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Supporting Information for Proteomics DOI 10.1002/pmic.200700415

Barbara Seliger, Sven P. Dressler, Rudolf Lichtenfels and Roland Kellner

Candidate biomarkers in renal cell carcinoma

ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com ID Family compartment Reg Paper ID compartment Reg Paper TU TU O75891 10-formyltetrahydrofolate cytoplasm u * Craven et al. 2006 P14550 aldo-keto reductase family 1, metabolism cytoplasm u Craven et al. 2006 dehydrogenase d Unwin et al. 2003 memberA1 n.d. Hoffmann et al. 2005 P31947 14-3-3 protein sigma proliferation cytoplasm n.d. Perego et al. 2003 (aldehyde reductase 2ALR) d Hwa et al. 2005 n.d. Bloom et al. 2006 d Perroud et al. 2006 P09543 2,3-cyclic-nucleotide 3- signal membrane / n.d. Hoffmann et al. 2005 u Poznanovic et al. 2005 phosphodiesterase transduction cell surface n.d. Seliger et al. 2003 P42126 3,2-trans-enoyl-CoA metabolism mitochondrion d Unwin et al. 2003 Q5U031 Aldo-keto reductase family 1, other unknown u Poznanovic et al. 2005 Q9BYC9 39S ribosomal protein L20 expression mitochondrion n.d. Hoffmann et al. 2005 membERB1 control P05062 aldolase B, fructose-bisphosphate metabolism cytoplasm d Perroud et al. 2006 Q99714 3-hydroxyacyl-CoA dehydrogenase type metabolism multiple n.d. Magni et al. 2005 P15121 Aldose reductase stress protein extracellular region h Lichtenfels et al. 2003 II compartment P31937 3-hydroxyisobutyrate dehydrogenase metabolism mitochondrion n.d. Magni et al. 2005 P02489 Alpha crystallin A chain stress protein cytoplasm n.d. Sarto et al. 1997 Q92931 3-Hydroxyisobutyryl coenzyme A metabolism mitochondrion d Unwin et al. 2003 P25325 3-mercaptopyruvate sulfurtransferase transport cytoplasm n.d. Bloom et al. 2006 P02511 Alpha crystallin B chain signal cytoplasm n.d. Magni et al. 2005 protein transduction n.d. Perego et al. 2003 P62273 40S ribosomal protein S29 expression cytoplasm n.d. Hoffmann et al. 2005 u Poznanovic et al. 2005 control n.d. Sarto et al. 1997 P22090 40S ribosomal protein S4, Y isoform 1 expression other n.d. Hoffmann et al. 2005 P06733 alpha enolase expression multiple n.d. Bloom et al. 2006 control control compartment n.d. Zhuang et al. 2006 P49189 4-trimethylaminobutyraldehyde metabolism cytoplasm d Unwin et al. 2003 P01009 Alpha-1-antitrypsin stress extracellular region u * Hwa et al. 2005 dehydrogenase protein n.d. Magni et al. 2005 P05387 60S acidic ribosomal protein P2 expression cytoplasm n.d. Sarto et al. 1997 P06733 Alpha-enolase expression multiple u Craven et al. 2006 control control compartment n.d. Magni et al. 2005 Q02543 60S ribosomal protein L18a. expression other n.d. Hoffmann et al. 2005 n.d. Perego et al. 2003 control u Poznanovic et al. 2005 P11021 78 kDa glucose-regulated protein stress ER n.d. Lichtenfels et al. 2002 u Unwin et al. 2003 protein n.d. Magni et al. 2005 P47710 Alpha-s1-casein transport extracellular region u Unwin et al. 2003 n.d. Perego et al. 2003 protein u Unwin et al. 2003 Q03154 Aminoacylase-1 metabolism cytoplasm d Balabanov et al. 2001 P24752 Acetyl-CoA acetyltransferase metabolism mitochondrion n.d. Magni et al. 2005 d Hwa et al. 2005 d Perroud et al. 2006 d Perroud et al. 2006 d Unwin et al. 2003 d Poznanovic et al. 2005 Q99798 Aconitate hydratase metabolism mitochondrion n.d. Magni et al. 2005 d Unwin et al. 2003 u Unwin et al. 2003 P80404 Aminobutyrate transaminase metabolism mitochondrion d Unwin et al. 2003 P60709 Actin, cytoplasmic 1 (beta-actin) cell motility cytoplasm d Craven et al. 2006 P04083 Annexin A1 signal cytoplasm n.d. Magni et al. 2005 n.d. Magni et al. 2005 transduction n.d. Perego et al. 2003 u Poznanovic et al. 2005 n.d. Zhuang et al. 2006 n.d. Sarto et al. 1997 u Unwin et al. 2003 n.d. Zhuang et al. 2006 u Unwin et al. 2003 P63261 Actin, cytoplasmic 2 (gamma-actin) cell motility cytoskeleton d Craven et al. 2006 P07355 Annexin A2 proliferation membrane / u Craven et al. 2006 ∅ Kellner et al. 2002 cell surface n.d. Zhuang et al. 2006 n.d. Magni et al. 2005 u Unwin et al. 2003 P27144 Adenylate kinase 3 metabolism mitochondrion u Craven et al. 2006 P12429 Annexin A3 signal cytoplasm n.d. Hoffmann et al. 2005 P54819 Adenylate kinase isoenzyme 2 metabolism mitochondrion n.d. Magni et al. 2005 transduction Q9Y6K8 Adenylate kinase isoenzyme 5 metabolism cytoplasm n.d. Magni et al. 2005 P09525 Annexin A4 signal cytoplasm n.d. Zhuang et al. 2006 P21695 a-Glycerol-3-phosphate metabolism cytoplasm d Balabanov et al. 2001 transduction u Perroud et al. 2006 Q9BSE5 metabolism mitochondrion d Dallmann et al. 2003 u Poznanovic et al. 2005 d Hwa et al. 2005 u Unwin et al. 2003 d Perroud et al. 2006 u Unwin et al. 2003 P05091 Aldehyde dehydrogenase 1 metabolism mitochondrion d Balabanov et al. 2001 u Zimmermann et al. 2004 n.d. Magni et al. 2005 n.d. Bloom et al. 2006 d Unwin et al. 2003 P08758 Annexin V signal cytoplasm n.d. Bloom et al. 2006 P00352 Aldehyde dehydrogenase 1 A1 metabolism cytoplasm n.d. Bloom et al. 2006 transduction u Perroud et al. 2006 u Craven et al. 2006 u Poznanovic et al. 2005 u * Craven et al. 2006 n.d. Seliger et al. 2003 d Poznanovic et al. 2005 O00244 Antioxidant protein 1 (ATOX1) stress protein cytoplasm n.d. Zhuang et al. 2006 P30837 Aldehyde dehydrogenase X metabolism mitochondrion n.d. Bloom et al. 2006 ID Protein Family compartment Reg Paper ID Protein Family compartment Reg Paper TU TU P02647 Apolipoprotein A1 metabolism extracellular region n.d. Magni et al. 2005 P12110 alpha 2(VI) chain CA26 splice cell adhesion extracellular region n.d. Magni et al. 2005 Q8NCW5 Apolipoprotein A1 binding protein unknown extracellular region u * Craven et al. 2006 isoform 2C2 P02649 Apolipoprotein E multiple multiple n.d. Magni et al. 2005 P12277 kinase B-type other cytoplasm d Unwin et al. 2003 compartment P04080 cystatin B (stefin B) other nucleus u Perroud et al. 2006 P00966 Arginosuccinate synthase metabolism cytoplasm u * Craven et al. 2006 P00167 Cytochrome b5 splice isoform 2 ion binding multiple n.d. Magni et al. 2005 d Perroud et al. 2006 compartment d Unwin et al. 2003 P20674 Cytochrome c oxidase polypeptide Va metabolism cytoplasm n.d. Sarto et al. 1997 O95376 Ariadne-2 protein homolog metabolism nucleus n.d. Zhuang et al. 2006 P10606 Cytochrome C oxidase polypeptide Vb transport mitochondrion n.d. Magni et al. 2005 P17174 Aspartate aminotransferase, cytoplasmic metabolism cytoplasm n.d. Bloom et al. 2006 protein P25705 ATP synthase alpha chain transport mitochondrion n.d. Magni et al. 2005 P14854 Cytochrome C oxidase polypeptide VIb transport mitochondrion n.d. Magni et al. 2005 protein protein P06576 ATP synthase beta chain transport mitochondrion n.d. Magni et al. 2005 P05783 18 transport cytoskeleton d Craven et al. 2006 protein n.d. Sarto et al. 1997 protein P30049 ATP synthase delta chain metabolism mitochondrion d Perroud et al. 2006 P08729 Cytokeratin 7 structural cytoskeleton d Craven et al. 2006 n.d. Sarto et al. 1997 molecule O75947 ATP synthase, H+ transporting, transport mitochondrion n.d. Magni et al. 2005 P30038 Delta-1-pyrroline-5-carboxylate metabolism mitochondrion n.d. Magni et al. 2005 mitochondrial F0 complex, subunit d protein d Perroud et al. 2006 dehydrogenase d Unwin et al. 2003 P53396 ATP-citrate synthase metabolism cytoplasm d Craven et al. 2006 Q13011 Delta3,5-delta2,4-dienoyl-CoA metabolism mitochondrion n.d. Magni et al. 2005 P13010 ATP-dependent DNA helicase 2 subunit expression nucleus d Craven et al. 2006 isomerase 2 control P36957 Dihydrolipoamide succinyltransferase metabolism mitochondrion n.d. Zhuang et al. 2006 Q92499 ATP-dependent RNA helicase DDX1 expression unknown n.d. Hoffmann et al. 2005 Q16555 Dihydropyrimidinase related protein-2 signal mitochondrion u Craven et al. 2006 control transduction Q93088 Betaine--homocysteine S- metabolism cytoplasm d Perroud et al. 2006 Q14566 DNA replication licensing factor MCM6 expression nucleus n.d. Hoffmann et al. 2005 methyltransferase d Unwin et al. 2003 control P30043 Biliverdin reductase B metabolism cytoplasm u Craven et al. 2006 Q9NZN4 EH domain containing protein 2 other membrane / u Craven et al. 2006 Q13509 b-Tubulin 4 structural cytoskeleton d Craven et al. 2006 cell surface n.d. Hoffmann et al. 2005 molecule P13804 Electron transferflavoprotein alpha- transport mitochondrion n.d. Magni et al. 2005 P05937 calbindin 1, 28kDa ion binding cytoplasm d Perroud et al. 2006 subunit protein Q99653 Calcium-binding protein p22 transport cytoplasm n.d. Magni et al. 2005 P24534 Elongation factor 1-beta expression other n.d. Perego et al. 2003 protein control n.d. Sarto et al. 1997 P02593 Calmodulin ion binding unknown n.d. Magni et al. 2005 P26641 Elongation factor 1-gamma expression other u Craven et al. 2006 n.d. Perego et al. 2003 control n.d. Hoffmann et al. 2005 P27797 Calreticulin multiple ER n.d. Magni et al. 2005 P13639 Elongation factor 2 expression cytoplasm d Craven et al. 2006 n.d. Perego et al. 2003 control n.d. Sarto et al. 1997 P49411 Elongator factor Tu expression mitochondrion n.d. Magni et al. 2005 P00915 Carbonic anhydrase 1 metabolism cytoplasm o Klade et al. 2001 control u Poznanovic et al. 2005 P30040 protein ERp29 transport ER n.d. Magni et al. 2005 u Unwin et al. 2003 protein P16152 Carbonyl reductase [NADPH] 1 metabolism cytoplasm u Poznanovic et al. 2005 P30084 Enoyl-CoA hydratase metabolism mitochondrion d Balabanov et al. 2001 P04040 Catalase stress protein other n.d. Sarto et al. 1997 d Hwa et al. 2005 n.d. Magni et al. 2005 P07339 Cathepsin D other multiple u Craven et al. 2006 d Perroud et al. 2006 compartment u * Craven et al. 2006 h Lichtenfels et al. 2003 n.d. Zhuang et al. 2006 P30042 ES1 protein homolog unknown mitochondrion n.d. Magni et al. 2005 Q5T178 CDC28 protein kinase regulatory subunit other unknown n.d. Hoffmann et al. 2005 Q9UPT5 Exocyst complex component Exo70 transport cytoplasm u Craven et al. 2006 1B protein O00299 chloride intracellular channel 1 signal multiple u Perroud et al. 2006 P47756 F-actin capping protein subunit beta cell motility cytoskeleton ∅ Kellner et al. 2002 transduction compartment Q16658 Fascin 1 proliferation cytoskeleton u Craven et al. 2006 Q9Y696 Chloride intracellular channel protein 4 transport multiple n.d. Seliger et al. 2003 u * Craven et al. 2006 protein compartment O15540 Fatty acid-binding protein, brain signal cytoplasm u Perroud et al. 2006 P09497 Clathrin light chain B transport golgi apparatus n.d. Magni et al. 2005 transduction u Seliger et al. 2005 protein P05413 Fatty acid-binding protein, heart proliferation cytoplasm d Poznanovic et al. 2005 P33240 Cleavage stimulation factor expression nucleus u Craven et al. 2006 h Seliger et al. 2005 control P07148 Fatty acid-binding protein, livER signal cytoplasm d Poznanovic et al. 2005 P23528 Cofilin-1 signal nucleus u Unwin et al. 2003 transduction d Seliger et al. 2005 transduction P02675 Fibrinogen beta chain signal extracellular region u Craven et al. 2006 P12109 Collagen alpha 1(VI) chain splice cell adhesion cytoskeleton n.d. Magni et al. 2005 transduction n.d. Magni et al. 2005 isoform n.d. Bloom et al. 2006 u Unwin et al. 2003 ID Protein Family compartment Reg Paper ID Protein Family compartment Reg Paper TU TU P02679 Fibrinogen gamma chain precursor signal other n.d. Zhuang et al. 2006 P04792 Heat shock 27 kDa protein stress multiple u Lichtenfels et al. 2002 transduction protein compartment n.d. Seliger et al. 2003 Q02790 FK506-binding protein 4 multiple multiple n.d. Seliger et al. 2003 u * Craven et al. 2006 compartment u Craven et al. 2006 Q14332 Frizzled-2 signal membrane / cell n.d. Hoffmann et al. 2005 n.d. Magni et al. 2005 transduction surface n.d. Perego et al. 2003 P09467 Fructose-1,6-bisphosphatase 1 metabolism unknown d Unwin et al. 2003 u Perroud et al. 2006 P04075 Fructose-bisphosphate aldolase A metabolism unknown u Craven et al. 2006 u Poznanovic et al. 2005 u Unwin et al. 2003 h Tremolada et al. 2005 Q13742 Fructose-bisphosphate aldolase B metabolism cytoplasm d Unwin et al. 2003 u Sarto et al. 2004 P07954 Fumarate hydratase metabolism mitochondrion n.d. Magni et al. 2005 n.d. Bloom et al. 2006 Q92945 FUSE binding protein 2 expression nucleus d Craven et al. 2006 P10809 heat shock 60kDa protein 1 stress mitochondrion n.d. Lichtenfels et al. 2002 control (chaperonin) protein n.d. Sarto et al. 1997 P09382 Galectin-1 signal multiple n.d. Magni et al. 2005 d Craven et al. 2006 transduction compartment n.d. Sarto et al. 1997 n.d. Magni et al. 2005 P17931 Galectin-3 structural multiple u Poznanovic et al. 2005 n.d. Perego et al. 2003 molecule compartment d Perroud et al. 2006 P09104 Gamma-enolase metabolism cytoplasm n.d. Seliger et al. 2003 P38646 Heat shock 70kDa protein stress mitochondrion n.d. Lichtenfels et al. 2002 n.d. Bloom et al. 2006 (mortalin, GRP75) protein n.d. Sarto et al. 1997 u Perroud et al. 2006 u * Craven et al. 2006 n.d. Zhuang et al. 2006 n.d. Magni et al. 2005 Q13630 GDP-L-fucose synthetase metabolism cytoplasm u Craven et al. 2006 P08238 heat shock 90kDa protein 1, beta stress cytoplasm n.d. Seliger et al. 2003 P11413 Glucose-6-phosphate dehydrogenase metabolism cytoplasm u Craven et al. 2006 protein n.d. Lichtenfels et al. 2002 d Craven et al. 2006 d Craven et al. 2006 P06744 Glucose-6-phosphate isomerase metabolism extracellular region d Craven et al. 2006 d Perroud et al. 2006 P00367 1 metabolism cytoplasm n.d. Magni et al. 2005 P08108 Heat shock cognate 70 kDa protein stress protein cytoplasm n.d. Lichtenfels et al. 2002 n.d. Perego et al. 2003 n.d. Sarto et al. 1997 P11142 Heat shock cognate 71 kDa protein stress cytoplasm n.d. Magni et al. 2005 P49448 Glutamate dehydrogenase 2 metabolism mitochondrion n.d. Magni et al. 2005 protein n.d. Perego et al. 2003 O94925 C, kidney isoform metabolism mitochondrion u Craven et al. 2006 P07900 Heat shock protein 90-a stress protein cytoplasm d Craven et al. 2006 P22352 peroxidase 3 stress extracellular region n.d. Magni et al. 2005 protein o Sarto et al. 1999 Q99729 Heterogeneous nuclear expression nucleus u Craven et al. 2006 P09211 Glutathione S- P metabolism cytoplasm n.d. Sarto et al. 1997 ribonucleoprotein A/B (isoform 2 or 3) control n.d. Perego et al. 2003 P09651 Heterogeneous nuclear expression multiple n.d. Hoffmann et al. 2005 h Lichtenfels et al. 2003 ribonucleoprotein A1 control compartment P48637 metabolism unknown u Craven et al. 2006 P22626 Heterogeneous nuclear expression nucleus d Craven et al. 2006 P78417 Glutathione transferase omega-1 metabolism cytoplasm n.d. Zhuang et al. 2006 ribonucleoprotein A2/B1 control Q9H4Y5 Glutathione transferase omega-2 metabolism cytoplasm d Poznanovic et al. 2005 P61978 Heterogeneous nuclear expression multiple n.d. Hoffmann et al. 2005 P08263 glutathione-S-transferase, alpha-class, metabolism cytoplasm d Perroud et al. 2006 ribonucleoprotein K control compartment omega 2 subunit P07910 Heteroproteinous nuclear ribonucleoproteinsexpression C1/C2 other n.d. Bloom et al. 2006 P04406 Glyceraldehyde -3-phosphate metabolism cytoplasm u Craven et al. 2006 control dehydrogenase (GAPDH) u Perroud et al. 2006 P49773 triad nucleotide binding protein signal multiple u Perroud et al. 2006 u Unwin et al. 2003 1 transduction compartment O14556 Glyceraldehyde-3-phosphate metabolism other u Poznanovic et al. 2005 P13747 HLA class I histocompatibility antigen, immune membrane / cell n.d. Hoffmann et al. 2005 dehydrogenase, testis-s... alpha chai... response surface P50440 amidinotransferase metabolism mitochondrion n.d. Magni et al. 2005 P01614 Ig kappa cahin V-II immune extracellular region d Poznanovic et al. 2005 d Perroud et al. 2006 response P11216 Glycogen phosphorylase, brain form metabolism unknown u Craven et al. 2006 P31939 IMP cyclohydrolase metabolism unknown u Craven et al. 2006 n.d. Magni et al. 2005 Q15181 Inorganic pyrophosphatase metabolism cytoplasm h Lichtenfels et al. 2003 Q92896 Golgi-apparatus protein 1 precursor signal golgi apparatus n.d. Zhuang et al. 2006 P48735 Isocitrate dehydrogenase (NADP) metabolism mitochondrion n.d. Magni et al. 2005 transduction P13645 10 proliferation cytoskeleton u Unwin et al. 2003 P62873 Guanine nucleotide-binding protein signal unknown d Unwin et al. 2003 P08727 Keratin, type I cytoskeletal 19 structural cytoskeleton n.d. Bloom et al. 2006 G(I)/G(S)/G(T) ... transduction molecule P35527 Keratin, type I cytoskeletal 9 structural cytoskeleton d Unwin et al. 2003 molecule P05787 Keratin, type II cytoskeletal 8 structural cytoskeleton d Craven et al. 2006 molecule u Kellner et al. 2002 ID Protein Family compartment Reg Paper ID Protein Family compartment Reg Paper TU TU P50053 Ketohexokinase metabolism cytoplasm d Hwa et al. 2005 P49821 NADH-ubiquinone 51 transport mitochondrion n.d. Magni et al. 2005 Q9ULJ1 KIAA1229 protein unknown unknown n.d. Seliger et al. 2003 kDa subunit protein P10072 Krueppel-related zinc finger protein (zinc fingerion binding 1 nucleus n.d. Zhuang et al. 2006 P28331 NADH-ubiquinone oxidoreductase 75 transport mitochondrion d Unwin et al. 2003 Q9P0G7 Lambda-crystallin metabolism unknown d Unwin et al. 2003 kDa subunit protein P02545 Lamin A/C proliferation nucleus n.d. Magni et al. 2005 P03886 NADH-ubiquinone oxidoreductase chain transport mitochondrion n.d. Sarto et al. 1997 n.d. Zhuang et al. 2006 1 protein P20700 Lamin B1 structural nucleus u Unwin et al. 2003 Q9BT67 NEDD4 family-interacting protein 1 signal membrane / cell n.d. Hoffmann et al. 2005 molecule n.d. Bloom et al. 2006 transduction surface Q03252 Lamin B2 other cytoplasm n.d. Magni et al. 2005 P40261 Nicotinamide N-methyltransferase other cytoplasm h Lichtenfels et al. 2003 Q9P2J5 Leucyl tRNA synthetase expression cytoplasm d Craven et al. 2006 Q9NR30 Nucleolar RNA helicase 2 expression nucleus n.d. Hoffmann et al. 2005 control control P00338 L-Lactate dehydrogenase A (LDH A) metabolism cytoplasm d Craven et al. 2006 P15531 Nucleoside diphosphate kinase A proliferation multiple d Craven et al. 2006 u Craven et al. 2006 (nm23) compartment u Perroud et al. 2006 P62937 Peptidyl-prolyl cis-trans isomerase A other cytoplasm d Craven et al. 2006 u Unwin et al. 2003 u Unwin et al. 2003 P07195 L-lactate dehydrogenase B chain metabolism cytoplasm d Unwin et al. 2003 P23284 Peptidyl-prolyl cis-trans isomerase B other ER u * Craven et al. 2006 d Unwin et al. 2003 Q3KQW3 Peptidylprolyl isomerase A, isoform 1 other cytoplasm u Poznanovic et al. 2005 O60449 Lymphocyte antigen 75 immune membrane / cell n.d. Hoffmann et al. 2005 P32119 Peroxiredoxin 2 (TSA) stress protein cytoplasm d Craven et al. 2006 response surface Q02809 Lysyl hydroxylase transport ER d Craven et al. 2006 P30044 Peroxiredoxin 5 stress mitochondrion u Craven et al. 2006 protein protein n.d. Magni et al. 2005 P40121 Macrophage-capping protein cell motility cytoplasm n.d. Zhuang et al. 2006 n.d. Perego et al. 2003 Q14764 Major vault protein other multiple n.d. Seliger et al. 2003 P30086 Phosphatidylethanolamine-binding expression cytoplasm n.d. Magni et al. 2005 compartment u Unwin et al. 2003 protein control n.d. Bloom et al. 2006 O95394 Phosphoacetylglucosamine mutase metabolism unknown n.d. Seliger et al. 2003 Q9UHC7 Makorin 1 other unknown n.d. Zhuang et al. 2006 Q16822 Phosphoenolpyruvate carboxykinase metabolism mitochondrion d Perroud et al. 2006 P11310 Medium-chain specific acyl-CoA metabolism mitochondrion d Unwin et al. 2003 d Unwin et al. 2003 dehydrogenase P35558 Phosphoenolpyruvate carboxykinase, metabolism cytoplasm d Unwin et al. 2003 O00264 Membrane-associated progesterone unknown membrane / n.d. Magni et al. 2005 cytosolic [GTP] cell surface Q01813 Phosphofructokinase isozyme C metabolism cytoplasm d Craven et al. 2006 P04731 Metallothionein-1A ion binding cytoplasm n.d. Zhuang et al. 2006 P36871 Phosphoglucomutase-1 metabolism cytoplasm u Craven et al. 2006 P80297 Metallothionein-1L ion binding unknown n.d. Zhuang et al. 2006 u Craven et al. 2006 Q02252 Methylmalonate-semialdehyde metabolism mitochondrion n.d. Magni et al. 2005 u Unwin et al. 2003 dehydrogenase P00558 Phosphoglycerate kinase 1 metabolism cytoplasm d Craven et al. 2006 P46821 Microtubule-associated protein 1B structural cytoskeleton n.d. Hoffmann et al. 2005 u Craven et al. 2006 molecule u Poznanovic et al. 2005 Q16891 Mitofilin membrane mitochondrion d Craven et al. 2006 u Unwin et al. 2003 n.d. Magni et al. 2005 P18669 Phosphoglycerate mutase 1 metabolism cytoplasm u Craven et al. 2006 P26038 Moesin cell motility cytoskeleton u Craven et al. 2006 n.d. Perego et al. 2003 n.d. Seliger et al. 2003 u Poznanovic et al. 2005 P05976 Myosin light chain 1, skeletal muscle structural cytoskeleton n.d. Sarto et al. 1997 u Unwin et al. 2003 isoform molecule n.d. Bloom et al. 2006 Q9P0J0 NADH dehydrogenase [ubiquinone] 1 multiple multiple a Alchanti et al. 2006 P22102 Phosphoribosylglycinamide metabolism cytoplasm u * Craven et al. 2006 alpha subcomplex subunit 13 (GRIM-19) compartment formyltransferase P78330 Phosphoserine phosphatase metabolism unknown u * Craven et al. 2006 227297 NADH dehydro-genase FeS protein transport mitochondrion n.d. Zhuang et al. 2006 Q96BW5 Phosphotriesterase-related gene metabolism unknown n.d. Zhuang et al. 2006 protein O60568 Procollagen-,2-oxoglutarate 5-dioxygenasemetabolism 3 ER n.d. Bloom et al. 2006 O75489 NADH-ubiquinone oxidoreductase transport mitochondrion u * Craven et al. 2006 P35232 Prohibitin stress protein membrane / cell n.d. Magni et al. 2005 protein surface Q16718 NADH-ubiquinone oxidoreductase transport mitochondrion n.d. Magni et al. 2005 P05165 Propionyl-CoA carboxylase alpha chain metabolism mitochondrion d Unwin et al. 2003 protein P51970 NADH-ubiquinone oxidoreductase 19 transport mitochondrion n.d. Magni et al. 2005 Q9UL46 proteasome (prosome, macropain) immune cytoplasm u Perroud et al. 2006 kDa subunit protein activator subunit 2 response n.d. Perego et al. 2003 Q06323 Proteasome activator subunit 1 immune cytoplasm n.d. Zhuang et al. 2006 O00217 NADH-ubiquinone oxidoreductase 23 stress protein mitochondrion n.d. Magni et al. 2005 response kDa subunit P25787 Proteasome subunit alpha type 2 metabolism cytoplasm n.d. Hoffmann et al. 2005 P19404 NADH-ubiquinone oxidoreductase 24 transport mitochondrion a Sarto et al. 1997 P60900 Proteasome subunit alpha type 6 metabolism cytoplasm n.d. Bloom et al. 2006 kDa subunit protein n.d. Magni et al. 2005 ID Protein Family compartment Reg Paper ID Protein Family compartment Reg Paper TU TU P28062 Proteasome subunit b immune cytoplasm u Craven et al. 2006 Q9P2R7 Succinate CoA [ADP forming] metabolism mitochondrion d Craven et al. 2006 response b chain, mitochondrial d Unwin et al. 2003 P30101 Protein disulfide isomerase A3 signal ER n.d. Magni et al. 2005 P51649 Succinate semialdehyde dehydrogenase metabolism mitochondrion d Unwin et al. 2003 transduction n.d. Perego et al. 2003 n.d. Bloom et al. 2006 P53597 succinate-CoA ligase, GDP-forming, metabolism mitochondrion d Perroud et al. 2006 P07237 Protein disulfide-isomerase multiple multiple n.d. Sarto et al. 1997 alpha subunit compartment n.d. Magni et al. 2005 P55809 Succinyl-CoA:3-ketoacid-coenzyme A metabolism mitochondrion n.d. Magni et al. 2005 n.d. Perego et al. 2003 transferase u Unwin et al. 2003 Q8NBJ7 Sulfatatase modifying factor 2 ion binding ER n.d. Magni et al. 2005 Q9H0A9 Putative protein C21orf56 unknown unknown n.d. Hoffmann et al. 2005 P00441 Superoxide dismutase [Cu-Zn] stress cytoplasm n.d. Perego et al. 2003 Q8TAP8 Putative uncharacterized protein unknown unknown n.d. Hoffmann et al. 2005 protein h Lichtenfels et al. 2003 C7orf47 P04179 Superoxide dismutase [Mn] stress mitochondrion n.d. Sarto et al. 1997 P11177 Pyruvate dehydro-genase component, ß metabolism mitochondrion n.d. Zhuang et al. 2006 protein n.d. Magni et al. 2005 P14618 Pyruvate kinase isozymes M1/M2 metabolism mitochondrion u Craven et al. 2006 n.d. Perego et al. 2003 u Perroud et al. 2006 u Poznanovic et al. 2005 u Poznanovic et al. 2005 u Unwin et al. 2003 u Unwin et al. 2003 u Unwin et al. 2003 Q15274 Quinolinate phosphoribosyltransferase signal unknown d Craven et al. 2006 o Sarto et al. 1999 transduction n.d. Bloom et al. 2006 P35241 Radixin structural cytoskeleton u Craven et al. 2006 Q15833 Syntaxin binding protein 2 (Unc18b) transport cytoplasm u Craven et al. 2006 molecule protein P46940 Ras GTPase-activating-like protein signal cytoskeleton n.d. Seliger et al. 2003 P78371 T-complex protein 1, beta subunit proliferation cytoplasm n.d. Magni et al. 2005 IQGAP1 transduction P48643 T-complex protein 1, e subunit metabolism cytoplasm d Craven et al. 2006 P23921 Ribonucleoside-diphosphate reductase expression cytoplasm n.d. Hoffmann et al. 2005 P50990 T-complex protein 1, y subunit metabolism cytoplasm d Craven et al. 2006 large subunit control P10599 Thioredoxin signal cytoplasm n.d. Sarto et al. 1997 P16083 Ribosyldihydronicotinamide transport cytoplasm d Unwin et al. 2003 transduction u Lichtenfels et al. 2003 dehydrogenase [quinone] protein Q16881 Thioredoxin reductase signal cytoplasm d Craven et al. 2006 Q9Y512 SAM50-like protein unknown mitochondrion u Craven et al. 2006 transduction P57086 SCAN domain-containing protein 1 expression nucleus n.d. Hoffmann et al. 2005 P30048 Thioredoxin-dependent peroxide expression mitochondrion n.d. Magni et al. 2005 control reductase control Q9NVA2 Septin 11 proliferation other u Craven et al. 2006 Q06830 Thioredoxin-dependent peroxide proliferation cytoplasm n.d. Magni et al. 2005 Q15019 Septin 2 (NEDD5) proliferation multiple d Craven et al. 2006 reductase 2 d Perroud et al. 2006 compartment u Craven et al. 2006 P19971 Thymidine phosphorylase multiple cytoskeleton u Unwin et al. 2003 Q96GA7 deyhdratase 2 metabolism unknown u Craven et al. 2006 u Unwin et al. 2003 Q9H288 Serologically defined breast expression unknown n.d. Hoffmann et al. 2005 Q01995 Transgelin ( SM22-alpha) proliferation cytoplasm u Klade et al. 2001 cancERantigen NY-BR-... control P55072 Transitional endoplasmic reticulum expression multiple n.d. Seliger et al. 2003 P02787 Serotransferrin ion binding extracellular region n.d. Magni et al. 2005 ATPase (vasolin containing protein, control compartment d Craven et al. 2006 P02768 Serum albumin transport extracellular region n.d. Sarto et al. 1997 VCP) protein n.d. Magni et al. 2005 P02766 Transthyretin transport extracellular region d Poznanovic et al. 2005 Q16836 Short chain 3-hydroxyacyl-CoA metabolism mitochondrion d Unwin et al. 2003 protein dehydrogenase P60174 Triosephosphate isomerase metabolism unknown n.d. Sarto et al. 1997 P16219 Short-chain specific acyl-CoA metabolism mitochondrion n.d. Sarto et al. 1997 u Craven et al. 2006 dehydrogenase n.d. Magni et al. 2005 Q14192 Skeletal muscle LIM-protein 3 expression nucleus n.d. Magni et al. 2005 n.d. Perego et al. 2003 control n.d. Perego et al. 2003 n.d. Bloom et al. 2006 Q9Y5X1 Sorting nexin-9 transport multiple n.d. Seliger et al. 2003 h Lichtenfels et al. 2003 protein compartment u Unwin et al. 2003 O75533 Splicing factor 3B subunit 1 expression nucleus n.d. Hoffmann et al. 2005 u Unwin et al. 2003 control u Unwin et al. 2003 P26368 Splicing factor U2AF 65 kDa expression nucleus u Craven et al. 2006 Q53HE2 Triosephosphate isomerase 1 variant metabolism unknown u Poznanovic et al. 2005 control P09493 Tropomyosin 1 alpha chain cell motility cytoskeleton n.d. Magni et al. 2005 P42224 STAT1-a expression nucleus d Craven et al. 2006 P06753 Tropomyosin alpha 3 chain cell motility cytoskeleton n.d. Magni et al. 2005 control n.d. Perego et al. 2003 P16949 Stathmin signal cytoplasm d Kellner et al. 2002 P67936 Tropomyosin alpha 4 chain cell motility cytoskeleton d Hwa et al. 2005 transduction n.d. Bloom et al. 2006 n.d. Magni et al. 2005 O95347 Structural maintenance of expression nucleus d Craven et al. 2006 P06753 Tropomyosin alpha-3 chain cell motility cytoskeleton ∅ Kellner et al. 2002 chromosome 2-like protein control P07951 Tropomyosin beta 2 chain structural cytoskeleton n.d. Magni et al. 2005 molecule ID Protein Family compartment Reg Paper ID Protein Family compartment Reg Paper TU TU Q25008 Tubulin alpha-1 chain (Alpha-tubulin 1) structural other n.d. Bloom et al. 2006 O75083 WD repeat protein 1 (AIP1) other cytoskeleton u Craven et al. 2006 molecule Q15072 Zinc finger expression nucleus n.d. Zhuang et al. 2006 Q71U36 Tubulin alpha-3 chain structural mitochondrion ∅ Kellner et al. 2002 control molecule ∅ Q9H4B7 Tubulin beta-1 chain structural cytoskeleton Kellner et al. 2002 *: comparison VHL + vs. VHL - RCC cell lines; ∅: not regulated; u: upregulated in RCC; d: downregulated in RCC; molecule n.d.: not determined; a: absent in RCC; o: only in RCC; h: heterogeneously regulated in RCC P68371 Tubulin beta-2 chain cell motility cytoskeleton n.d. Seliger et al. 2003 d Craven et al. 2006 u * Craven et al. 2006 n.d. Zhuang et al. 2006 P07437 Tubulin beta-5 chain cell motility cytoskeleton d Craven et al. 2006 u * Craven et al. 2006 n.d. Perego et al. 2003 u Perroud et al. 2006 O75347 Tubulin-specific chaperone A other cytoplasm n.d. Bloom et al. 2006 Q9UJW2 Tubulointerstitial nephritis antigen cell adhesion extracellular region n.d. Magni et al. 2005

P22695 Ubiquinol-cytochrome c reductase transport mitochondrion u * Craven et al. 2006 complex core protein 2 protein P07919 Ubiquinol-cytochrome C reductase transport mitochondrion n.d. Magni et al. 2005 complex protein 11 kDa protein P31930 Ubiquinol-cytochrome C reductase transport mitochondrion d Craven et al. 2006 core complex protein 1 protein n.d. Magni et al. 2005 d Unwin et al. 2003 P47985 Ubiquinol-cytocrome C reductase transport mitochondrion a Sarto et al. 1997 -sulfur subunit protein n.d. Magni et al. 2005 P62988 Ubiquitin multiple nucleus n.d. Sarto et al. 1997 P09936 Ubiquitin carboxyl-terminal metabolism cytoplasm u * Craven et al. 2006 isozyme L1 h Lichtenfels et al. 2003 h Seliger et al. 2007 Q92890 Ubiquitin fusion degradation protein 1 proliferation unknown u Craven et al. 2006 homolog Q5JV78 Ubiquitin specific protease 45 ion binding unknown n.d. Hoffmann et al. 2005 P22314 Ubiquitin-activating E1 expression unknown n.d. Seliger et al. 2003 control P61086 Ubiquitin-conjugating enzyme E2 expression cytoplasm u * Craven et al. 2006 control Q9NYL9 Ubiquitous tropomodulin structural cytoskeleton n.d. Magni et al. 2005 molecule n.d. Perego et al. 2003 P38606 Vacuolar ATPase metabolism membrane / cell u * Craven et al. 2006 surface Q12907 Vesicular integral-membrane protein VP- transport multiple n.d. Magni et al. 2005 36 protein compartment P08670 Vimentin cell motility cytoskeleton n.d. Bloom et al. 2006 d Craven et al. 2006 u Craven et al. 2006 u * Hwa et al. 2005 n.d. Magni et al. 2005 n.d. Perego et al. 2003 n.d. Seliger et al. 2003 n.d. Hoffmann et al. 2005 d Kellner et al. 2002 u Unwin et al. 2003 P21796 Voltage-dependent anion-selective transport mitochondrion n.d. Magni et al. 2005 channel protein 1 (VDAC-1) protein P45880 Voltage-dependent anion-selective transport mitochondrion n.d. Magni et al. 2005 channel protein 2 (VDAC-2) protein n.d. Perego et al. 2003 Supporting Information Figure 1. Classification of differentially expressed identified by classical proteomics The charts display the data sets following the classification of differentially expressed proteins in RCC identified by proteomics according to their functional protein classes. Distribution in (A) biopsy probes (198 proteins), (B) primary cell lines (85 proteins), (C) established cell lines (41 proteins), (D) all systems (262 proteins).

Supporting Information Figure 1

A) B) cell motility / structural cell motility / molecule structural 12% transport protein molecule expression stress protein transport protein 13% 8% control 12% 7% stress protein 5% expression 8% signal transduction control 7% 13% signal transduction 9% metabolism proliferation 8% proliferation 36% 4% other other metabolism 17% 12% 29%

C) D)

transport protein cell motility / transport protein cell motility / stress protein 7% structural 12% structural signal 7% molecule molecule expression transduction stress protein 9% control 17% 7% 5% 8% expression proliferation signal control 5% transduction 12% 8%

other proliferation 10% 5% metabolism other metabolism 35% 16% 37%