Supporting Information for Proteomics DOI 10.1002/Pmic.200500072

Supporting Information for Proteomics DOI 10.1002/pmic.200500072

Peter Nilsson, Linda Paavilainen, Karin Larsson, Jenny dling, Mrten Sundberg, Ann-Catrin Andersson, Caroline Kampf, Anja Persson, Cristina Al-Khalili Szigyarto, Jenny Ottosson, Erik Bjrling, Sophia Hober, Henrik Wernrus, Kenneth Wester, Fredrik Pontn and Mathias Uhlen

Towards a human proteome atlas: High-throughput generation of mono-specific antibodies for tissue profiling

ª 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Supplementary Table 1 Towards a human proteome atlas

Antibody ID Ensembl Gene ID Gene name Gene description 1 HPRK140001 ENSG00000151456 C14orf145 (HUGO ID) ND 2 HPRK140003 ENSG00000100439 ABHD4 (HUGO ID) ABHYDROLASE DOMAIN CONTAINING 4. 3 HPRK140004 ENSG00000100811 YY1 (HUGO ID) TRANSCRIPTIONAL REPRESSOR PROTEIN YY1 (YIN AND YANG 1) (YY-1) (DELTA TRANSCRIP 4 HPRK140006 ENSG00000157379 DHRS1 (HUGO ID) DEHYDROGENASE/REDUCTASE (SDR FAMILY) MEMBER 1; DEHYDROGENASE/REDUCTASE S 5 HPRK140007 ENSG00000165516 KLHDC2 (HUGO ID) KELCH DOMAIN CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANT 6 HPRK140008 ENSG00000182338 ISGF3G (HUGO ID) TRANSCRIPTIONAL REGULATOR ISGF3 GAMMA SUBUNIT (IFN-ALPHA RESPONSIVE TRANSC 7 HPRK140009 ENSG00000100557 C14orf105 (HUGO ID) ND 8 HPRK140010 ENSG00000100836 PABPN1 (HUGO ID) POLY(A) BINDING PROTEIN, NUCLEAR 1; OCULOPHARYNGEAL MUSCULAR DYSTROPHY; PO 9 HPRK140011 ENSG00000131980 AND1_HUMAN (SWISSPROT ID) ACIDIC NUCLEOPLASMIC DNA-BINDING PROTEIN 1 (AND-1). 10 HPRK140012 ENSG00000165588 OTX2 (HUGO ID) HOMEOBOX PROTEIN OTX2. 11 HPRK140013 ENSG00000071246 NM_014909 (RefSeq ID) ND 12 HPRK140014 ENSG00000100450 GZMH (HUGO ID) GRANZYME H PRECURSOR (EC 3.4.21.-) (CYTOTOXIC T-LYMPHOCYTE PROTEINASE) (CATHE 13 HPRK140015 ENSG00000100600 LGMN (HUGO ID) LEGUMAIN PRECURSOR (EC 3.4.22.34) (ASPARAGINYL ENDOPEPTIDASE) (PROTEASE, CYST 14 HPRK140016 ENSG00000100697 DICER1 (HUGO ID) ENDORIBONUCLEASE DICER (EC 3.1.26.-) (HELICASE WITH RNASE MOTIF) (HELICASE-MOI). 15 HPRK140017 ENSG00000100813 ACINUS (HUGO ID) APOPTOTIC CHROMATIN CONDENSATION INDUCER IN THE NUCLEUS (ACINUS). 16 HPRK140018 ENSG00000100868 Y297_HUMAN (SWISSPROT ID) ND 17 HPRK140019 ENSG00000100749 VRK1 (HUGO ID) VACCINIA RELATED KINASE 1; VACCINIA-RELATED KINASE-1. 18 HPRK140020 ENSG00000183032 SLC25A21 (HUGO ID) MITOCHONDRIAL 2-OXODICARBOXYLATE CARRIER. 19 HPRK140021 ENSG00000081181 ARG2 (HUGO ID) ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY 20 HPRK140022 ENSG00000100439 ABHD4 (HUGO ID) ABHYDROLASE DOMAIN CONTAINING 4. 21 HPRK140023 ENSG00000100697 DICER1 (HUGO ID) ENDORIBONUCLEASE DICER (EC 3.1.26.-) (HELICASE WITH RNASE MOTIF) (HELICASE-MOI). 22 HPRK140024 ENSG00000140043 ZADH1 (HUGO ID) ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 1. 23 HPRK140025 ENSG00000140006 NM_080666 (RefSeq ID) ND 24 HPRK140027 ENSG00000100664 EIF5 (HUGO ID) EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). 25 HPRK140028 ENSG00000178974 FBXO34 (HUGO ID) F-BOX ONLY PROTEIN 34. 26 HPRK140029 ENSG00000119699 TGFB3 (HUGO ID) TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3). 27 HPRK140030 ENSG00000133965 NM_033426 (RefSeq ID) ND 28 HPRK140031 ENSG00000090061 CCNK (HUGO ID) CYCLIN K. 29 HPRK140032 ENSG00000169413 RNASE6 (HUGO ID) RIBONUCLEASE K6 PRECURSOR (EC 3.1.27.-) (RNASE K6). 30 HPRK140033 ENSG00000131966 ACTR10 (HUGO ID) ACTIN-RELATED PROTEIN 10 (HARP11). 31 HPRK140034 ENSG00000176784 Q8N9A6 (SPTREMBL ID) ND 32 HPRK140035 ENSG00000020426 MNAT1 (HUGO ID) CDK-ACTIVATING KINASE ASSEMBLY FACTOR MAT1 (RING FINGER PROTEIN MAT1) (MENAG 33 HPRK140036 ENSG00000100906 NFKBIA (HUGO ID) NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING Transcript removed from current Ensembl version 34 HPRK140037 ENSG00000179627 ND (20.34c.1); one other transcript 35 HPRK140038 ENSG00000100714 MTHFD1 (HUGO ID) C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC (C1-THF SYNTHASE) [INCLUDES: METH 36 HPRK140039 ENSG00000136367 ZFHX2 (HUGO ID) ZINC FINGER HOMEOBOX PROTEIN 2. 37 HPRK140040 ENSG00000130235 NM_032714 (RefSeq ID) ND 38 HPRK140041 ENSG00000140006 NM_080666 (RefSeq ID) ND 39 HPRK140042 ENSG00000151413 C14orf127 (HUGO ID) ND 40 HPRK140043 ENSG00000166126 AMN (HUGO ID) AMNIONLESS PROTEIN PRECURSOR 41 HPRK140044 ENSG00000165591 NM_174912 (RefSeq ID) ND 42 HPRK140045 ENSG00000100578 Y586_HUMAN (SWISSPROT ID) ND 43 HPRK140046 ND ND ND 44 HPRK140047 ND ND ND 45 HPRK140048 ND ND ND 46 HPRK140049 ND ND ND 47 HPRK140050 ND ND ND 48 HPRK140056 ND ND ND 49 HPRK140057 ND ND ND 50 HPRK140058 ND ND ND 51 HPRK140059 ND ND ND 52 HPRK140060 ND ND ND 53 HPRK140064 ND ND ND 54 HPRK140065 ND ND ND 55 HPRK140066 ND ND ND 56 HPRK140069 ENSG00000151320 AKAP6 (HUGO ID) A-KINASE ANCHOR PROTEIN 6 (PROTEIN KINASE A ANCHORING PROTEIN 6) (PRKA6) (A-KINA 57 HPRK140071 ENSG00000100888 HELSNF1 (HUGO ID) CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN HELSNF1 (HELICASE WITH SNF2 DOMA 58 HPRK140072 ENSG00000139913 C14orf21 (HUGO ID) ND 59 HPRK140073 ENSG00000174373 Q9Y408 (SPTREMBL ID) SIMILAR TO TUBERIN-LIKE PROTEIN 1 (FRAGMENT). 60 HPRK140074 ENSG00000119599 WDR21 (HUGO ID) WD-REPEAT PROTEIN 21 61 HPRK140075 ENSG00000012963 C14orf130 (HUGO ID) ND 62 HPRK140076 ENSG00000140043 ZADH1 (HUGO ID) ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 1. 63 HPRK140077 ENSG00000023608 SNAPC1 (HUGO ID) SNRNA ACTIVATING PROTEIN COMPLEX 43 KDA SUBUNIT (SNAPC 43 KDA SUBUNIT) (PROXIM 64 HPRK140078 ENSG00000133984 SYNJ2BP (HUGO ID) SYNAPTOJANIN 2 BINDING PROTEIN (MITOCHONDRIAL OUTER MEMBRANE PROTEIN 25). 65 HPRK140079 ENSG00000100664 EIF5 (HUGO ID) EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). 66 HPRK140081 ENSG00000140092 FBLN5 (HUGO ID) FIBULIN-5 PRECURSOR (FIBL-5) (DEVELOPMENTAL ARTERIES AND NEURAL CREST EGF-LIKE 67 HPRK140082 ENSG00000165417 GTF2A1 (HUGO ID) TRANSCRIPTION INITIATION FACTOR IIA ALPHA AND BETA CHAINS (TFIIA P35 AND P19 SUBU 68 HPRK140083 ENSG00000165934 CPSF2 (HUGO ID) CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA 69 HPRK140084 ENSG00000099814 Q9Y4F5 (SPTREMBL ID) ND 70 HPRK140085 ENSG00000100764 PSMC1 (HUGO ID) 26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). Transcript removed from current Ensembl version 71 HPRK140086 ENSG00000185567 ND (20.34c.1); one other transcript (no translation) 72 HPRK140088 ENSG00000183790 Q96DQ3 (SPTREMBL ID) ND 73 HPRK140089 ENSG00000184577 Gene removed from current database (20.34c.1) ND 74 HPRK140090 ENSG00000157227 MMP14 (HUGO ID) MATRIX METALLOPROTEINASE-14 PRECURSOR (EC 3.4.24.-) (MMP-14) (MEMBRANE-TYPE MA 75 HPRK140091 ENSG00000129566 TEP1 (HUGO ID) TELOMERASE-ASSOCIATED PROTEIN 1; TELOMERASE PROTEIN COMPONENT 1. 76 HPRK140092 ENSG00000165894 Q96DE2 (SPTREMBL ID) ND 77 HPRK140093 ENSG00000136305 CIDEB (HUGO ID) CELL DEATH ACTIVATOR CIDE-B (CELL DEATH-INDUCING DFFA-LIKE EFFECTOR B). 78 HPRK140094 ENSG00000100906 NFKBIA (HUGO ID) NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING 79 HPRK140095 ENSG00000100591 AHSA1 (HUGO ID) ACTIVATOR OF 90 KDA HEAT SHOCK PROTEIN ATPASE HOMOLOG 1 (AHA1) (P38) (HSPC322) 80 HPRK140096 ENSG00000100938 GMPR2 (HUGO ID) GMP REDUCTASE 2 (EC 1.7.1.7) (GUANOSINE 5'-MONOPHOSPHATE OXIDOREDUCTASE 2) (G 81 HPRK140097 ENSG00000100567 PSMA3 (HUGO ID) PROTEASOME SUBUNIT ALPHA TYPE 3 (EC 3.4.25.1) (PROTEASOME COMPONENT C8) (MACR 82 HPRK140098 ENSG00000100784 RPS6KA5 (HUGO ID) RIBOSOMAL PROTEIN S6 KINASE, 90KDA, POLYPEPTIDE 5 ISOFORM A; MITOGEN- AND STRE 83 HPRK140099 ENSG00000100644 HIF1A (HUGO ID) HYPOXIA-INDUCIBLE FACTOR 1 ALPHA (HIF-1 ALPHA) (HIF1 ALPHA) (ARNT INTERACTING PRO 84 HPRK140111 ND ND ND 85 HPRK140112 ND ND ND 86 HPRK140113 ND ND ND 87 HPRK140117 ND ND ND 88 HPRK140119 ND ND ND 89 HPRK140120 ND ND ND 90 HPRK140135 ND ND ND 91 HPRK140140 ND ND ND 92 HPRK220001 ENSG00000133422 K852_HUMAN (SWISSPROT ID) ND 93 HPRK220002 ENSG00000177663 IL17R (HUGO ID) INTERLEUKIN-17 RECEPTOR PRECURSOR (IL-17 RECEPTOR). 94 HPRK220003 ENSG00000130487 NM_138433 (RefSeq ID) ND 95 HPRK220004 ENSG00000182424 NM_152669 (RefSeq ID) ND 96 HPRK220005 ENSG00000100425 BRD1 (HUGO ID) BROMODOMAIN-CONTAINING PROTEIN 1 (BR140-LIKE PROTEIN). 97 HPRK220006 ENSG00000100357 ADSL (HUGO ID) ADENYLOSUCCINATE LYASE (EC 4.3.2.2) (ADENYLOSUCCINASE) (ASL) (ASASE). 98 HPRK220007 ENSG00000100239 K685_HUMAN (SWISSPROT ID) ND 99 HPRK220008 ENSG00000100382 ND ND 100 HPRK220009 ENSG00000180957 PITPN (HUGO ID) PHOSPHATIDYLINOSITOL TRANSFER PROTEIN BETA ISOFORM (PTDINS TRANSFER PROTEIN Transcript removed from current database 101 HPRK220010 ENSG00000183664 ND (19.34a.1), one other transcripts 102 HPRK220011 ENSG00000025708 ECGF1 (HUGO ID) THYMIDINE PHOSPHORYLASE PRECURSOR (EC 2.4.2.4) (TDRPASE) (TP) (PLATELET-DERIVED 103 HPRK220012 ENSG00000100094 NM_020315 (RefSeq ID) ND 104 HPRK220013 ENSG00000099942 CRKL (HUGO ID) CRK-LIKE PROTEIN 105 HPRK220014 ENSG00000099942 CRKL (HUGO ID) CRK-LIKE PROTEIN 106 HPRK220015 ENSG00000172404 NM_145174 (RefSeq ID) HSC3 107 HPRK220016 ENSG00000100220 NM_014306 (RefSeq ID) SIMILAR TO C. ELEGENS HYPOTHETICAL 55.2 KD PROTEIN F16A11.2. 108 HPRK220018 ENSG00000186998 NM_133455 (RefSeq ID) EMILIN AND MULTIMERIN-DOMAIN CONTAINING PROTEIN 1; PUTATIVE EMU1. 109 HPRK220019 ENSG00000093009 CDC45L (HUGO ID) CDC45-RELATED PROTEIN (PORC-PI-1). 110 HPRK220021 ND ND ND 111 HPRK220022 ND ND ND 112 HPRK220023 ENSG00000184164 NM_024324 (RefSeq ID) ND 113 HPRK220024 ND ND ND 114 HPRK220025 ND ND ND 115 HPRK220026 ND ND ND 116 HPRK220027 ENSG00000100241 SBF1 (HUGO ID) SET BINDING FACTOR 1 (SBF1) (MYOTUBULARIN-RELATED PROTEIN 5). 117 HPRK220028 ENSG00000133422 K852_HUMAN (SWISSPROT ID) ND 1 (4) Supplementary Table 1 Towards a human proteome atlas

Antibody ID Ensembl Gene ID Gene name Gene description 118 HPRK220029 ND ND ND 119 HPRK220030 ND ND ND 120 HPRK220031 ND ND ND 121 HPRK220032 ND ND ND 122 HPRK220033 ND ND ND 123 HPRK220034 ENSG00000128346 C22orf23 (HUGO ID) ND 124 HPRK220035 ENSG00000185838 GNB1L (HUGO ID) GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 1 (G PROTEIN BETA 125 HPRK220036 ENSG00000099995 SF3A1 (HUGO ID) SPLICING FACTOR 3 SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 114) (SAP 114) (SF3A 126 HPRK220037 ND ND ND 127 HPRK220038 ENSG00000100281 HMG2L1 (HUGO ID) HIGH-MOBILITY GROUP PROTEIN 2-LIKE 1 (HMGBCG PROTEIN). 128 HPRK220039 ENSG00000100150 Y645_HUMAN (SWISSPROT ID) ND 129 HPRK220040 ENSG00000100024 UPB1 (HUGO ID) BETA-UREIDOPROPIONASE (EC 3.5.1.6) (BETA-ALANINE SYNTHASE) (N-CARBAMOYL-BETA-A 130 HPRK220041 ND ND ND 131 HPRK220042 ENSG00000100077 ADRBK2 (HUGO ID) BETA-ADRENERGIC RECEPTOR KINASE 2 (EC 2.7.1.126) (BETA-ARK-2) (G-PROTEIN COUPLED 132 HPRK220043 ENSG00000170420 APOL6 (HUGO ID) APOLIPOPROTEIN L6 (APOLIPOPROTEIN L-VI) (APOL-VI). 133 HPRK220044 ENSG00000100425 BRD1 (HUGO ID) BROMODOMAIN-CONTAINING PROTEIN 1 (BR140-LIKE PROTEIN). 134 HPRK220046 ND ND ND 135 HPRK220047 ENSG00000100395 L3MBTL2 (HUGO ID) LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE 2 PROTEIN (L(3)MBT-LIKE 2 PROTEIN) (H-L(3)MBT- 136 HPRK220048 ENSG00000100284 TOM1 (HUGO ID) TARGET OF MYB PROTEIN 1. 137 HPRK220049 ENSG00000100151 PRKCABP (HUGO ID) PRKCA-BINDING PROTEIN (PROTEIN KINASE C-ALPHA BINDING PROTEIN) (PROTEIN INTERA 138 HPRK220050 ENSG00000128203 NM_020437 (RefSeq ID) SIMILAR TO ASPARTATE BETA HYDROXYLASE (ASPH). 139 HPRK220051 ENSG00000100034 PPM1F (HUGO ID) CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE PHOSPHATASE (EC 3.1.3.16) (CAM-KINA 140 HPRK220052 ENSG00000170638 YV03_HUMAN (SWISSPROT ID) ND 141 HPRK220053 ENSG00000161180 NM_152612 (RefSeq ID) ND 142 HPRK220054 ENSG00000100416 TRMU_HUMAN (SWISSPROT ID) TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). 143 HPRK220055 ENSG00000184381 PLA2G6 (HUGO ID) 85 KDA CALCIUM-INDEPENDENT PHOSPHOLIPASE A2 (EC 3.1.1.4) (IPLA2) (CAI- PLA2) (GROUP 144 HPRK220056 ENSG00000159873 NM_173510 (RefSeq ID) ND 145 HPRK220057 ENSG00000100142 POLR2F (HUGO ID) DNA-DIRECTED RNA POLYMERASE II 14.4 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB6) (RPB14.4) (R 146 HPRK220058 ENSG00000185339 TCN2 (HUGO ID) TRANSCOBALAMIN II PRECURSOR (TCII) (TC II). 147 HPRK220059 ENSG00000100154 KA43_HUMAN (SWISSPROT ID) TPR REPEAT CONTAINING PROTEIN KIAA1043 148 HPRK220060 ENSG00000170288 Gene removed from current database (20.34c.1) ND 149 HPRK220061 ENSG00000179007 APOBEC3D (HUGO ID) APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC POLYPEPTIDE-LIKE 3D. 150 HPRK220063 ND ND ND 151 HPRK220064 ND ND ND 152 HPRK220065 ND ND ND 153 HPRK220066 ND ND ND 154 HPRK220067 ND ND ND 155 HPRK220071 ENSG00000100412 ACO2 (HUGO ID) ACONITATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.3) (CITRATE HYDRO-LYAS 156 HPRK220072 ENSG00000100116 GCAT (HUGO ID) 2-AMINO-3-KETOBUTYRATE COENZYME A LIGASE, MITOCHONDRIAL PRECURSOR (EC 2.3.1.2 157 HPRK220073 ENSG00000070413 DGCR2 (HUGO ID) INTEGRAL MEMBRANE PROTEIN DGCR2/IDD PRECURSOR. 158 HPRK220074 ENSG00000182482 O76052 (SPTREMBL ID) ND 159 HPRK220075 ENSG00000183773 NM_144704 (RefSeq ID) ND 160 HPRK220077 ND ND ND 161 HPRK220078 ND ND ND 162 HPRK220079 ND ND ND 163 HPRK220081 ND ND ND 164 HPRK220088 ND ND ND 165 HPRK220097 ND ND ND 166 HPRK220100 ND ND ND 167 HPRK230015 ENSG00000101938 NRL1_HUMAN (SWISSPROT ID) NEURALIN PRECURSOR (VENTROPTIN). 168 HPRK230021 ENSG00000102145 GATA1 (HUGO ID) ERYTHROID TRANSCRIPTION FACTOR (GATA-1) (ERYF1) (GF-1) (NF-E1). 169 HPRK230022 ENSG00000102145 GATA1 (HUGO ID) ERYTHROID TRANSCRIPTION FACTOR (GATA-1) (ERYF1) (GF-1) (NF-E1). 170 HPRK230023 ENSG00000102218 RP2 (HUGO ID) XRP2 PROTEIN 171 HPRK230024 ENSG00000102225 PCTK1 (HUGO ID) SERINE/THREONINE-PROTEIN KINASE PCTAIRE-1 172 HPRK230025 ENSG00000102241 HTATSF1 (HUGO ID) HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSC 173 HPRK230026 ENSG00000102271 KLHL4 (HUGO ID) KELCH-LIKE PROTEIN 4. 174 HPRK230028 ENSG00000102393 GLA (HUGO ID) ALPHA-GALACTOSIDASE A PRECURSOR (EC 3.2.1.22) (MELIBIASE) (ALPHA-D- GALACTOSIDE 175 HPRK230032 ENSG00000155721 NSBP1 (HUGO ID) NUCLEOSOMAL BINDING PROTEIN 1. 176 HPRK230034 ENSG00000165192 ASB11 (HUGO ID) ANKYRIN REPEAT AND SOCS BOX CONTAINING PROTEIN 11 (ASB-11). 177 HPRK230035 ENSG00000101940 WDR13 (HUGO ID) WD-REPEAT PROTEIN 13. 178 HPRK230036 ENSG00000126945 HNRPH2 (HUGO ID) HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H' (HNRNP H') (FTP-3). 179 HPRK230037 ENSG00000130827 PLXNA3 (HUGO ID) PLEXIN A3 PRECURSOR (PLEXIN 4) (TRANSMEMBRANE PROTEIN SEX). 180 HPRK230039 ENSG00000072315 TRPC5 (HUGO ID) SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). 181 HPRK230040 ENSG00000101882 NM_024528 (RefSeq ID) ND 182 HPRK230041 ENSG00000036473 OTC (HUGO ID) ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCAS 183 HPRK230042 ENSG00000049769 ND ND Transcript removed from current database 184 HPRK230043 ENSG00000147144 NM_033626 (RefSeq ID); JM11 PROTEIN (19.34a.1), one other transcripts 185 HPRK230044 ENSG00000147168 IL2RG (HUGO ID) CYTOKINE RECEPTOR COMMON GAMMA CHAIN PRECURSOR (GAMMA-C) (INTERLEUKIN- 2 R 186 HPRK230045 ENSG00000147234 Q96JK8 (SPTREMBL ID) ND 187 HPRK230046 ENSG00000147383 NSDL_HUMAN (SWISSPROT ID) NAD(P)-DEPENDENT STEROID DEHYDROGENASE (EC 1.1.1.-) (H105E3 PROTEIN). 188 HPRK230048 ENSG00000160211 G6PD (HUGO ID) GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). 189 HPRK230049 ENSG00000090776 EFNB1 (HUGO ID) EPHRIN-B1 PRECURSOR (EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 2) (LERK-2) ( 190 HPRK230050 ENSG00000101938 NRL1_HUMAN (SWISSPROT ID) NEURALIN PRECURSOR (VENTROPTIN). 191 HPRK230053 ENSG00000156920 GPR112 (HUGO ID) G-PROTEIN COUPLED RECEPTOR 112. 192 HPRK230059 ENSG00000156504 NM_145284 (RefSeq ID) ND 193 HPRK230060 ENSG00000000005 TNMD_HUMAN (SWISSPROT ID) TENOMODULIN (TEM) (HTEM) (CHONDROMODULIN-I LIKE PROTEIN) (CHM1L) (HCHM1L) (MYO 194 HPRK230061 ENSG00000126947 NM_016608 (RefSeq ID) ALEX1 PROTEIN; ARM PROTEIN LOST IN EPITHELIAL CANCERS, X CHROMOSOME, 1. 195 HPRK230062 ENSG00000130985 UBE1 (HUGO ID) UBIQUITIN-ACTIVATING ENZYME E1 (A1S9 PROTEIN). 196 HPRK230063 ENSG00000131831 RAI2 (HUGO ID) RETINOIC ACID-INDUCED PROTEIN 2. 197 HPRK230064 ENSG00000131831 RAI2 (HUGO ID) RETINOIC ACID-INDUCED PROTEIN 2. 198 HPRK230065 ENSG00000068400 GRIPAP1 (HUGO ID) GRIP-ASSOCIATED PROTEIN 1. 199 HPRK230066 ENSG00000089289 IGBP1 (HUGO ID) IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANS 200 HPRK230067 ENSG00000165769 ND ND 201 HPRK230068 ENSG00000102096 PIM2 (HUGO ID) SERINE/THREONINE-PROTEIN KINASE PIM-2 (EC 2.7.1.37) (PIM-2H). 202 HPRK230069 ENSG00000068366 NM_004458 (RefSeq ID) LONG-CHAIN-FATTY-ACID--COA LIGASE 4 (EC 6.2.1.3) (LONG-CHAIN ACYL-COA SYNTHETASE 203 HPRK230070 ENSG00000068394 NM_015698 (RefSeq ID) T54 PROTEIN. 204 HPRK230071 ENSG00000130234 ACE2 (HUGO ID) ANGIOTENSIN I CONVERTING ENZYME 2 PRECURSOR; ANGIOTENSIN CONVERTING ENZYME 205 HPRK230072 ENSG00000130985 UBE1 (HUGO ID) UBIQUITIN-ACTIVATING ENZYME E1 (A1S9 PROTEIN). 206 HPRK230074 ENSG00000126016 AMOT (HUGO ID) ANGIOMOTIN. 207 HPRK230075 ENSG00000130021 FAM16AX (HUGO ID) GS1 PROTEIN (PROTEIN FAM16AX). 208 HPRK230076 ENSG00000131724 IL13RA1 (HUGO ID) INTERLEUKIN-13 RECEPTOR ALPHA-1 CHAIN PRECURSOR (IL-13R-ALPHA-1) (IL- 13RA-1) (CD2 209 HPRK230077 ENSG00000169188 APEX2 (HUGO ID) APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 210 HPRK230078 ENSG00000050030 Q8IVE9 (SPTREMBL ID) ND 211 HPRK230079 ENSG00000078596 ITM2A (HUGO ID) INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). 212 HPRK230080 ENSG00000086712 CXorf15 (HUGO ID) CHROMOSOME X OPEN READING FRAME 15; LIPOPOLYSACCHARIDE SPECIFIC RESPONSE-5 Transcript removed from current database 213 HPRK230081 ENSG00000147231 NM_018015 (RefSeq ID); No description (19.34a.1), one other transcripts 214 HPRK230083 ENSG00000072315 TRPC5 (HUGO ID) SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). 215 HPRK230084 ENSG00000089820 ARHGAP4 (HUGO ID) RHO-GTPASE-ACTIVATING PROTEIN 4 (RHO-GAP HEMATOPOIETIC PROTEIN C1) (P115). Transcript removed from current database 216 HPRK230085 ENSG00000102401 NM_177947 (RefSeq ID); ALEX3 PROTEIN; ARM PROTEIN LOST IN EPITHELIAL CANCERS, X CH (19.34a.1), two other transcripts 217 HPRK230086 ENSG00000176896 NM_152634 (RefSeq ID) ND 218 HPRK230087 ENSG00000181491 Gene removed from current database (19.34a.1) ND 219 HPRK230088 ENSG00000122121 XPNPEP2 (HUGO ID) XAA-PRO AMINOPEPTIDASE 2 PRECURSOR (EC 3.4.11.9) (X-PRO AMINOPEPTIDASE 2) (MEMB 220 HPRK230089 ENSG00000165370 GPR101 (HUGO ID) G PROTEIN-COUPLED RECEPTOR 101. 221 HPRK230090 ENSG00000169057 MECP2 (HUGO ID) METHYL-CPG-BINDING PROTEIN 2 (MECP-2 PROTEIN) (MECP2). 222 HPRK230091 ENSG00000071872 FLNA (HUGO ID) FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) 223 HPRK230092 ENSG00000133131 NM_024657 (RefSeq ID) ND 224 HPRK230093 ENSG00000169188 APEX2 (HUGO ID) APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 225 HPRK230094 ENSG00000008056 SYN1 (HUGO ID) SYNAPSIN I (BRAIN PROTEIN 4.1). 226 HPRK230095 ENSG00000050030 Q8IVE9 (SPTREMBL ID) ND 227 HPRK230096 ENSG00000102048 ASB9 (HUGO ID) ANKYRIN REPEAT AND SOCS BOX CONTAINING PROTEIN 9 (ASB-9). 228 HPRK230097 ENSG00000171365 CLCN5 (HUGO ID) CHLORIDE CHANNEL PROTEIN 5 (CLC-5). 229 HPRK230098 ENSG00000123572 ND ND 230 HPRK230100 ENSG00000130054 TED_HUMAN (SWISSPROT ID) TED PROTEIN 231 HPRK230101 ENSG00000130826 DKC1 (HUGO ID) DYSKERIN (NUCLEOLAR PROTEIN NAP57) (CBF5 HOMOLOG). 232 HPRK230103 ENSG00000156531 PHF6 (HUGO ID) PHD-LIKE ZINC FINGER PROTEIN. 233 HPRK230104 ENSG00000134588 USP26 (HUGO ID) UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 26 (EC 3.1.2.15) (UBIQUITIN THIOLESTERASE 234 HPRK230105 ENSG00000067829 IDH3G (HUGO ID) ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL PRECURSOR (EC 2 (4) Supplementary Table 1 Towards a human proteome atlas

Antibody ID Ensembl Gene ID Gene name Gene description 235 HPRK230106 ENSG00000073009 IKBKG (HUGO ID) NF-KAPPAB ESSENTIAL MODULATOR (NEMO) (NF-KAPPAB ESSENTIAL MODIFIER) (INHIBITOR 236 HPRK230107 ENSG00000101811 CSTF2 (HUGO ID) CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA S 237 HPRK230108 ENSG00000102032 RENBP (HUGO ID) N-ACYLGLUCOSAMINE 2-EPIMERASE (EC 5.1.3.8) (GLCNAC 2-EPIMERASE) (N-ACETYL-D-GLU 238 HPRK230109 ENSG00000166389 NM_152583 (RefSeq ID) ND 239 HPRK230110 ENSG00000171493 Q96QH7 (SPTREMBL ID) DJ54B20.4 (NOVEL KRAB BOX CONTAINING C2H2 TYPE ZINC FINGER PROTEIN 240 HPRK230111 ENSG00000179542 NM_173078 (RefSeq ID) ND 241 HPRK230112 ENSG00000007350 TKTL1 (HUGO ID) TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED 242 HPRK230114 ENSG00000102313 ND ND 243 HPRK230115 ENSG00000130830 MPP1 (HUGO ID) 55 KDA ERYTHROCYTE MEMBRANE PROTEIN (P55) (MEMBRANE PROTEIN, PALMITOYLATED 244 HPRK230117 ENSG00000102010 BMX (HUGO ID) CYTOPLASMIC TYROSINE-PROTEIN KINASE BMX (EC 2.7.1.112) (BONE MARROW KINASE BMX 245 HPRK230118 ENSG00000102269 Gene removed from current database (19.34a.1) ND 246 HPRK230119 ENSG00000165675 COVA1 (HUGO ID) CYTOSOLIC OVARIAN CARCINOMA ANTIGEN 1 (APK1 ANTIGEN). Transcript removed from current database 247 HPRK230120 ENSG00000178443 ND (19.34a.1), one other transcripts 248 HPRK230121 ENSG00000147118 Q96QH9 (SPTREMBL ID) DJ54B20.2 (NOVEL KRAB BOX CONTAINING C2H2 TYPE ZINC FINGER PROTEIN) (FRAGMENT) 249 HPRK230123 ND ND ND 250 HPRK230124 ND ND ND 251 HPRK230125 ENSG00000082458 DLG3 (HUGO ID) PRESYNAPTIC PROTEIN SAP102 (SYNAPSE-ASSOCIATED PROTEIN 102) (NEUROENDOCRINE 252 HPRK230126 ENSG00000068354 OATL1 (HUGO ID) MG81 PROTEIN (FRAGMENT). 253 HPRK230127 ENSG00000102032 RENBP (HUGO ID) N-ACYLGLUCOSAMINE 2-EPIMERASE (EC 5.1.3.8) (GLCNAC 2-EPIMERASE) (N-ACETYL-D-GLU 254 HPRK230128 ENSG00000158337 ND ND 255 HPRK230129 ENSG00000102057 KCND1 (HUGO ID) POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 1; SHAL-TYP 256 HPRK230131 ENSG00000165769 ND ND 257 HPRK230132 ENSG00000062096 ARSF (HUGO ID) ARYLSULFATASE F PRECURSOR (EC 3.1.6.-) (ASF). Transcript removed from current database 258 HPRK230133 ENSG00000101974 A11C_HUMAN (SWISSPROT ID); POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IG (EC (19.34a.1), two other transcripts 259 HPRK230134 ENSG00000147082 CCNB3 (HUGO ID) CYCLIN B3 ISOFORM 1. 260 HPRK230135 ENSG00000158443 Gene removed from current database (19.34b.2) ND 261 HPRK230136 ENSG00000175553 Q9ULL0 (SPTREMBL ID) ND 262 HPRK230137 ENSG00000155961 RAB39B (HUGO ID) RAS-RELATED PROTEIN RAB-39B. 263 HPRK230138 ENSG00000089472 HEPH (HUGO ID) HEPHAESTIN ISOFORM A. 264 HPRK230139 ENSG00000071872 FLNA (HUGO ID) FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) 265 HPRK230140 ENSG00000169306 IL1RAPL2 (HUGO ID) INTERLEUKIN 1 RECEPTOR ACCESSORY PROTEIN-LIKE 1; X-LINKED INTERLEUKIN-1 RECEPT 266 HPRK230141 ENSG00000169891 REPS2 (HUGO ID) RALBP1 ASSOCIATED EPS DOMAIN CONTAINING 2; PARTNER OF RAL-BINDING PROTEIN 1. 267 HPRK230142 ENSG00000063587 ZNF275 (HUGO ID) ZINC FINGER PROTEIN 275. 268 HPRK230143 ENSG00000178777 Gene removed from current database (20.34c.1) ND 269 HPRK230145 ENSG00000036473 OTC (HUGO ID) ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCAS 270 HPRK230146 ENSG00000147383 NSDL_HUMAN (SWISSPROT ID) NAD(P)-DEPENDENT STEROID DEHYDROGENASE (EC 1.1.1.-) (H105E3 PROTEIN). 271 HPRK230147 ENSG00000181191 PJA1 (HUGO ID) UBIQUITIN PROTEIN LIGASE PRAJA1 272 HPRK230148 ENSG00000068400 GRIPAP1 (HUGO ID) GRIP-ASSOCIATED PROTEIN 1. 273 HPRK230149 ENSG00000076716 GPC4 (HUGO ID) GLYPICAN-4 PRECURSOR (K-GLYPICAN). 274 HPRK230150 ENSG00000155008 ND ND 275 HPRK230151 ENSG00000174129 Gene removed from current database (20.34c.1) ND 276 HPRK230152 ENSG00000174678 Q8TAA0 (SPTREMBL ID) SIMILAR TO PRAM-1 PROTEIN, PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECUL 277 HPRK230153 ND ND ND 278 HPRK230154 ENSG00000133132 NM_019007 (RefSeq ID) ND Transcript removed from current database 279 HPRK230155 ENSG00000101974 A11C_HUMAN (SWISSPROT ID); POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IG (EC (19.34a.1), two other transcripts 280 HPRK230156 ENSG00000158443 Gene removed from current database (19.34b.2) ND 281 HPRK230157 ENSG00000089289 IGBP1 (HUGO ID) IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANS 282 HPRK230159 ENSG00000158423 Q8N443 (SPTREMBL ID) ND 283 HPRK230160 ENSG00000102053 ND ND 284 HPRK230161 ENSG00000165243 Gene removed from current database (20.34c.1) ND 285 HPRK230162 ND ND ND 286 HPRK230163 ENSG00000169153 Gene removed from current database (20.34c.1) ND 287 HPRK230165 ENSG00000130054 TED_HUMAN (SWISSPROT ID) TED PROTEIN 288 HPRK230167 ND ND ND 289 HPRK230169 ND ND ND 290 HPRK230170 ND ND ND 291 HPRK230172 ENSG00000147234 Q96JK8 (SPTREMBL ID) ND 292 HPRK230174 ND ND ND 293 HPRK230175 ENSG00000173698 GPR64 (HUGO ID) G PROTEIN-COUPLED RECEPTOR 64; G PROTEIN-COUPLED RECEPTOR, EPIDIDYMIS-SPECIF 294 HPRK230176 ENSG00000160211 G6PD (HUGO ID) GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). 295 HPRK230177 ENSG00000102053 ND ND 296 HPRK230178 ND ND ND 297 HPRK230179 ENSG00000086712 CXorf15 (HUGO ID) CHROMOSOME X OPEN READING FRAME 15; LIPOPOLYSACCHARIDE SPECIFIC RESPONSE-5 298 HPRK230181 ND ND ND 299 HPRK230184 ND ND ND 300 HPRK230186 ND ND ND 301 HPRK230187 ND ND ND 302 HPRK230188 ND ND ND Transcript removed from current database 303 HPRK230189 ENSG00000147231 NM_018015 (RefSeq ID); No description (19.34a.1), one other transcripts 304 HPRK230199 ND ND ND 305 HPRK230202 ND ND ND 306 HPRK230205 ND ND ND 307 HPRK230206 ND ND ND 308 HPRK230213 ND ND ND 309 HPRK230214 ND ND ND 310 HPRK230215 ND ND ND 311 HPRK230217 ND ND ND 312 HPRK230219 ND ND ND 313 HPRK230220 ND ND ND 314 HPRK230222 ND ND ND 315 HPRK230223 ND ND ND 316 HPRK230224 ND ND ND 317 HPRK230225 ND ND ND 318 HPRK230229 ND ND ND 319 HPRK230233 ND ND ND 320 HPRK230234 ND ND ND 321 HPRK230235 ND ND ND 322 HPRK230236 ND ND ND 323 HPRK230238 ND ND ND 324 HPRK230244 ND ND ND 325 HPRK230256 ND ND ND 326 HPRK230257 ND ND ND 327 HPRK230263 ND ND ND 328 HPRK230275 ND ND ND 329 HPRK230278 ND ND ND 330 HPRK240001 ENSG00000099715 PCDH11Y (HUGO ID) PROTOCADHERIN 11 Y-LINKED ISOFORM A; PROTOCADHERIN Y; PROTOCADHERIN 22. 331 HPRK240002 ND ND ND 332 HPRK240005 ND ND ND 333 HPRK240006 ND ND ND 334 HPRK240007 ND ND ND 335 HPRK240009 ND ND ND 336 HPRK250001 ENSG00000140416 TPM2 (HUGO ID) TROPOMYOSIN 1 ALPHA CHAIN (ALPHA-TROPOMYOSIN). 337 HPRK250003 ENSG00000109436 O94958 (SPTREMBL ID) ND 338 HPRK250006 ENSG00000134986 C5orf13 (HUGO ID) NEURONAL PROTEIN 3.1 (P311 PROTEIN). 339 HPRK250008 ENSG00000139083 ETV6 (HUGO ID) TRANSCRIPTION FACTOR ETV6 (ETS-RELATED PROTEIN TEL1) (TEL) (ETS TRANSLOCATION 340 HPRK250012 ENSG00000170396 ND ND 341 HPRK250015 ENSG00000038945 MSR1 (HUGO ID) MACROPHAGE SCAVENGER RECEPTOR TYPES I AND II (MACROPHAGE ACETYLATED LDL R 342 HPRK250019 ENSG00000135919 SERPINE2 (HUGO ID) GLIA DERIVED NEXIN PRECURSOR (GDN) (PROTEASE NEXIN I) (PN-1) (PROTEASE INHIBITOR 343 HPRK250020 ENSG00000136026 CKAP4 (HUGO ID) TRANSMEMBRANE PROTEIN (63KD), ENDOPLASMIC RETICULUM/GOLGI INTERM; TRANSMEM Transcript removed from current database 344 HPRK250025 ENSG00000150593 PDCD4 (HUGO ID); PROGRAMMED CELL DEATH 4 ISOFORM 1; PROGRAMMED CELL DEATH 4 (19.34a.1), one other transcript Transcript removed from current database 345 HPRK250026 ENSG00000151914 BPAG1 (HUGO ID); BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLO (19.34a.1), four other transcripts 346 HPRK250027 ENSG00000022267 Q9NZ40 (SPTREMBL ID) SKELETAL MUSCLE LIM-PROTEIN 1 (SLIM 1) (SLIM) (FOUR AND A HALF LIM DOMAINS PROTE 347 HPRK250028 ENSG00000125827 KG62_HUMAN (SWISSPROT ID) THIOREDOXIN-LIKE PROTEIN KIAA1162 PRECURSOR. 348 HPRK250029 ENSG00000147394 ZNF185 (HUGO ID) ZINC FINGER PROTEIN 185 (LIM-DOMAIN PROTEIN ZNF185) (P1-A). 3 (4) Supplementary Table 1 Towards a human proteome atlas

Antibody ID Ensembl Gene ID Gene name Gene description 349 HPRK250030 ENSG00000150527 MGEA6 (HUGO ID) MENINGIOMA-EXPRESSED ANTIGEN 6/11 (MEA6) (MEA11). 350 HPRK250031 ENSG00000119042 SATB2 (HUGO ID) ND 351 HPRK250032 ENSG00000121373 NKGD_HUMAN (SWISSPROT ID) NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN (NKG2-D ACTIVATING NK RECEPTOR) (NK C Transcript removed from current database 352 HPRK250033 ENSG00000158321 AUTS2 (HUGO ID); AUTISM SUSCEPTIBILITY GENE 2 PROTEIN (19.34a.1), one other transcript 353 HPRK250034 ENSG00000108679 LGALS3BP (HUGO ID) GALECTIN 3 BINDING PROTEIN; L3 ANTIGEN; MAC-2-BINDING PROTEIN; SERUM PROTEIN 90K 354 HPRK250035 ENSG00000136960 ENPP2 (HUGO ID) ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 2 (E-NPP 2) (PHOSPHODIES 355 HPRK250036 ENSG00000158006 PAFAH2 (HUGO ID) PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE 2, CYTOPLASMIC (EC 3.1.1.47) (SERINE 356 HPRK250037 ENSG00000165322 ARHGAP12 (HUGO ID) RHO GTPASE ACTIVATING PROTEIN 12 357 HPRK250038 ENSG00000172379 ARNT2 (HUGO ID) ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR 2 (ARNT PROTEIN 2). Transcript removed from current database 358 HPRK250039 ENSG00000168452 EGFL8 (HUGO ID); PALMITOYL-PROTEIN THIOESTERASE 2 PRECURSOR (EC 3.1.2.22) (PALMIT (19.34a.1), four other transcripts 359 HPRK250041 ENSG00000136960 ENPP2 (HUGO ID) ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 2 (E-NPP 2) (PHOSPHODIES 360 HPRK250043 ENSG00000176887 SOX11 (HUGO ID) TRANSCRIPTION FACTOR SOX-11 361 HPRK250044 ENSG00000106211 HSPB1 (HUGO ID) HEAT SHOCK 27 KDA PROTEIN (HSP 27) (STRESS-RESPONSIVE PROTEIN 27) (SRP27) (ESTRO 362 HPRK250045 ENSG00000112144 ICK (HUGO ID) INTESTINAL CELL KINASE ISOFORM A; MAK-RELATED KINASE; SERINE/THREONINE PROTEIN Transcript removed from current database 363 HPRK250046 ENSG00000113552 (20.34c.1), three other transcripts (same Mol GNPI (HUGO ID); Weight) 364 HPRK250047 ENSG00000131773 KHDRBS3 (HUGO ID) KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 3; SAM68-LIK 365 HPRK250048 ENSG00000108679 LGALS3BP (HUGO ID) GALECTIN 3 BINDING PROTEIN; L3 ANTIGEN; MAC-2-BINDING PROTEIN; SERUM PROTEIN 90K 366 HPRK250049 ENSG00000106443 PHF14 (HUGO ID) ND Transcript removed from curren database 367 HPRK250050 ENSG00000120885 CLU (HUGO ID); CLUSTERIN PRECURSOR (COMPLEMENT-ASSOCIATED PROTEIN SP-40,40) (C (20.34a.1); One other transcript 368 HPRK250051 ND ND ND 369 HPRK250052 ENSG00000143443 AF1Q_HUMAN (SWISSPROT ID) PROTEIN AF1Q. 370 HPRK250054 ND ND ND 371 HPRK250055 ENSG00000067445 TRO (HUGO ID) TROPHININ 372 HPRK250056 ENSG00000070882 OSBPL3 (HUGO ID) OXYSTEROL BINDING PROTEIN-RELATED PROTEIN 3 (OSBP-RELATED PROTEIN 3) (ORP-3). 373 HPRK250057 ND ND ND 374 HPRK250058 ENSG00000176887 SOX11 (HUGO ID) TRANSCRIPTION FACTOR SOX-11 375 HPRK250059 ND ND ND 376 HPRK250060 ENSG00000070882 OSBPL3 (HUGO ID) OXYSTEROL BINDING PROTEIN-RELATED PROTEIN 3 (OSBP-RELATED PROTEIN 3) (ORP-3). 377 HPRK250061 ND ND ND 378 HPRK250062 ND ND ND 379 HPRK250063 ND ND ND 380 HPRK250064 ND ND ND 381 HPRK250065 ENSG00000085265 FCN1 (HUGO ID) FICOLIN 1 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 1) (FICOLIN 382 HPRK250066 ND ND ND 383 HPRK250067 ND ND ND 384 HPRK250068 ND ND ND 385 HPRK250071 ND ND ND 386 HPRK250072 ND ND ND 387 HPRK250073 ND ND ND 388 HPRK250074 ND ND ND 389 HPRK250075 ENSG00000112144 ICK (HUGO ID) INTESTINAL CELL KINASE ISOFORM A; MAK-RELATED KINASE; SERINE/THREONINE PROTEIN 390 HPRK250076 ENSG00000136026 CKAP4 (HUGO ID) TRANSMEMBRANE PROTEIN (63KD), ENDOPLASMIC RETICULUM/GOLGI INTERM; TRANSMEM 391 HPRK250078 ND ND ND 392 HPRK250079 ND ND ND 393 HPRK250080 ND ND ND 394 HPRK250081 ND ND ND 395 HPRK250082 ND ND ND 396 HPRK250099 ND ND ND 397 HPRK260001 ND ND ND 398 HPRK260002 ND ND ND 399 HPRK260003 ND ND ND 400 HPRK260004 ND ND ND 401 HPRK260005 ND ND ND 402 HPRK260006 ND ND ND 403 HPRK260007 ND ND ND 404 HPRK260009 ND ND ND 405 HPRK260010 ND ND ND 406 HPRK260011 ND ND ND 407 HPRK260012 ND ND ND 408 HPRK260013 ND ND ND 409 HPRK260014 ND ND ND 410 HPRK260016 ND ND ND 411 HPRK270001 ENSG00000128573 FOXP2 (HUGO ID) FORKHEAD BOX PROTEIN P2 (CAG REPEAT PROTEIN 44) (TRINUCLEOTIDE REPEAT- CONTA 412 HPRK270002 ENSG00000128573 FOXP2 (HUGO ID) FORKHEAD BOX PROTEIN P2 (CAG REPEAT PROTEIN 44) (TRINUCLEOTIDE REPEAT- CONTA 413 HPRK280001 ND ND ND 414 HPRK280006 ND ND ND 415 HPRK280007 ND ND ND 416 HPRK280010 ND ND ND 417 HPRK300001 ENSG00000081237 PTPRC (HUGO ID) LEUKOCYTE COMMON ANTIGEN PRECURSOR (EC 3.1.3.48) (L-CA) (CD45 ANTIGEN) (T200). 418 HPRK300002 ENSG00000091831 ESR1 (HUGO ID) ESTROGEN RECEPTOR (ER) (ESTRADIOL RECEPTOR) (ER-ALPHA). 419 HPRK300004 ENSG00000148773 MKI67 (HUGO ID) ANTIGEN KI-67. Transcript removed from current database 420 HPRK300005 ENSG00000126337 KRTHA5 (HUGO ID); KERATIN, TYPE I CUTICULAR HA5 (HAIR KERATIN, TYPE I HA5). (20.34c.1), two other transcripts (same Mol Weight)

Transcript removed from current database 421 HPRK300006 ENSG00000126337 KRTHA5 (HUGO ID); KERATIN, TYPE I CUTICULAR HA5 (HAIR KERATIN, TYPE I HA5). (20.34c.1), two other transcripts (same Mol Weight)

Transcript removed from current database 422 HPRK300007 ENSG00000126337 KRTHA5 (HUGO ID); KERATIN, TYPE I CUTICULAR HA5 (HAIR KERATIN, TYPE I HA5). (20.34c.1), two other transcripts (same Mol Weight) 423 HPRK300008 ENSG00000141510 TP53 (HUGO ID) CELLULAR TUMOR ANTIGEN P53 (TUMOR SUPPRESSOR P53) (PHOSPHOPROTEIN P53) (ANT 424 HPRK300009 ENSG00000142515 KLK3 (HUGO ID) PROSTATE SPECIFIC ANTIGEN PRECURSOR (EC 3.4.21.77) (PSA) (GAMMA- SEMINOPROTEIN 425 HPRK300010 ND ND ND 426 HPRK300013 ND ND ND 427 HPRK300014 ND ND ND 428 HPRK300018 ENSG00000091831 ESR1 (HUGO ID) ESTROGEN RECEPTOR (ER) (ESTRADIOL RECEPTOR) (ER-ALPHA). 429 HPRK300019 ENSG00000081237 PTPRC (HUGO ID) LEUKOCYTE COMMON ANTIGEN PRECURSOR (EC 3.1.3.48) (L-CA) (CD45 ANTIGEN) (T200). 430 HPRK320001 ENSG00000141736 ERBB2 (HUGO ID) RECEPTOR PROTEIN-TYROSINE KINASE ERBB-2 PRECURSOR (EC 2.7.1.112) (P185ERBB2) (N 431 HPRK320003 ND ND ND 432 HPRK320004 ND ND ND Transcript removed from curren database 433 HPRK320005 ENSG00000160200 CBS (HUGO ID); CYSTATHIONINE BETA-SYNTHASE (EC 4.2.1.22) (SERINE SULFHYDRASE) (BE (20.34a.1); Two other transcripts 434 HPRK320006 ENSG00000100665 SERPINA3 (HUGO ID) PLASMA SERINE PROTEASE INHIBITOR PRECURSOR (PCI) (PROTEIN C INHIBITOR) (PLASMIN 435 HPRK320008 ENSG00000102024 PLS3 (HUGO ID) T-PLASTIN 436 HPRK320012 ENSG00000170086 SERPINA1 (HUGO ID) ALPHA-1-ANTITRYPSIN PRECURSOR (ALPHA-1 PROTEASE INHIBITOR) (ALPHA-1- ANTIPROTE 437 HPRK320013 ND ND ND 438 HPRK990001 ND ND ND 439 HPRK990002 ND ND ND 440 HPRK990005 ND ND ND 441 HPRK990006 ND ND ND 442 HPRK990007 ND ND ND 443 HPRK990008 ND ND ND 444 HPRK990009 ND ND ND 445 HPRK990010 ND ND ND 446 HPRK990011 ND ND ND

4 (4) Supplementary Table 2 Towards a human proteome atlas

Tissue type Topography code 1 Adrenal gland 93000 2 Appendix 66000 3 Breast 04000 4 Bronchus 26000 5 Bone marrow 06000 6 Cerebellum X6000 7 Cerebral cortex X2020 8 Cervix, uterine 83000 9 Colon 67000 10 Duodenum 64300 11 Endometruim 1 84000 12 Endometruim 2 84000 13 Epidydimis 79100 14 Esophagus 62000 15 Fallopian tube 86100 16 Gall bladder 57000 17 Heart muscle 32000 18 Hippocampus X2570 19 Kidney 71000 20 Lateral ventricle X1600 21 Liver 56000 22 Lung 28000 23 Lymph node 8000 24 Nasopharynx 23000 25 Oral mucosa 51000 26 Ovary 87000 27 Pancreas 59000 28 Parathyroid gland 97000 29 Placenta 88100 30 Prostate 77100 31 Rectum 68000 32 Salivary gland 55100 33 Seminal vesicle 77500 34 Skeletal muscle 13000 35 Skin 01000 36 Small intestine 65000 37 Smooth muscle 1X300 38 Soft tissue 1 1X000 39 Soft tissue 2 1X000 40 Spleen 07000 41 Stomach 1 62350 42 Stomach 2 63700 43 Testes 78000 44 Thyroid gland 96000 45 Tonsil 61100 46 Urinary tract 74000 47 Vagina 81000 48 Vulval- anal skin 80100/69000

1 (1) Supplementary Table 3 Towards a human proteome

Example of Immuno- Antibody ID Main Staining Feature stained Tissue

Intensity Localisation 1 HPRK140001 Weak Cytoplasmic Stomach 2 HPRK140003 Weak Granular Heart muscle 3 HPRK140004 Strong Cytoplasmic Placenta 4 HPRK140006 Medium Cytoplasmic Kidney 5 HPRK140008 Medium Nuclear Skin 6 HPRK140010 Strong Nuclear Pancreas 7 HPRK140012 Medium Nuclear Hippocampus 8 HPRK140013 Weak Cytoplasmic Colon 9 HPRK140015 Medium Granular Endometrium 10 HPRK140017 Medium Nuclear Colon 11 HPRK140018 Strong Cytoplasmic Urinary tract 12 HPRK140019 Strong Nuclear Breast 13 HPRK140020 Medium Extra-cellular Skin 14 HPRK140021 Strong Cytoplasmic Kidney 15 HPRK140024 Medium Nuclear Bronchus 16 HPRK140030 Medium Granular Skin 17 HPRK140031 Strong Membraneous Stomach 18 HPRK140032 Strong Granular Liver 19 HPRK140040 Medium Cytoplasmic Stomach 20 HPRK140041 Medium Cytoplasmic Placenta 21 HPRK140043 Strong Cytoplasmic Kidney 22 HPRK140058 Strong Nuclear Cerebral cortex 23 HPRK140064 Medium Nuclear Esophagus 24 HPRK140103 Medium Nuclear Testes 25 HPRK140106 Medium Membraneous Small intestine 26 HPRK140107 Medium Nuclear Lymph node 27 HPRK140108 Medium Cytoplasmic Skeletal muscle 28 HPRK220001 Strong Nuclear Urinary tract 29 HPRK220002 Strong Nuclear Testes 30 HPRK220004 Medium Cytoplasmic Vessels 31 HPRK220005 Medium Cytoplasmic Heart muscle 32 HPRK220006 Strong Nuclear Placenta 33 HPRK220008 Strong Membraneous Salivary gland 34 HPRK220009 Medium Cytoplasmic Urinary tract 35 HPRK220011 Weak Nuclear Breast 36 HPRK220012 Medium Nuclear Cerebellum 37 HPRK220013 Medium Cytoplasmic Gall bladder 38 HPRK220016 Strong Nuclear Ovary 39 HPRK220018 Strong Granular Stomach 40 HPRK220021 Medium Granular Cerebral cortex 41 HPRK220022 Weak Membraneous Skeletal muscle 42 HPRK220024 Medium Cytoplasmic Liver 43 HPRK220025 Medium Granular Colon 44 HPRK220027 Strong Cytoplasmic Lymph node 45 HPRK220030 Strong Nuclear Ovary 46 HPRK220031 Medium Extra-cellular Esophagus 47 HPRK220032 Strong Cytoplasmic Urinary tract 48 HPRK220033 Weak Granular Colon 49 HPRK220036 Strong Nuclear Skin 50 HPRK220038 Medium Nuclear Testes 51 HPRK220040 Weak Cytoplasmic Liver 52 HPRK220042 Strong Nuclear Stomach 53 HPRK220044 Strong Nuclear Testes 54 HPRK220047 Medium Cytoplasmic Heart muscle 55 HPRK220048 Weak Cytoplasmic Urinary tract 56 HPRK220056 Weak Nuclear Bone marrow 57 HPRK220064 Strong Nuclear Tonsil 58 HPRK220066 Strong Cytoplasmic Cerebellum 59 HPRK230001 Strong Cytoplasmic Salivary gland 60 HPRK230002 Strong Nuclear Testes 61 HPRK230003 Medium Cytoplasmic Soft tissue 62 HPRK230004 Medium Nuclear Heart muscle 63 HPRK230005 Medium Granular Fallopian tube 64 HPRK230007 Medium Cytoplasmic Red blood cells 65 HPRK230008 Strong Cytoplasmic Lymph node 66 HPRK230009 Medium Granular Cerebral cortex 67 HPRK230011 Medium Nuclear Testes 68 HPRK230015 Medium Membraneous Colon 69 HPRK230016 Strong Cytoplasmic Pancreas 70 HPRK230017 Medium Cytoplasmic Skin 71 HPRK230019 Weak Cytoplasmic Skeletal muscle 72 HPRK230020 Medium Granular Liver 73 HPRK230021 Strong Nuclear Testes 74 HPRK230022 Strong Nuclear Bone marrow 75 HPRK230024 Strong Cytoplasmic Liver 76 HPRK230025 Strong Nuclear Lymph node 77 HPRK230027 Strong Cytoplasmic Pancreas 78 HPRK230028 Medium Granular Endometrium 79 HPRK230036 Strong Nuclear Kidney 80 HPRK230037 Medium Granular Fallopian tube 81 HPRK230039 Medium Nuclear Cerebral cortex Supplementary Table 3 Towards a human proteome

Example of Immuno- Antibody ID Main Staining Feature stained Tissue

Intensity Localisation 82 HPRK230040 Medium Membraneous Pancreas 83 HPRK230041 Strong Granular Liver 84 HPRK230042 Medium Cytoplasmic Soft tissue 85 HPRK230046 Medium Cytoplasmic Adrenal gland 86 HPRK230049 Strong Cytoplasmic Spleen 87 HPRK230055 Medium Membraneous Stomach 88 HPRK230062 Medium Nuclear Kidney 89 HPRK230069 Strong Cytoplasmic Kidney 90 HPRK230071 Medium Cytoplasmic Stomach 91 HPRK230081 Strong Cytoplasmic Cerebral cortex 92 HPRK230085 Strong Cytoplasmic Liver 93 HPRK230088 Medium Cytoplasmic Small intestine 94 HPRK230095 Strong Cytoplasmic Vessels 95 HPRK230096 Medium Cytoplasmic Spleen 96 HPRK230097 Strong Nuclear Lymph node 97 HPRK230101 Strong Nuclear Cerebral cortex 98 HPRK230112 Medium Granular Hippocampus 99 HPRK230114 Medium Nuclear Stomach 100 HPRK230119 Weak Cytoplasmic Soft tissue 101 HPRK230125 Medium Cytoplasmic Soft tissue 102 HPRK230127 Strong Cytoplasmic Stomach 103 HPRK230129 Strong Cytoplasmic Heart muscle 104 HPRK230135 Medium Cytoplasmic Skeletal muscle 105 HPRK230141 Weak Cytoplasmic Cerebellum 106 HPRK230154 Medium Cytoplasmic Small intestine 107 HPRK250001 Medium Cytoplasmic Vessels 108 HPRK250003 Strong Membraneous Testes 109 HPRK250006 Medium Granular Cerebral cortex 110 HPRK250007 Strong Membraneous Kidney 111 HPRK250008 Medium Cytoplasmic Appendix 112 HPRK250009 Medium Extra-cellular Urinary tract 113 HPRK250013 Strong Cytoplasmic Kidney 114 HPRK250016 Medium Cytoplasmic Epididymis 115 HPRK250018 Strong Nuclear Cerebral cortex 116 HPRK250020 Strong Cytoplasmic Placenta 117 HPRK250027 Medium Cytoplasmic Skeletal muscle 118 HPRK250030 Medium Cytoplasmic Cerebral cortex 119 HPRK250031 Strong Nuclear Cerebral cortex 120 HPRK250033 Medium Nuclear Esophagus 121 HPRK250034 Medium Granular Pancreas 122 HPRK250044 Strong Cytoplasmic Vagina 123 HPRK250047 Medium Nuclear Prostate 124 HPRK250049 Strong Nuclear Lymph node 125 HPRK250050 Medium Granular Tonsil 126 HPRK250053 Strong Cytoplasmic Placenta 127 HPRK250054 Medium Cytoplasmic Kidney 128 HPRK250059 Medium Cytoplasmic Urinary tract 129 HPRK250060 Weak Cytoplasmic Placenta 130 HPRK250061 Medium Nuclear Thyroid gland 131 HPRK250062 Strong Cytoplasmic Cerebral cortex 132 HPRK250063 Medium Nuclear Cervix, uterine 133 HPRK250064 Medium Granular Heart muscle 134 HPRK250066 Medium Cytoplasmic Testes 135 HPRK250067 Strong Membraneous Small intestine 136 HPRK250068 Strong Nuclear Lymph node 137 HPRK250071 Medium Granular Bone marrow 138 HPRK250072 Strong Granular Liver 139 HPRK250074 Medium Membraneous Fallopian tube 140 HPRK250076 Strong Cytoplasmic Cerebellum 141 HPRK250077 Medium Cytoplasmic Skeletal muscle 142 HPRK250079 Strong Granular Endometrium 143 HPRK250080 Medium Nuclear Hippocampus 144 HPRK250081 Medium Membraneous Testes 145 HPRK250082 Strong Cytoplasmic Testes 146 HPRK260003 Strong Cytoplasmic Cerebral cortex 147 HPRK260005 Strong Membraneous Breast 148 HPRK260007 Strong Nuclear Lymph node 149 HPRK260009 Medium Cytoplasmic Skeletal muscle 150 HPRK270001 Strong Nuclear Lung 151 HPRK270002 Strong Nuclear Ovary 152 HPRK990002 Weak Cytoplasmic Breast 153 HPRK990003 Strong Cytoplasmic Stomach 154 HPRK990008 Medium Cytoplasmic Cerebellum Supplementary Table 4 Towards a human proteome atlas

Antibody characteristics for four msAbs and corresponding commercially available mAbs. Concentration* Antibody name Distributor/producer Clone Dilution (µg/ml) LCA/CD45 msAb In-house - 1:100 2.60 LCA/CD45 mAb Dakocytomation 2B11+PD7/26 1:500 0.66 Estrogen receptor msAb In-house - 1:200 0.90 Estrogen receptor mAb Novocastra 6F11 1:150 0.50 Ki67 msAb In-house - 1:300 0.77 Ki67 mAb Dakocytomation MIB-1 1:100 0.80 HER-2 msAb In-house - 1:20 2.00 HER-2 mAb Novocastra CBE-356 1:50 0.86 * Relates to concentration after dilution, i.e., working dilution.

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