.64 19.36 49.07±152.71 26.36 78.42±239.37 7648 1735.72 30.63 13.87 19.44±87.31 18.18 41.55±199.18 7711 1741.73 30.33 34.68 58.37±120.9 34.55 68.63±135.8 7772 1746.93 19.46 7.51 26.52±165.84 6.36 14.66±68.76 7778 1747.79 38.94 12.72 27.3±102.57 10.91 32.78±121.64 8185 1793.89 32.41 80.92 621.18±1243.56 65.45 437.41±655.38 8222 1797.93 23.94 23.12 7824.98±52161.59 9.09 1096.23±8000.1 8225 1798.72 36.72 28.03 80.75±205.79 40.91 104.52±210.47 8322 1809.87 32.43 34.1 136.76±621.25 32.73 115.61±349.72 8371 1814.77 30.55 15.03 17.8±60.28 16.36 19.11±55.2 8694 1852.89 25.02 35.55 726.49±2265.43 24.55 404.04±1403.67 8739 1859.78 31.03 20.52 95.14±274.85 16.36 62.96±182.54 8755 1860.83 21.44 67.34 847.85±1071.96 70 1042.9±3087.15 8878 1873.83 31.95 19.94 65.09±262.56 19.09 46.99±162.09 8946 1878.95 21.43 30.35 4328.53±30533.2 12.73 258.81±2013.26 9003 1885.80 30.70 16.47 11.94±33.5 20.91 13.84±37.59

9061 1892.88 24.45 39.88 181.28±418.07 38.18 127.22±290.25

9121 1899.81 22.44 21.68 60±168.23 35.45 96.33±180.75 9385 1931.01 21.36 14.16 181.75±824.81 10.91 132.52±648.72 9588 1955.88 28.03 54.05 248.59±345.53 51.82 198.73±306.76 10081 2021.03 21.75 32.95 3666.8±19863.53 20.91 778.94±3840.19 10200 2040.88 39.28 27.75 99.57±559.73 19.09 48.88±179.93

10706 2109.94 21.05 25.14 27.37±74.77 32.73 46.56±88.08 10745 2115.00 26.31 22.54 308.55±1118.81 16.36 156.58±572.41 10838 2130.97 32.98 39.31 59.91±141.26 34.55 42.07±103.25

11343 2207.09 43.40 21.1 89±305.79 40.91 218.19±698.57 11348 2207.89 31.76 14.45 14.6±49.21 10.91 11.04±51.88 11407 2215.09 41.43 7.8 9.65±43.81 4.55 8.92±41.85

11536 2233.01 22.45 60.12 222.82±334.96 59.09 169.28±287.66 11672 2249.01 22.50 40.17 101.19±203.53 37.27 86.04±210.11

11802 2269.04 39.25 56.07 196.63±387.16 50.91 200.17±417.83

11905 2282.01 40.35 26.3 338.93±1280.08 17.27 434.4±2328.52 11977 2292.08 20.81 24.28 58.86±164.57 32.73 69.65±167.07 12210 2320.02 23.28 15.03 11.42±34.97 30 18.34±35.36

12312 2332.04 26.70 13.01 9.6±32.79 23.64 19.07±55.58

12707 2384.06 33.80 17.63 56.59±174.41 11.82 32.32±122.12

13322 2500.18 20.94 17.05 29.43±117.58 20 38.24±110.89

13763 2574.13 20.50 18.79 24.55±75.61 27.27 29.92±66.93 13845 2586.74 36.41 27.17 65.05±170.65 30 83.72±221.44 13932 2601.23 35.83 2.6 2.59±21.66 3.64 6.26±38.44

14224 2647.21 23.52 47.98 108.85±203.27 52.73 99.18±147.76

14251 2653.24 23.91 8.67 23.48±100.33 16.36 33.85±101.73

14253 2654.20 23.89 80.64 434.03±424.79 89.09 557.86±506.77

14255 2655.15 22.23 25.72 31.57±77.37 38.18 43.04±77.74

14316 2663.22 21.72 30.64 37.57±71.89 40 54.46±88.77 14586 2714.20 19.42 4.05 15.68±126.07 7.27 59.94±564.21 14737 2743.11 35.11 12.14 20.89±78.59 22.73 36.07±101.9

14943 2777.32 21.50 44.8 156.75±299.24 41.82 148.86±286.86

15400 2853.33 23.85 35.55 378.07±936.28 38.18 263.4±654.46

16053 2982.49 20.49 17.05 4085.28±27791.01 4.55 95.56±644.03

16219 3023.39 24.65 23.7 175.01±483.21 20 169.64±866.85

16283 3037.60 24.23 18.5 4008.7±25741.02 6.36 238.17±2124.61

16632 3114.42 30.34 44.22 130.97±216.8 38.18 132.23±230.3

16811 3158.42 29.80 74.57 1151.8±1483.44 66.36 784.14±909.53

16970 3194.65 20.85 26.88 14479.19±103520.25 13.64 1344.45±7415.29 17307 3271.41 29.37 13.01 15.15±51.68 20.91 18.57±51.44 17317 3273.72 22.30 25.14 28502.55±239181.24 10 138.24±880.17

17614 3341.69 21.12 36.99 14471.56±82932.18 24.55 6349.33±39198.4 17983 3441.61 31.36 76.59 8770.19±7704.92 79.09 9829.64±8733.25

18106 3478.42 41.58 45.66 386.99±938.6 62.73 646.63±1100.06

18941 3745.68 26.64 38.73 142.11±243.64 46.36 128.4±181.54

18981 3759.86 19.39 36.71 1361.7±6009.19 25.45 827.05±3593.28 19288 3873.85 31.49 15.32 59.39±282.4 12.73 27.13±122.12

19346 3906.80 24.28 27.75 219.25±685.92 28.18 225.64±1185.97

20775 5026.26 26.46 5.49 4.6±28.69 9.09 15±60.08

20853 5211.35 27.53 17.92 62.72±229.67 15.45 78.33±288.69

21031 5800.43 19.63 26.88 313.38±794.06 30.91 239.98±649.52 21321 8559.22 19.49 26.3 697.44±4056.1 21.82 1678.64±12397.57 21329 8837.17 21.08 69.08 2700.01±5815.43 63.64 1471.99±3416.68

21470 11721.51 19.56 23.99 2664.51±19224.93 14.55 365.55±2057.94

21471 11737.74 19.59 25.72 2389.95±12241.19 21.82 23222.43±187499.82

* Abbreviations: Amp, amplitude; AUC, Area under the ROC curve; CE-MS, capillary electrophoresis mass † 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 recurrent UBC

Sequence information

Peptide- Amino acid Sequence‡ Protein name SwissProt Accession ID ID† Low-density lipoprotein receptor-related protein 1747 DCGDNSDEEN LRP2 2 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 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 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 3651 MYVSGpPGpPGpP Collagen alpha-1(XVII) chain, COL17A1 COL17A1 4152 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 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 Sodium/potassium-transporting ATPase subunit 7648 TGLSMDGGGSPKGDVDPF ATNG gamma 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 Rho guanine nucleotide exchange factor 25, 9121 TQPPEEETLSQAPESEE ARHGEF25 ARHGEF25 9385 AARLEALKENGGARLAEY Apolipoprotein A-I APOA1 9588 DGVWNGMIGEVFYQRAD Glutamate receptor ionotropic, NMDA1 GRIN2D 10200 GppGESGREGApGAEGSPGRDG Collagen alpha-1(I) chain COL1A1 Disintegrin and metalloproteinase domain- 10706 KPGDGDSFYSDIPPGVSTNSA ADAM22 containing protein 22 10745 DEPPQSPWDRVKDLATVY Apolipoprotein A-I APOA1 10838 GpTGpIGPpGpAGQPGDKGEGGAP Collagen alpha-1(III) chain CO3A1 11343 EAEDLQVGQVELGGGPGAGSLQP Insulin INS 11348 11407 AAAAQGTAPPQDGEQPAESPEPP Diacylglycerol kinase kappa DGKK 11536 NGDDGEAGKPGRpGERGPpGPQG Collagen alpha-1(I) chain CO1A1 11672 NGDDGEAGKPGRPGERGppGpQG Collagen alpha-1(I) chain CO1A1 Thioredoxin-dependent peroxide reductase, 11802 TFVCPTEIVAFSDKANEFHD PRDX3 mitochondrial 11905 QNGEpGGKGERGApGEKGEGGppG Collagen alpha-1(III) chain, COL3A1 COL3A1 11977 EHGPPPPPDERDHSHGPPLPQ Histidine-rich glycoprotein HRG1 12210 GDSMDRIEKDRLqGMAPAAGAD Collagen alpha-1(XVII) chain, COL17A1 COL17A1 12312 TGGPpGENGKPGEpGpKGDAGApGAP Collagen alpha-1(III) chain COL3A1 12707 GPIGppGVRGSVGEAGpEGPPGEpGP Collagen alpha-2(V) chain COL5A2 13322 GPpGKNGDDGEAGKpGRpGERGPPGP Collagen alpha-1(I) chain CO1A1 1-phosphatidylinositol 4,5-bisphosphate 13763 ELDCWDGKGEDQEPIITHGKAMC PLCB4 phosphodiesterase beta-4, PLCB4 13845 13932 LAPEPLSAPPGSPPPSAAPTSATSNSSN Homeobox protein Hox-B3 HOXB3 NRGERGSEGSPGHpGQPGPpGPPGApG 14224 Collagen alpha-1(III) chain CO3A1 P DGKTGPpGpAGQDGRPGPPGpPGARGQ 14251 Collagen alpha-1(I) chain COL1A1 AG 14253 ERGEAGIpGVpGAKGEDGKDGSpGEpGA Collagen alpha-1(III) chain CO3A1 DGVSGGEGKGGSDGGGSHRKEGEEADA 14255 CD99 antigen, CD99 CD99 PG GGEGKGGSDGGGSHRKEGEEADAPGVI 14316 CD99 antigen CD99 PG 14586 SH3 and multiple ankyrin repeat domains protein 14737 EVEMKPDSSPSEVPEGVSETEGALQI SHANK2 2 GPPGESGREGApGAEGSPGRDGSPGAK 14943 Collagen alpha-1(I) chain COL1A1 GDR TGARGLVGEpGpAGSKGESGNKGEpGSA 15400 Collagen alpha-2(I) chain COL1A2 GPQ DGLQAAFTTAHELGHVFNMPHDDAKQC A disintegrin and metalloproteinase with 16219 ADAMTS1 A thrombospondin motifs 1, ADAMTS1 LTPEEKSAVTALWGKVNVDEVGGEALGR 16283 Hemoglobin subunit beta, HBB HBB L pGPPGSpGPAGPTGKQGDRGEAGAQGP 16632 Collagen alpha-1(II) chain COL2A1 MGpSGpAG GLPGPKGEKGApGDFGpRGDQGQDGAA 16811 Collagen alpha-1(XXIII) chain COL23A1 GpPGPpG 17307 PAGDRGPRGERGPpGppGRDGEDGPTG 17317 Collagen alpha-2(I) chain COL1A2 PPGPpGP PpGPSGpRGQPGVMGFpGPKGNDGAP 17983 Collagen alpha-1(III) chain COL3A1 GKNGERGGPGG DGTESSEDSFSFTVTDGTHTDFYVFPDTV FRAS1-related extracellular matrix protein 2, 18106 FREM2 FE FREM2 DGQPGPKGDQGEKGERGTPGIGGFpGP 18941 Collagen alpha-1(VII) chain COL7A1 SGNDGSAGpPGpp RERpQNQQpHRAQRSPQQqPSRLHRpQ 18981 Collagen alpha-2(XI) chain COL11A2 NQE 19288 SNGNpGPPGPSGSPGKDGPPGpAGNTG 19346 Collagen alpha-1(III) chain COL3A1 ApGSpGVSGPKGDAGQPG GAGPGSGSnVSMNQQNPqAPQAqSLG 20775 GMHVNGAPPLMqASMQGGVPAPGQM Cleavage stimulation factor subunit 2 CSTF2 P DGETGAAGppGPAGPAGERGEqGAPGP 20853 SGFQGLPGPPGPPGEGGKpGDQGVPGE Collagen alpha-1(II) chain, COL2A1 COL2A1 AGAPG 21031 21321 21329 IQRTPKIQVYSRHPAENGKSNFLNcYVSGF HPSDIEVDLLKNGERIEKVEHSDLSFSKD 21470 Beta-2-microglobulin B2M WSFYLLYYTEFTPTEKDEYAcRVNHVTLSQ PKIVKWDRDM IQRTPKIQVYSRHPAENGKSNFLNcYVSGF HPSDIEVDLLKNGERIEKVEHSDLSFSKD 21471 Beta-2-microglobulin B2M WSFYLLYYTEFTPTEKDEYAcRVNHVTLSQ PKIVKWDRDm * 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 carcinoma.

† Peptide identification number. ‡ Lower case p, k and m indicate hydroxyproline, hydroxylysine and oxidized methionine. | Wilcoxon P value . || Benjamini/ Hochberg (FDR adjustment) Supplementary Table S5. List of all the peptides that were included in the peptide biomarker panels for detecting primary and recurrent UBC

RECURRENCE BIOMARKER PANEL CE-MS characteristics Distribution in Recurrent UBC cases Distribution in negative for (n=109) recurrence controls (n=316)

Peptide- CE migration time Mass [Da] Frequency Mean Amp ± STD Frequency Mean Amp ± STD ID† [min]

1747 1096.33 35.81 33.90 78.26±185.76 27.53 73.26±180.08 1907 1113.47 27.24 15.25 48.78±152.8 30.38 111.28±218.67 1944 1116.47 36.90 10.17 21.73±86.81 12.03 33.62±128.82 2032 1126.51 25.59 16.10 18.86±50.59 23.73 44.13±123.5 2451 1170.64 21.36 21.19 427.76±1807.33 5.38 37.66±347.66 2522 1178.71 19.19 22.88 81.87±222.96 9.18 39.07±329.15 2543 1180.62 21.29 21.19 113.94±716.98 5.06 15.84±135.79 2592 1186.53 22.31 75.42 385.68±468.44 68.04 332.67±394.45 2597 1187.34 36.35 29.66 350.17±1044.17 12.34 174.73±791.18 2794 1209.52 39.52 22.03 39.1±97 25.95 57.93±134.92 2801 1210.37 36.45 2801 1070.17±1475.77 56.65 720.86±1210.82 2858 1216.54 24.59 78.81 981.09±1089.66 85.13 945.83±1051.3 3183 1250.64 20.57 56.78 618.55±2523.77 34.81 408.69±4320.64 3202 1252.64 21.63 20.34 329.75±2303.72 8.23 36.67±186.51 3223 1255.48 35.73 21.19 201.99±743.91 17.41 381.82±3324.78 3651 1299.58 22.37 66.95 263.12±273.91 50.95 173.27±232.72 4152 1349.41 36.43 43.22 258.28±418.29 46.52 284.45±399.02 4270 1360.62 22.65 44.07 107.16±256.26 39.24 70.38±128.18 4532 1392.63 27.65 3.39 1.34±7.59 6.96 4.05±18.58 4535 1392.67 39.08 13.56 31.34±92.73 16.77 130.11±931.15 4759 1416.64 28.20 22.88 19.84±45.92 10.44 10.75±41.51 4957 1436.73 23.26 22.03 187.87±655.14 6.33 21.62±172.64 5216 1464.66 31.31 53.39 1832.21±7623.44 27.85 874.95±13157.77 5423 1491.73 39.89 74.58 721.91±1029.13 71.84 763.47±1028.76 5438 1493.63 21.97 43.22 145.61±257.97 44.62 195.08±336.77 5444 1493.80 22.91 24.58 4259.48±16541.02 15.51 940.5±5991.78 5673 1522.73 22.99 30.51 326.31±1107.04 35.44 207.12±483.61 5705 1526.69 23.89 59.32 108.86±157.8 56.33 103.92±169.8 5781 1535.69 30.14 39.83 3641.18±13669.75 17.41 1274.13±16160.76 5998 1560.75 19.56 6.78 6.66±28.21 10.13 11.84±44.97 6355 1600.69 29.84 59.32 240.12±306.7 38.61 146.19±257.64 6373 1602.74 29.19 69.49 209.28±216.9 56.33 144.71±174.48 6498 1615.66 40.87 29.66 2121.34±8179.13 6.33 835.7±13027.81 6571 1622.72 26.99 76.27 277.1±280.31 62.66 197.99±251.53 6708 1636.74 22.52 79.66 11644.4±11270.12 93.04 12927.6±8626.19 6924 1659.76 31.06 20.34 15.75±44.41 8.54 5.81±21.84 6985 1667.79 40.64 53.39 393.93±595.75 37.97 306.15±645.58 6998 1668.81 40.58 29.66 499.21±985.37 38.61 815.66±1258.2 7390 1708.78 31.16 50.00 1020.04±1364.81 45.25 897.24±1201.83 7502 1720.69 19.64 11.02 19.95±83.36 7.91 12.07±48.78 7648 1735.72 30.63 22.88 49.81±155.7 14.56 24.55±78.48 7711 1741.73 30.33 37.29 62.95±116.08 21.84 44.43±184.64 7772 1746.93 19.46 22.88 137.4±507.73 9.49 31.35±141.79 7778 1747.79 38.94 22.03 69.82±309.26 9.81 21.87±101.87 8185 1793.89 32.41 83.05 760.29±1209.93 69.94 481.04±804.77 8222 1797.93 23.94 21.19 6895.78±27274.9 7.59 1487.84±14934.39 8225 1798.72 36.72 37.29 103.01±203.05 23.42 59.01±169.73 8322 1809.87 32.43 46.61 133.87±289.93 27.22 81.67±266.41 8371 1814.77 30.55 22.03 32.45±80.51 9.81 17.59±96.39 8694 1852.89 25.02 44.07 859.58±2535.16 22.78 308.96±1680.52 8739 1859.78 31.03 26.27 135.7±322.11 15.19 63.55±206.18 8755 1860.83 21.44 77.12 1005.53±1127.57 64.87 671.36±897.49 8878 1873.83 31.95 42.37 138.93±255.81 24.05 111.45±296.34 8946 1878.95 21.43 22.03 3505.35±19689.5 12.34 752.2±8568.02 9003 1885.80 30.70 34.75 40±74.55 19.94 18.89±81.52 9061 1892.88 24.45 43.22 163.91±477.39 26.58 77.34±231.2 9121 1899.81 22.44 44.07 158.26±285.93 35.76 123.59±249.72 9385 1931.01 21.36 21.19 782.72±4275.57 7.91 138.56±811.39 9588 1955.88 28.03 55.08 238.99±360.92 51.58 224.92±314.32 10200 2040.88 39.28 26.27 138.26±658.76 12.66 22.6±88.13 10706 2109.94 21.05 30.51 42.36±94.31 26.90 35.27±77.9 10745 2115.00 26.31 22.88 300.7±1086.82 9.18 106.71±590.45 10838 2130.97 32.98 46.61 73.87±158.44 31.01 43.47±99.58 11343 2207.09 43.40 44.92 387.96±804.19 43.35 409.72±1252.65 11348 2207.89 31.76 7.63 10.82±46.79 8.23 14.87±92.3 11407 2215.09 41.43 25.42 41.46±105.29 12.03 22.26±91.56 11536 2233.01 22.45 65.25 217.37±289.37 55.70 167.43±240.36 11672 2249.01 22.50 34.75 103.15±235.4 34.18 102.18±341.16 11802 2269.04 39.25 64.41 225.93±382.13 48.73 156.17±310.11 11905 2282.01 40.35 27.97 701.25±3097.88 11.71 81.61±391.7 11977 2292.08 20.81 30.51 60.51±135.67 25.63 50.42±128.55 12210 2320.02 23.28 23.73 18.88±42.79 18.04 15.58±43.13 12312 2332.04 26.70 13.56 14.74±50.97 11.39 14.68±79.9 12707 2384.06 33.80 24.58 76.16±217.77 15.82 47.69±180.41 13322 2500.18 20.94 20.34 34.26±106.73 17.72 27.9±75.52 13763 2574.13 20.50 14.41 18.37±57.24 22.47 32.45±86.03 13845 2586.74 36.41 41.53 107.71±193.33 25.95 58.09±150.8 13932 2601.23 35.83 27.97 128.61±921.66 10.76 12.81±65.71 14224 2647.21 23.52 52.54 106.19±177.92 49.68 107.26±184.58 14251 2653.24 23.91 18.64 37.62±100.87 12.03 36.49±132.78 14253 2654.20 23.89 83.90 619.83±548.32 86.08 665.86±576.25 14255 2655.15 22.23 29.66 55.25±130.74 38.29 64.4±129 14316 2663.22 21.72 35.59 63.44±152.92 39.24 54.56±94.5 14586 2714.20 19.42 20.34 307.46±1013.04 8.86 122.32±842.33 14737 2743.11 35.11 17.80 25.03±85.55 17.09 32.09±98.35 14943 2777.32 21.50 55.93 259.29±474.31 41.14 147.65±299.81 15400 2853.33 23.85 44.07 452.71±1469.7 26.90 132.23±394.51 16219 3023.39 24.65 26.27 143.37±568.8 12.34 66.62±541.22 16283 3037.60 24.23 15.25 1149.41±4556.14 7.59 255.33±3367.58 16632 3114.42 30.34 61.02 297.41±362.31 49.37 188.4±280.8 16811 3158.42 29.80 79.66 1369.99±1487.69 67.72 1050.91±1273.3 17307 3271.41 29.37 13.56 13.78±47.9 17.09 23.98±88.43 17317 3273.72 22.30 16.10 27917.12±271355.79 9.81 750.34±7796.28 17983 3441.61 31.36 70.34 10267.63±9012.62 65.19 9628.21±9265.7 18106 3478.42 41.58 52.54 509.9±1097.97 52.85 757.81±1582.99 18941 3745.68 26.64 45.76 119.73±188.16 51.58 138.82±183.67 18981 3759.86 19.39 35.59 630.15±2191.11 19.30 394.16±1715.76 19288 3873.85 31.49 29.66 91.53±226.44 14.87 59.99±285.36 19346 3906.80 24.28 44.07 188.94±519.24 27.22 151.88±650.59

20775 5026.26 26.46 21.19 40.86±112.77 7.91 26.51±154.43

20853 5211.35 27.53 15.25 46.52±173.87 27.85 106.76±266.39 21031 5800.43 19.63 43.22 657.35±1592.23 27.53 320.02±1082.98 21321 8559.22 19.49 28.81 1196.56±4224.9 15.19 291.88±2103.34 21329 8837.17 21.08 66.95 2142.8±3251.17 57.28 1520.45±3724.58

21470 11721.51 19.56 22.88 643.97±2985.8 10.76 2304.55±27155.44 21471 11737.74 19.59 31.36 1366.09±5772.47 15.19 14890.45±219406.57 * 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 carcinoma.

† Peptide identification number. ‡ Lower case p, k and m indicate hydroxyproline, hydroxylysine and oxidized methionine. | Wilcoxon P value . || Benjamini/ Hochberg (FDR adjustment)