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TABLE S2 Ipi GN DESCRIPTION Mean H/L # Pep CLDN1

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TABLE S2 Ipi GN DESCRIPTION Mean H/L # Pep CLDN1 TABLE S2 ALL RATIOS ARE REPORTED HEAVY / LIGHT 2H_TE_L+/H ipi GN DESCRIPTION Mean H/L # Pep CLDN1 IPI00000691 CLDN1 claudin-1. isoform 1 of chromodomain helicase-dna- CHD4 IPI00000846 CHD4 binding protein 4. 1.03 4 OCLN IPI00003373 OCLN occludin. SPOCK2 IPI00006128 SPOCK2 testican-2 precursor. KLF5 IPI00015934 KLF5 krueppel-like factor 5. 1.02 1 CBFB IPI00016746 CBFB core-binding factor subunit beta. 0.98 1 ADD1 IPI00019901 ADD1 isoform 1 of alpha-adducin. basement membrane-specific heparan sulfate proteoglycan core HSPG2 IPI00024284 HSPG2 proteinprecursor. glioma tumor suppressor candidate region GLTSCR2 IPI00024567 GLTSCR2 gene 2 protein. 1.18 5 QARS IPI00026665 QARS glutaminyl-trna synthetase. 1.19 11 S100A9 IPI00027462 S100A9 protein s100-a9. 0.80 134 PRDX6 IPI00220301 PRDX6 peroxiredoxin-6. 0.89 56 PDCD4 IPI00240675 PDCD4 programmed cell death 4 isoform 2. 0.67 1 tumor-associated calcium signal EpCAM IPI00296215 TACSTD1 transducer 1 precursor. 1.19 12 tumor-associated calcium signal Trop2 IPI00297910 TACSTD2 transducer 2 precursor. 0.85 10 neutrophil gelatinase-associated lipocalin LCN2 IPI00299547 LCN2 precursor. 1.06 13 ELAVL1 IPI00301936 ELAVL1 elav-like protein 1. 1.06 6 tumor necrosis factor, alpha-induced TNFAIP2 IPI00304866 TNFAIP2 protein 2. 1.07 19 VAMP3 IPI00549343 VAMP3 vesicle-associated membrane protein 3. IPI00553177 IPI00553177 SERPINA1 alpha-1-antitrypsin precursor. 0.13 29 SNX5 IPI00295209 SNX5 sorting nexin-5. 1.82 1 CDH17 IPI00290089 CDH17 Cadherin-17 precursor BAG4 IPI00030695 BAG4 bag family molecular chaperone regulator 4. isoform long of double-stranded rna- IPI00000001 STAU1 binding protein staufen homolog 1. 0.96 15 IPI00000015 SFRS4 splicing factor, arginine/serine-rich 4. 1.11 2 IPI00000024 PCDH1 isoform 1 of protocadherin-1 precursor. isoform delta-1 of serine/threonine-protein phosphatase 2a 56 kdaregulatory subunit IPI00000030 PPP2R5D delta isoform. 1.05 5 isoform 1 of interleukin-1 receptor IPI00000045 IL1RN antagonist protein precursor. 1.14 6 IPI00000051 PFDN1 prefoldin subunit 1. 1.08 4 IPI00000105 MVP major vault protein. 1.00 10 IPI00000151 ITGB6 integrin beta-6 precursor. ligase iii, dna, atp-dependent isoform beta IPI00000156 LIG3 precursor. 0.99 3 IPI00000181 MRPS24 mitochondrial 28s ribosomal protein s24. IPI00000184 SCOC hrihfb2072 protein (fragment). IPI00000279 - hypothetical protein lerepo4. 1.03 10 IPI00000330 C9orf80 hspc043 protein. 1.05 3 IPI00000335 HINT2 histidine triad nucleotide-binding protein 2. 1.07 12 IPI00000398 NUSAP1 liver nuclear protein. 1.21 4 IPI00000494 RPL5 60s ribosomal protein l5. 1.20 26 IPI00000495 PCID1 pnas-125. 1.14 1 IPI00000581 OTUB1 hypothetical protein dkfzp564e242. 1.16 12 IPI00000634 CCDC6 coiled-coil domain-containing protein 6. bag family molecular chaperone regulator IPI00000643 BAG2 2. 1.19 7 IPI00000685 CDK7 cell division protein kinase 7. isoform 1 of programmed cell death IPI00000690 PDCD8 protein 8, mitochondrial precursor. 1.06 2 IPI00000692 CLIC3 chloride intracellular channel protein 3. isoform 1 of ubiquitin carboxyl-terminal IPI00000728 USP15 hydrolase 15. u3 small nucleolar rna-associated protein IPI00000733 UTP18 18 homolog. 1.29 6 isoform 1 of proteasome subunit beta type IPI00000783 PSMB8 8 precursor. 0.95 5 proteasome subunit beta type 6 IPI00000811 PSMB6 precursor. IPI00000816 YWHAE 14-3-3 protein epsilon. 1.04 88 39s ribosomal protein l16, mitochondrial IPI00000821 MRPL16 precursor. isoform 1 of pleckstrin homology domain- IPI00000856 PLEKHC1 containing family c member 1. IPI00000858 RDBP isoform 1 of negative elongation factor e. 0.96 2 IPI00000861 LASP1 isoform 1 of lim and sh3 domain protein 1. 1.06 32 IPI00000873 VARS valyl-trna synthetase. 1.13 3 IPI00000875 EEF1G elongation factor 1-gamma. 1.29 64 150 kda oxygen-regulated protein IPI00000877 HYOU1 precursor. 1.02 31 IPI00000948 TBL2 transducin beta-like 2 protein. probable mitochondrial import receptor IPI00000980 TOMM7 subunit tom7 homolog. 1.03 4 IPI00001091 AFG3L2 afg3-like protein 2. 0.95 1 cdna flj11153 fis, clone place1006917, IPI00001134 RBM7 weakly similar to hsh49protein. IPI00001159 GCN1L1 gcn1-like protein 1. 1.15 2 isoform a of gc-rich sequence dna-binding IPI00001364 C21orf66 factor homolog. echinoderm microtubule-associated IPI00001466 EML4 protein-like 4. isoform 1 of epithelial discoidin domain- IPI00001477 DDR1 containing receptor 1precursor. mitochondrial import inner membrane IPI00001541 TIMM9 translocase subunit tim9. 1.01 16 mitochondrial import inner membrane IPI00001543 TIMM10 translocase subunit tim10. 0.96 7 IPI00001568 ATP6V1D vacuolar atp synthase subunit d. 1.08 2 mitochondrial import inner membrane IPI00001589 TIMM13 translocase subunit tim13. 1.02 7 IPI00001632 KIAA1522 hypothetical protein loc57648. 0.87 6 IPI00001636 ATXN10 ataxin-10. 0.93 3 IPI00001639 KPNB1 importin beta-1 subunit. 1.39 8 IPI00001661 RCC1 rcc1 protein. 0.91 10 isoform 2 of nuclear protein localization IPI00001676 NPLOC4 protein 4 homolog. 1.20 7 isoform 1 of apoptosis-associated speck- IPI00001699 PYCARD like protein containing acard. 1.19 7 IPI00001716 PUS1 trna pseudouridine synthase a. isoform 1 of phosphoserine IPI00001734 PSAT1 aminotransferase. 1.24 3 IPI00001754 F11R junctional adhesion molecule a precursor. 1.19 5 IPI00001757 RBM8A isoform 1 of rna-binding protein 8a. 1.04 24 IPI00001871 PAWR prkc apoptosis wt1 regulator protein. 0.87 27 IPI00001883 SNX9 sorting nexin-9. 0.70 1 IPI00001890 COPG coatomer subunit gamma. 1.76 4 IPI00001922 ST14 suppressor of tumorigenicity protein 14. 1.15 4 IPI00001960 CLIC4 chloride intracellular channel protein 4. 0.87 19 26s proteasome non-atpase regulatory IPI00002134 PSMD5 subunit 5. 1.49 2 transforming acidic coiled-coil-containing IPI00002135 TACC3 protein 3. 1.02 2 IPI00002149 SAR1B gtp-binding protein sar1b. 0.94 2 brca2 and cdkn1a-interacting protein IPI00002203 BCCIP isoform bccipbeta. 1.14 3 IPI00002230 AADACL1 arylacetamide deacetylase-like 1. lipopolysaccharide-responsive and beige- IPI00002255 LRBA like anchor protein. IPI00002270 C6orf211 protein c6orf211. nuclear fragile x mental retardation- IPI00002349 NUFIP2 interacting protein 2. 1.03 8 atp-binding cassette sub-family d member IPI00002372 ABCD3 3. lutheran blood group glycoprotein IPI00002406 BCAM precursor. 0.99 15 IPI00002408 AMIGO2 hypothetical protein flj21908. 0.94 4 IPI00002412 PPT1 palmitoyl-protein thioesterase 1 precursor. 1.02 1 cdna flj13187 fis, clone nt2rp3004242, weakly similar to putativerho/rac guanine IPI00002424 PLEKHF2 nucleotide exchange factor. 1.06 1 IPI00002441 SDC1 syndecan-1 precursor. IPI00002460 ANXA7 isoform 1 of annexin a7. 0.97 2 IPI00002495 EPN1 isoform 1 of epsin-1. 1.08 4 gdp-mannose pyrophosphorylase b IPI00002496 GMPPB isoform 1. serine hydroxymethyltransferase, IPI00002520 SHMT2 mitochondrial precursor. 1.05 34 atp synthase coupling factor 6, IPI00002521 ATP5J mitochondrial precursor. 0.94 16 IPI00002525 NENF neudesin precursor. 1.01 10 IPI00002535 FKBP2 fk506-binding protein 2 precursor. 0.99 21 IPI00002564 XRCC1 dna-repair protein xrcc1. 1.44 2 IPI00002624 PLRG1 isoform 1 of pleiotropic regulator 1. 1.08 2 IPI00002790 SEL1L isoform 1 of sel-1 homolog precursor. IPI00002821 RPL14 60s ribosomal protein l14. 0.99 18 IPI00002824 CSRP2 cysteine and glycine-rich protein 2. 0.93 1 mitogen-activated protein kinase 14 IPI00002857 MAPK14 isoform 2. 1.28 2 IPI00002922 TBL1XR1 f-box-like/wd repeat protein tbl1xr1. cdna flj12750 fis, clone nt2rp2001168, IPI00002926 VPS37B weakly similar to verprolin. 1.12 3 IPI00002966 HSPA4 heat shock 70 kda protein 4. 0.98 38 IPI00003084 DRAP1 dr1-associated protein 1. 0.91 7 isoform iib of prolyl 4-hydroxylase alpha-2 IPI00003128 P4HA2 subunit precursor. 0.94 3 phosphoribosyl pyrophosphate synthetase- IPI00003168 PRPSAP2 associated protein 2. proteasome subunit beta type 7 IPI00003217 PSMB7 precursor. 1.49 2 IPI00003269 THBS4 hypothetical protein loc345651. dna-directed rna polymerases i, ii, and iii IPI00003309 POLR2H 17.1 kda polypeptide. IPI00003327 ARL3 adp-ribosylation factor-like protein 3. 0.93 7 guanine nucleotide-binding protein IPI00003348 GNB2 g(i)/g(s)/g(t) subunit beta 2. 1.25 4 IPI00003362 HSPA5 hypothetical protein. 1.11 201 isoform 1 of splicing factor, IPI00003377 SFRS7 arginine/serine-rich 7. 0.78 1 IPI00003386 RBX1 ring-box protein 1. 1.05 2 isoform smn of survival motor neuron IPI00003394 SMN2 protein. IPI00003406 DBN1 drebrin. 0.89 6 IPI00003419 C11orf58 small acidic protein. 0.83 2 dnaj (hsp40) homolog, subfamily c, IPI00003438 DNAJC8 member 8. 1.06 14 isoform 1 of gamma-interferon-inducible IPI00003443 IFI16 protein ifi-16. 1.05 1 IPI00003479 MAPK1 mitogen-activated protein kinase 1. 0.97 5 2,4-dienoyl-coa reductase, mitochondrial IPI00003482 DECR1 precursor. isoform 1 of thyroid receptor-interacting IPI00003505 TRIP13 protein 13. 116 kda u5 small nuclear IPI00003519 EFTUD2 ribonucleoprotein component. 1.04 14 ezrin-radixin-moesin-binding IPI00003527 SLC9A3R1 phosphoprotein 50. 0.82 19 cofactor required for sp1 transcriptional IPI00003562 CRSP9 activation subunit 9. eukaryotic translation elongation factor 1 IPI00003588 EEF1E1 epsilon-1. 1.03 2 IPI00003627 ACTL6A isoform 1 of actin-like protein 6a. isoform 2 of endoplasmic reticulum-golgi IPI00003635 ERGIC1 intermediate compartmentprotein 1. IPI00003704 RBM4 isoform 1 of rna-binding protein 4. 0.86 1 rna-binding motif, single-stranded- IPI00003706 RBMS2 interacting protein 2. 1.16 4 IPI00003766 ETHE1 ethe1 protein, mitochondrial precursor. 0.92 1 IPI00003768 PES1 isoform 1 of pescadillo homolog 1. dual specificity mitogen-activated
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