Supporting Information for Proteomics DOI /pmic

Supporting Information for Proteomics DOI 10.1002/pmic.200401063 Linda L. Manza, Sheryl L. Stamer, Amy-Joan L. Ham, Simona G. Codreanu and Daniel C. Liebler Sample preparation and digestion for proteomic analyses using spin filters ã 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de

Supplemental Table 1, "Sample preparation and digestion for proteomic analyses using spin filters", Manza et al. Cytosolic protein identifications Protein Accession # Peptide 14-3-3 protein beta/alpha gi 4507949 R.VISSIEQK.T 14-3-3 protein beta/alpha K.AVTEQGHELSNEER.N 14-3-3 protein tau gi 5803227 K.TELIQK.A 26S proteinase chain 5a gi 2134662 R.LQAQQDAVNIVC*HSK.T 40S ribosomal protein S10 gi 4506679 K.HPELADK.N 40S ribosomal protein S12 gi 133742 K.LGEWVGLC*K.I 40S ribosomal protein S12 K.TALIHDGLAR.G 40S ribosomal protein S18 gi 6755368 K.YSQVLANGLDNK.L 40S ribosomal protein S23 gi 4506701 K.ANPFGGASHAK.G 40S ribosomal protein S3 gi 15718687 K.GGKPEPPAMPQPVPTA.- 40S ribosomal protein S3 K.KPLPDHVSIVEPK.D 40S ribosomal protein S6 gi 6677809 K.QGVLTHGR.V 40S ribosomal protein S7 gi 4506741 R.TLTAVHDAILEDLVFPSEIVGK.R 40S ribosomal protein S8 gi 4506743 K.ISSLLEEQFQQGK.L 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase gi 20127454 R.YGMNPHQTPAQLYTLQPK.L 60 kda heat shock protein (Hsp60) gi 129379 R.TALLDAAGVASLLTTAEVVVTEIPK.E 60 kda heat shock protein (Hsp60) K.LVQDVANNTNEEAGDGTTTATVLAR.S 60 kda heat shock protein (Hsp60) R.ALMLQGVDLLADAVAVTMGPK.G 60 kda heat shock protein (Hsp60) R.IQEIIEQLDVTTSEYEK.E 60 kda heat shock protein (Hsp60) K.VGGTSDVEVNEK.K 60 kda heat shock protein (Hsp60) K.VGEVIVTK.D 60 kda heat shock protein (Hsp60) K.LSDGVAVLK.V 60 kda heat shock protein (Hsp60) R.VTDALNATR.A 60 kda heat shock protein (Hsp60) R.TVIIEQSWGSPK.V 60 kda heat shock protein (Hsp60) K.LSDGVAVLK.V 60 kda heat shock protein (Hsp60) R.GYISPYFINTSK.G 60 kda heat shock protein (Hsp60) K.QSKPVTTPEEIAQVATISANGDK.E 60S acidic ribosomal protein P0 gi 4506667 K.AFLADPSAFVAAAPVAAATTAAPAAAAAPAK.V 60S acidic ribosomal protein P1 R.GHLENNPALEK.L 60S acidic ribosomal protein P1 gi 4506669 K.AAGVNVEPFWPGLFAK.A 60S acidic ribosomal protein P2 gi 4506671 R.YVASYLLAALGGNSSPSAK.D 60S acidic ribosomal protein P2 K.VISELNGK.N

60S ribosomal protein gi 4506597 K.HSGNITFDEIVNIAR.Q 60S ribosomal protein L13a gi 6912634 R.LAHEVGWK.Y 60S ribosomal protein L14 gi 7513316 K.GTAAAAAAAAAAAAAAAK.V 60S ribosomal protein L18a gi 11415026 R.AHSIQIMK.V 60S ribosomal protein L28 gi 13904866 R.SQKPVMVK.R 60S ribosomal protein L29 gi 4506629 K.AQAAAPASVPAQAPK.R 60S ribosomal protein L30 gi 4506631 K.TGVHHYSGNNIELGTAC*GK.Y 60S ribosomal protein L31 gi 4506633 R.IHGVGFK.K 60S ribosomal protein L4 gi 16579885 K.AAAAAAALQAK.S accessory protein BAP31 K.VNLQNNPGAMEHFHMK.L accessory protein BAP31 gi 5031675 K.GAAVDGGK.L acetyl-coenzyme A acetyltransferase 1 gi 4557237 R.TPIGSFLGSLSLLPATK.L acetyl-coenzyme A acetyltransferase 2 gi 5174389 R.ATVAPEDVSEVIFGHVLAAGC*GQNPVR.Q Acidic leucine-rich nuclear phosphoprotein 32 gi 5454088 K.LPNLTHLNLSGNK.L Acidic leucine-rich nuclear phosphoprotein 32 gi 6912604 R.VSGGLEVLAEK.C aconitase 2 gi 4501867 K.DSSGQHVDVSPTSQR.L Actin gi 71611 K.EITALAPSTMK.I Actin K.YPIEHGIITNWDDMEK.I Actin R.HQGVMVGMGQK.D actinin, alpha 4 gi 12025678 R.QFASQANVVGPWIQTK.M Acyl-CoA-binding protein (ACBP) gi 118276 K.TKPSDEEMLFIYGHYK.Q adenylate kinase 2 isoform b gi 7524346 R.AVLLGPPGAGK.G adenylate kinase 2 isoform b R.LAENFC*VC*HLATGDMLR.A adenylate kinase 3 gi 8051579 R.IAQNFGLQHLSSGHFLR.E adenylyl cyclase-associated protein gi 5453595 K.AGAAPYVQAFDSLLAGPVAEYLK.I adenylyl cyclase-associated protein R.SALFAQINQGESITHALK.H Aldehyde dehydrogenase family 7 member A1 gi 25108887 R.VGNPWDPNVLYGPLHTK.Q Aldose Reductase gi 576362 R.NLVVIPK.S Aldose Reductase K.YKPAVNQIEC*HPYLTQEK.L Alpha-actinin 1 gi 112959 K.YLDIPK.M Alpha-actinin1 R.LDHLAEK.F antigen identified by monoclonal antibody Ki-67 gi 19923217 K.QESGSEIHVEVK.A Antioxidant protein 2 (1-Cys peroxiredoxin) gi 4758638 R.VATPVDWK.D anti-sigma cross-reacting protein homolog I gi 2134764 K.ITDLANLSAANHDAAIFPGGFGAAK.N aspartate aminotransferase 2 precursor gi 4504069 R.ISVAGVTSSNVGYLAHAIHQVTK.- ATPase, Na+/K+ transporting, alpha 1 polypeptide gi 21361181 R.AVFQANQENLPILK.R

ATPase, Na+/K+ transporting, alpha 1 polypeptide K.IVEIPFNSTNK.Y ATPB_HUMAN ATP synthase beta chain, mitochondrial precursor gi 114549 R.FLSQPFQVAEVFTGHMGK.L ATP-citrate (pro-s-)-lyase (Citrate cleavage enzyme) ATP-citrate (pro-s-)-lyase (Citrate cleavage enzyme) gi 20141248 R.SGGMSNELNNIISR.T R.LLQDHPWLLSQNLVVKPDQLIK.R ATP-citrate (pro-s-)-lyase (Citrate cleavage enzyme) K.GVTIIGPATVGGIKPGC*FK.I autoantigen La gi 10835067 K.VQFQGK.K beta-tubulin - human gi 2119276 K.NSSYFVEWIPNNVK.T beta-tubulin - human R.ISVYYNEATGGK.Y beta-tubulin - human R.IMNTFSVVPSPK.V beta-tubulin - human K.LAVNMVPFPR.L beta-tubulin - human R.SGPFGQIFRPDNFVFGQSGAGNNWAK.G beta-tubulin - human R.LHFFMPGFAPLTSR.G biliverdin reductase gi 7512303 K.SGSLENVPNVGVNK.N calreticulin gi 913148 -.EPAVYFK.E calreticulin precursor gi 4757900 K.IDDPTDSKPEDWDKPEHIPDPDAK.K calumenin precursor gi 4502551 R.VHHEPQLSDK.V carbonyl reductase 1 gi 4502599 R.GQAAVQQLQAEGLSPR.F cathepsin D preproprotein [Homo sapiens] gi 4503143 K.LLDIAC*WIHHK.Y Cdc42 gi 2624582 K.QKPITPETAEK.L Chain A, Human Mitochondrial Aldehyde Dehydrogenase Complex gi 6137677 K.LGPALATGNVVVMK.V chaperonin containing TCP1, subunit 4 (delta) gi 5453605 R.FSNISAAK.A chaperonin containing TCP1, subunit 6A (zeta 1) gi 4502643 K.DGNVLLHEMQIQHPTASLIAK.V chaperonin containing TCP1, subunit 7 (eta) gi 5453607 K.LLDVVHPAAK.T chromosome 21 open reading frame 33 gi 5031691 K.NLSTFAVDGK.D citrate synthase precursor gi 4758076 K.IVPNVLLEQGK.A clathrin heavy chain gi 4758012 R.LAELEEFINGPNNAHIQQVGDR.C cofilin 1 (non-muscle) gi 5031635 K.LGGSAVISLEGKPL.- cofilin 1 (non-muscle) K.VFNDMK.V COX17 homolog, cytochrome c oxidase assembly protein gi 5031645 K.GEEHC*GHLIEAHK.E creatine kinase-b gi 21536286 K.TDLNPDNLQGGDDLDPNYVLSSR.V

creatine kinase-b R.FC*TGLTQIETLFK.S creatine kinase-b K.SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR.D creatine kinase-b R.FPAEDEFPDLSAHNNHMAK.V cyclophilin A gi 1041969 -.VNPTVFFDIAVDGEPLGR.X Cyclophilin A gi 2981731 K.HTGPGILSMANAGPNTNGSQFFIC*TAK.T Cyclophilin B gi 118090 K.HVVFGK.V cystatin B gi 4503117 R.VFQSLPHENKPLTLSNYQTNK.A cytosolic malate dehydrogenase gi 5174539 K.NVIIWGNHSSTQYPDVNHAK.V D-3-phosphoglycerate dehydrogenase gi 23308577 K.NAGNC*LSPAVIVGLLK.E D-3-phosphoglycerate dehydrogenase K.GTIQVITQGTSLK.N D-3-phosphoglycerate dehydrogenase R.ALVDHENVISC*PHLGASTK.E D-dopachrome tautomerase gi 7512375 R.LC*AAAASILGKPADR.V desmoplakin (DPI, DPII) gi 4758200 R.NNYDEEIISLK.N Dihydrolipoamide succinyltransferase gi 1709442 K.AKPAEAPAAAAPK.A DnaJ (Hsp40) homolog, subfamily A, member 1 gi 4504511 R.IHQIGPGMVQQIQSVC*MEC*QGHGER.I dnak-type molecular chaperone HSP70-2 gi 2119728 K.SINPDEAVAYGAAVQAAILMGDK.S dnak-type molecular chaperone HSP70-2 K.SENVQDLLLLDVAPLSLGLETAGGVMTALIK.R dnak-type molecular chaperone HSPA1L gi 2119712 K.ELEQVC*NPIISGLYQGAGGPGPGGFGAQGPK.G dnak-type molecular chaperone HSPA1L K.EIAEAYLGYPVTNAVITVPAYFNDSQR.Q dnak-type molecular chaperone HSPA1L K.AFYPEEISSMVLTK.M dnak-type molecular chaperone HSPA1L K.FGDPVVQSDMK.H dnak-type molecular chaperone HSPA1L K.SAVEDEGLK.G dnak-type molecular chaperone HSPA1L K.NQVALNPQNTVFDAK.R dnak-type molecular chaperone HSPA1L K.LLQDFFNGR.D dnak-type molecular chaperone HSPA1L K.QTQIFTTYSDNQPGVLIQVYEGER.A dnak-type molecular chaperone HSPA1L K.NALESYAFNMK.S dnak-type molecular chaperone HSPA1L K.AFYPEEISSMVLTK.M dnak-type molecular chaperone HSPA1L K.AQIHDLVLVGGSTR.I dnak-type molecular chaperone HSPA1L R.LVNHFVEEFK.R dnak-type molecular chaperone HSPA1L K.HWPFQVINDGDKPK.V dnak-type molecular chaperone HSPA-2 gi 7441839 K.VQVEYK.G dystrophin gi 87340 R.LETELK.E E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K) gi 119040 K.SC*GELFDSLNLGHQALFQEK.V E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K) R.LLLLSSVRPAIIPTEEQQQQQEEAR.R electron-transfer-flavoprotein, beta polypeptide gi 4503609 K.VETTEDLVAK.L electron-transfer-flavoprotein, beta polypeptide K.IEVIKPGDLGVDLTSK.L Elongation factor 1-alpha 1 (EF-1-alpha-1) gi 4503471 K.IGGIGTVPVGR.V

Elongation factor 1-alpha 1 (EF-1-alpha-1) R.YEEIVK.E Elongation factor 1-alpha 1 (EF-1-alpha-1) R.VETGVLKPGMVVTFAPVNVTTEVK.S Elongation factor 1-alpha 1 (EF-1-alpha-1) K.DGNASGTTLLEALDC*ILPPTRPTDKPLR.L Elongation factor 2 (EF-2) gi 4503483 R.YVEPIEDVPC*GNIVGLVGVDQFLVK.T Elongation factor 2 (EF-2) K.NPADLPK.L Elongation factor 2 (EF-2) R.YFDPANGK.F Elongation factor 2 (EF-2) R.VFSGLVSTGLK.V Elongation factor 2 (EF-2) R.GHVFEESQVAGTPMFVVK.A Elongation factor 2 (EF-2) R.NMSVIAHVDHGK.S enolase 1; phosphopyruvate hydratase gi 4503571 R.GNPTVEVDLFTSK.G enolase 1; phosphopyruvate hydratase R.IEEELGSK.A enolase 1; phosphopyruvate hydratase K.FTASAGIQVVGDDLTVTNPK.R enolase 1; phosphopyruvate hydratase K.LAMQEFMILPVGAANFR.E enolase 1; phosphopyruvate hydratase R.GNPTVEVDLFTSK.G enolase 1; phosphopyruvate hydratase R.HIADLAGNSEVILPVPAFNVINGGSHAGNK.L enolase 1; phosphopyruvate hydratase K.LAQANGWGVMVSHR.S enolase alpha, lung-specific gi 7657062 K.DATNVGDEGGFAPNILENK.E enolase alpha, lung-specific K.VNQIGSVTESLQAC*K.L enolase alpha, lung-specific R.IGAEVYHNLK.N eukaryotic translation elongation factor 1 gi 4758862 R.QIPVLQTNNGPSLTGLTTIAAHLVK.Q Eukaryotic translation initiation factor 4 gamma gi 1170510 K.IHNAENIQPGEQK.Y eukaryotic translation initiation factor 5A; eif5a gi 4503545 K.VHLVGIDIFTGK.K Ezrin (p81) (Cytovillin) gi 119717 K.FVIKPIDK.K F-actin capping protein alpha-1 subunit; Cap Z gi 5453597 K.IIENAENEYQTAISENYQTMSDTTFK.A F-actin capping protein alpha-1 subunit; Cap Z R.EGAAHAFAQYNMDQFTPVK.I F-actin capping protein beta subunit gi 13124696 K.NLSDLIDLVPSLC*EDLLSSVDQPLK.I Familial Als Mutant G37r Cuznsod gi 2982080 R.HVGDLGNVTADK.D Familial Als Mutant G37r Cuznsod R.TLVVHEK.A filamin 1 (actin-binding protein-280) gi 4503745 R.NGHVGISFVPK.E fructose-1,6-bisphosphate aldolase A gi 253292 -.PYQYPALTPEQK.K fumarate hydratase gi 68293 R.THTQDAVPLTLGQEFSGYVQQVK.Y fumarate hydratase K.LHDALDAK.S fumarate hydratase K.IPVHPNDHVNK.S Gamma enolase gi 5803011 R.HIAQLAGNSDLILPVPAFNVINGGSHAGNK.L glioblastoma amplified sequence gi 4503937 K.LQFHNVKPEC*LEAYNK.I glucose phosphate isomerase, GPI gi 189238 K.TLAQLNPESSLFIIASK.T glucose phosphate isomerase, GPI R.SNTPILVDGK.D

glucose phosphate isomerase, GPI R.VWYVSNIDGTHIAK.T glucose phosphate isomerase, GPI R.VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK.M glucose-regulated protein precursor gi 16507237 K.NQLTSNPENTVFDAK.R glucose-regulated protein precursor R.ITPSYVAFTPEGER.L glucose-regulated protein precursor R.LIGDAAK.N glucose-regulated protein precursor K.TKPYIQVDIGGGQTK.T glucose-regulated protein precursor K.VTHAVVTVPAYFNDAQR.Q glucose-regulated protein precursor K.VLEDSDLK.K glutamyl-prolyl trna synthetase gi 4758294 K.NPEVGLKPVWYSPK.V Glyceraldehyde 3-phosphate dehydrogenase gi 120643 K.IISNASC*TTNC*LAPLAK.V glyceraldehyde-3-phosphate dehydrogenase gi 7669492 R.VPTANVSVVDLTC*R.L glyceraldehyde-3-phosphate dehydrogenase R.GALQNIIPASTGAAK.A glyceraldehyde-3-phosphate dehydrogenase R.VIISAPSADAPMFVMGVNHEK.Y glyceraldehyde-3-phosphate dehydrogenase K.VIHDNFGIVEGLMTTVHAITATQK.T glyceraldehyde-3-phosphate dehydrogenase K.AGAHLQGGAK.R glyoxalase I gi 5729842 K.ATLELTHNWGTEDDATQSYHNGNSDPR.G GTP-binding nuclear protein RAN (TC4) (Ran GTPase) gi 5453555 K.LVLVGDGGTGK.T GTP-binding nuclear protein RAN (TC4) (Ran GTPase) K.NLQYYDISAK.S heat shock 10kD protein 1 (chaperonin 10) gi 4504523 K.VLLPEYGGTK.V heat shock 10kD protein 1 (chaperonin 10) K.VLQATVVAVGSGSK.G Heat shock 70 kda protein 1 (HSP70.1) gi 462325 K.AAAIGIDLGTTYSC*VGVFQHGK.V HEAT SHOCK 70 KDA PROTEIN 4 gi 6226869 K.LNLQNK.Q heat shock 70kDa protein 6 (HSP70B') gi 4504515 R.TTPSYVAFTDTER.L heat shock 70kDa protein 6 (HSP70B') R.IINEPTAAAIAYGLDR.R heat shock 70kDa protein 6 (HSP70B') K.DNNLLGR.F heat shock 70kDa protein 6 (HSP70B') R.VEILANDQGNR.T heat shock 70kDa protein 6 (HSP70B') R.TTPSYVAFTDTER.L heat shock 70kDa protein 6 (HSP70B') K.ATAGDTHLGGEDFDNR.L heat shock 70kDa protein 8 isoform 1 gi 5729877 K.SINPDEAVAYGAAVQAAILSGDK.S heat shock 70kDa protein 9B precursor gi 24234688 R.VEAVNMAEGIIHDTETK.M heat shock 70kDa protein 9B precursor R.QAVTNPNNTFYATK.R heat shock 70kDa protein 9B precursor R.ASNGDAWVEAHGK.L heat shock protein 90-beta gi 72222 K.YIDQEELNK.T heat shock protein 90-beta R.TLTLVDTGIGMTK.A heat shock protein 90-beta K.HLEINPDHPIVETLR.Q

Heat shock protein HSP 90-alpha (HSP 86) gi 123678 K.LGIHEDSQNR.K Heat shock protein HSP 90-alpha (HSP 86) K.HLEINPDHSIIETLR.Q Heat shock protein HSP 90-alpha (HSP 86) K.HIYYITGETK.D Heat-shock protein 105 kda gi 2495344 R.GC*ALQC*AILSPAFK.V Heat-shock protein 105 kda K.IEVPLYSLLEQTHLK.V Heat-shock protein 105 kda R.NHAAPFSK.V histone-binding protein gi 477321 K.HLVMGDIPAAVNAFQEAASLLGK.K hnrnp A2/B1, isoform B1 gi 14043072 R.EESGKPGAHVTVK.K hnrnp C-like protein gi 420052 K.YHNVGLSK.C hnrnp K isoform b gi 13384620 R.IITITGTQDQIQNAQYLLQNSVK.Q hnrnp U gi 284156 K.SSGPTSLFAVTVAPPGAR.Q Human Carbonic Anhydrase gi 2098448 K.VGSAKPGLQK.V HUMAN Elongation factor 1-delta gi 25453472 R.GVVQELQQAISK.L HUMAN Elongation factor 1-delta K.KPALVAK.S HUMAN Glutathione S-transferase P (GSTP1-1) gi 4504183 K.ALPGQLKPFETLLSQNQGGK.T Human Heart L-Lactate Dehydrogenase gi 13786847 K.SLADELALVDVLEDK.L Human Heart L-Lactate Dehydrogenase K.GEMMDLQHGSLFLQTPK.I Human Heart L-Lactate Dehydrogenase R.GLTSVINQK.L Human Heart L-Lactate Dehydrogenase K.FIIPQIVK.Y Human Muscle Aldolase gi 229674 K.GVVPLAGTNGETTTQGLDGLSER.C Human Muscle Aldolase K.GILAADESTGSIAK.R Human Muscle Aldolase K.DGADFAK.W Human Muscle Aldolase R.ALANSLAC*QGK.Y Human Muscle Aldolase K.IGEHTPSALAIMENANVLAR.Y Human Muscle Aldolase K.ALSDHHIYLEGTLLKPNMVTPGHAC*TQK.F Human Muscle L-Lactate Dehydrogenase gi 13786849 K.DYNVTANSK.L Human P32, Acidic Mitochondrial Matrix Protein gi 4930073 K.VEEQEPELTSTPNFVVEVIK.N human PGP 9.5 homologue gi 236733 -.MQLKPMEXDPEMLNK.V Human Platelet Profilin gi 3891601 K.TFVNITPAEVGVLVGK.D Human Platelet Profilin R.SSFYVNGLTLGGQK.C Human Platelet Profilin K.STGGAPTFNVTVTK.T HUMAN Putative GTP-binding protein gi 25453240 K.IHTDFEK.G HUMAN Stress-induced-phosphoprotein 1 gi 5803181 K.NPVIAQK.I HUMAN T-complex protein 1, epsilon subunit gi 24307939 R.AFADALEVIPMALSENSGMNPIQTMTEVR.A HUMAN T-complex protein 1, epsilon subunit K.IAILTC*PFEPPKPK.T HUMAN T-complex protein 1, epsilon subunit R.VAIEHLDK.I HUMAN T-complex protein 1, gamma subunit gi 20455521 R.AVAQALEVIPR.T

HUMAN T-complex protein 1, gamma subunit R.NVLLDPQLVPGGGASEMAVAHALTEK.S HUMAN T-complex protein 1, gamma subunit R.EIQVQHPAAK.S hypothetical protein DKFZp434K0126.1 gi 11265337 K.AIANEC*QANFISIK.G lactate dehydrogenase, LDH-A gi 237993 R.NVNIFK.F laminin receptor 1 (67kD, ribosomal protein SA) gi 9845502 R.ADHQPLTEASYVNLPTIALC*NTDSPLR.Y macrophage myristoylated alanine-rich C kinase substrate gi 13491174 R.GDVTAEEAAGASPAK.A malate dehydrogenase gi 7431153 K.VIVVGNPANTNC*LTASK.S Malate dehydrogenase, mitochondrial precursor gi 6648067 K.VAVLGASGGIGQPLSLLLK.N Malate dehydrogenase, mitochondrial precursor R.IQEAGTEVVK.A Malate dehydrogenase, mitochondrial precursor R.LTLYDIAHTPGVAADLSHIETK.A methionine adenosyltransferase II, alpha gi 5174529 K.TC*NVLVALEQQSPDIAQGVHLDR.N methionine--trna ligase gi 2135628 K.TSPKPAVVETVTTAKPQQIQALMDEVTK.Q mitochondrial short-chain enoyl-coenzyme A hydratase 1 gi 12707570 K.IC*PVETLVEEAIQC*AEK.I mitochondrial short-chain enoyl-coenzyme A hydratase 2 K.NNTVGLIQLNRPK.A murine mammary tumor integration site 6 gi 4503521 R.MLFDYLADK.H myc far upstream element-binding protein gi 1082624 K.AGLVIGK.G myristoylated alanine-rich PKC substrate (MARCKS) gi 11125772 K.GEPAAAAAPEAGASPVEK.E myristoylated alanine-rich PKC substrate (MARCKS) K.GEAAAERPGEAAVASSPSK.A N8 gene product long isoform gi 1488414 K.ASAAFSSVGSVITK.K N-acetylglucosamine-specific receptor 1 precursor gi 627551 R.INEILSNALK.R nef protein [Human immunodeficiency virus 1] gi 23954662 R.ENSSLLHPICQHGMDDEER.E neuropolypeptide h3 gi 913159 K.WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK.V NKEF-B homolog/thiol-dependent antioxidant protein gi 1488366 -.IGKPAPDFK.A N-Terminal Actin-Crosslinking Domain From Human Fimbrin gi 2780868 K.AYFHLLNQIAPK.G nuclease sensitive element-binding protein 1 gi 423015 K.GAEAANVTGPGGVPVQGSK.Y nucleolin gi 4885511 K.VEGTEPTTAFNLFVGNLNFNK.S Nucleoside diphosphate kinase A (NDK A) gi 4557797 R.VMLGETNPADSKPGTIR.G Nucleoside diphosphate kinase A (NDK A) R.NIIHGSDSVESAEK.E nucleosomal binding protein 1 gi 13540523 K.ITEAPASEK.E

ORF 56 gi 18846023 K.EQLLVSR.H ornithine aminotransferase, OAT gi 1168056 R.WLAVDYENVRPDIVLLGK.A oxysterol binding protein gi 4505531 R.GATVLPANTPGNVGSGK.D PAI-1 mrna-binding protein gi 7661626 R.RPDQQLQGEGK.I PAI-1 mrna-binding protein R.KPNEGADGQWK.K PDZ and LIM domain 1 gi 13994151 K.VAASIGNAQK.L peptidylprolyl cis-trans isomerase gi 4503729 K.GEHSIVYLKPSYAFGSVGK.E peptidylprolyl isomerase F (cyclophilin F) gi 5031987 R.VIPSFMC*QAGDFTNHNGTGGK.S peroxiredoxin 1 gi 4505591 K.ATAVMPDGQFK.D peroxiredoxin 1 R.LVQAFQFTDK.H peroxiredoxin 1 K.LNC*QVIGASVDSHFC*HLAWVNTPK.K peroxiredoxin 1 K.HGEVC*PAGWKPGSDTIKPDVQK.S peroxiredoxin 1 K.IGHPAPNFK.A Peroxiredoxin 2 gi 2507169 R.GLFIIDGK.G Peroxiredoxin 2 K.ATAVVDGAFK.E peroxiredoxin 3 gi 5802974 K.AFQYVETHGEVC*PANWTPDSPTIKPSPAASK.E peroxiredoxin 3 K.NGGLGHMNIALLSDLTK.Q Peroxiredoxin 4 (Prx-IV) (Thioredoxin peroxidase) gi 5453549 R.GLFIIDDK.G peroxiredoxin 5 gi 6912238 K.ALNVEPDGTGLTC*SLAPNIISQL.- peroxiredoxin 5 K.GVLFGVPGAFTPGC*SK.T Peroxisomal acyl-coenzyme A thioester hydrolase 2 gi 12644291 R.GLAPEQPVTLR.A Phenylalanyl-tRNA synthetase beta chain gi 12643818 K.AVHISNPK.T phosphoglycerate kinase 1 gi 4505763 K.AC*ANPAAGSVILLENLR.F phosphoglycerate kinase 1 R.GC*ITIIGGGDTATC*C*AK.W phosphoglycerate kinase 1 K.AC*ANPAAGSVILLENLR.F phosphoglycerate kinase 1 K.ALESPERPFLAILGGAK.V phosphoglycerate kinase 1 K.VSHVSTGGGASLELLEGK.V phosphoglycerate kinase 1 R.AHSSMVGVNLPQK.A phosphoglycerate kinase 2 gi 20270259 K.LGDVYVNDAFGTAHR.A phosphoglycerate mutase 1 gi 4505753 K.NLKPIKPMQFLGDEETVR.K Phosphoglycerate mutase 2 gi 130353 K.AMEAVAAQGK.A Phosphoglycerate mutase 2 R.VLIAAHGNSLR.G phosphoglycerate mutase processed protein gi 26006838 R.ALPFWNEEIVPQIK.E phosphoglycerate mutase processed protein R.SYDVPPPPMEPDHPFYSNISK.D phosphopyruvate hydratase human gi 105934 R.AAVPSGASTGIYEALELR.D phosphopyruvate hydratase human K.VNQIGSVTESIQAC*K.L

phosphopyruvate hydratase human R.SGETEDTFIADLVVGLC*TGQIK.T phosphoribosylaminoimidazole carboxylase gi 5453539 K.ITSC*IFQLLQEAGIK.T Phosphoribosylformylglycinamidine synthase gi 12230514 R.LNFSTPTSTNIVSVC*R.A phosphorylase kinase, alpha 1 (muscle) gi 4505779 K.QEIITK.L phosphoserine aminotransferase gi 17402893 K.FGTINIVHPK.L plastin 3 precursor gi 7549809 K.TISSSLAVVDLIDAIQPGC*INYDLVK.S pol protein [Human immunodeficiency virus type 1] gi 9938495 K.IEEQLK.E poly(rc)-binding protein 3 gi 10092617 R.LVVPASQC*GSLIGK.G potassium inwardly-rectifying channel J1 isoform a gi 4504837 K.LCLLIR.V prefoldin 2 gi 12408675 K.GAVSAEQVIAGFNR.L probable protein 55.11 homolog p67 gi 7513235 R.VGQAVDVVGQAGKPK.T procollagen-proline gi 20070125 R.TGPAATTLPDGAAAESLVESSEVAVIGFFK.D procollagen-proline R.NNFEGEVTK.E procollagen-proline K.DHENIVIAK.M procollagen-proline K.HNQLPLVIEFTEQTAPK.I profilin 2 isoform a gi 16753215 K.SQGGEPTYNVAVGR.A progesterone membrane binding protein gi 5453916 K.VFDVTK.G programmed cell death 5 gi 4759224 R.LSNLALVKPEK.T Proliferation-associated protein 2G4 gi 13632817 K.VAHSFNC*TPIEGMLSHQLK.Q Protein CGI-126 (Protein HSPC155) gi 6831734 R.VVSEIPVLK.T Protein disulfide isomerase A6 precursor gi 5031973 R.GSTAPVGGGAFPTIVER.E protein disulfide isomerase related protein gi 4758304 R.TQEEIVAK.V protein disulfide isomerase related protein K.FIEEHATK.L protein disulfide-isomerase gi 2135267 K.YGVSGYPTLK.I protein kinase C inhibitor protein-1 gi 4507953 K.GIVDQSQQAYQEAFEISK.K protein kinase C inhibitor protein-1 R.VVSSIEQK.T protein kinase C substrate gi 4506077 K.LGGSPTSLGTWGSWIGPDHDK.F purine nucleoside phosphorylase gi 4557801 K.ANHEEVLAAGK.Q Putative nucleoside diphosphate kinase (NDK) (NDP kinase) gi 3914116 R.NIIHGSDSVK.S pyrophosphatase (inorganic) gi 11056044 K.GISC*MNTTLSESPFK.C Pyruvate kinase-3 gi 4505839 R.AEGSDVANAVLDGADC*IMLSGETAK.G Pyruvate kinase-3 K.GADFLVTEVENGGSLGSK.K Pyruvate kinase-3 K.GVNLPGAAVDLPAVSEK.D Pyruvate kinase-3 R.GDLGIEIPAEK.V

Pyruvate kinase-3 Pyruvate kinase-3 Pyruvate kinase-3 Pyruvate kinase-3 Pyruvate kinase-3 R.TATESFASDPILYRPVAVALDTK.G R.NTGIIC*TIGPASR.S K.VFLAQK.M R.AGKPVIC*ATQMLESMIK.K R.LNFSHGTHEYHAETIK.N ras-related C3 botulinum toxin substrate 1 isoform gi 9845511 K.LTPITYPQGLAMAK.E replication protein A1, 70kDa gi 4506583 K.AAGPSLSHTSGGTQSK.V replication protein A3, 14kDa gi 4506587 R.INAGMLAQFIDKPVC*FVGR.L ribosomal protein HL6, cytosolic gi 423071 K.VLATVTKPVGGDK.N ribosomal protein L13, cytosolic gi 542770 K.LATQLTGPVMPVR.N RNA-binding protein regulatory subunit gi 6005749 K.EGPYDVVVLPGGNLGAQNLSESAAVK.E RNA-binding protein regulatory subunit K.VTTHPLAK.D SEB4B protein - human gi 481241 R.FVNVVPTFGK.K SECIS binding protein 2 gi 21359955 K.NVSIPSSEALSSDPSYNK.E secretory carrier membrane protein 1 gi 16445416 K.TVQTAAANAASTAASSAAQNAFK.G Ser/Thr protein phosphatase 2A (PP2A, subunit A, PR65-alpha) gi 231443 R.AISHEHSPSDLEAHFVPLVK.R similar to tubulin alpha 1 [Mus musculus] gi 20903441 K.AYHEQLSVAEITNAC*FEPANQMVK.C spectrin alpha chain, nonerythroid gi 88622 R.ELELQK.E sperm surface protein gi 7513346 K.ERPISLGIFPLPAGDGLLTPDAQK.G stromal cell-derived factor 2-like 1 gi 11545743 R.LTHVLTGK.N Talin 1 gi 14916725 K.GTEWVDPEDPTVIAENELLGAAAAIEAAAK.K Talin 1 K.AVSSAIAQLLGEVAQGNENYAGIAAR.D Talin 1 R.ELVAQGK.V Talin 1 R.GVGAAATAVTQALNELLQHVK.A Talin 1 R.LASEAKPAAVAAENEEIGSHIK.H tankyrase, TRF1-interacting ankyrin-related gi 13376842 K.GANINEK.T T-complex protein 1, alpha subunit gi 135538 R.SLLVIPNTLAVNAAQDSTDLVAK.L T-complex protein 1, alpha subunit R.SQNVMAAASIANIVK.S T-complex protein 1, theta subunit (TCP-1-theta) gi 9988062 K.ANEVISK.L template activating factor-i gi 2136258 K.KPRPPPALGPEETSASAGLPK.K Thermostable Mutant Of Human Superoxide Dismutase gi 27065826 K.GLTEGLHGFHVHEFGDNTAGC*TSAGPHFNPLSR.K Thioredoxin gi 1827675 K.VGEFSGANK.E Threonyl-tRNA synthetase, cytoplasmic gi 20178337 R.NELSGALTGLTR.V

transaldolase 1 gi 5803187 K.IHLDEK.S Transcription factor BTF3 gi 115143 R.LAEALPK.Q transcription factor NF-AT 90K chain gi 1082856 R.LNQLKPGLQYK.L transcription factor ZFM1 gi 7513392 R.HNLITEMVALNPDFKPPADYKPPATR.V transketolase gi 4507521 K.ILATPPQEDAPSVDIANIR.M transketolase R.TSRPENAIIYNNNEDFQVGQAK.V transketolase R.VLDPFTIKPLDR.K transketolase K.ISSDLDGHPVPK.Q translocase of inner mitochondrial membrane 9 gi 7305581 K.VQIAVANAQELLQR.M triosephosphate isomerase 1 gi 4507645 K.ELASQPDVDGFLVGGASLKPEFVDIINAK.Q triosephosphate isomerase 1 K.VTNGAFTGEISPGMIK.D triosephosphate isomerase 1 K.VVLAYEPVWAIGTGK.T triosephosphate isomerase 1 K.SNVSDAVAQSTR.I triosephosphate isomerase 1 K.VPADTEVVC*APPTAYIDFAR.Q triosephosphate isomerase 1 R.EAGITEK.V triosephosphate isomerase 1 R.HVFGESDELIGQK.V triosephosphate isomerase 1 K.TATPQQAQEVHEK.L triosephosphate isomerase 1 K.VAHALAEGLGVIAC*IGEK.L tubulin alpha 6 gi 14389309 K.TIGGGDDSFNTFFSETGAGK.H tubulin alpha 6 K.VGINYQPPTVVPGGDLAK.V tubulin alpha 6 K.DVNAAIATIK.T tubulin alpha 6 R.AVFVDLEPTVIDEVR.T tubulin alpha 6 R.IHFPLATYAPVISAEK.A tubulin alpha 6 R.QLFHPEQLITGK.E Tubulin beta-1 chain gi 135448 R.EIVHIQAGQC*GNQIGAK.F tubulin, beta, 2 gi 5174735 R.INVYYNEATGGK.Y tubulin, beta, 2 K.LTTPTYGDLNHLVSATMSGVTTC*LR.F tumor necrosis factor type 1 receptor associated protein gi 7706485 R.AQLLQPTLEINPR.H Tumor rejection antigen-1 (gp96) gi 4507677 R.SGYLLPDTK.A Tumor rejection antigen-1 (gp96) K.NLLHVTDTGVGMTR.E Tumor rejection antigen-1 (gp96) R.FQSSHHPTDITSLDQYVER.M tyrosine 3-monooxgenase/tryptophan 5-monooxgenase activatio gi 9507245 R.EQLVQK.A U5 snrnp-specific protein, 116 kd gi 4759280 R.GGGQIIPTAR.R Ubiquitin C-terminal esterase L1 gi 21361091 K.NEAIQAAHDAVAQEGQC*R.V Ubiquitin C-terminal esterase L1 K.QTIGNSC*GTIGLIHAVANNQDK.L

ubiquitin-activating enzyme E1 gi 23510338 R.IYDDDFFQNLDGVANALDNVDAR.M ubiquitin-activating enzyme E1 R.AAVATFLQSVQVPEFTPK.S ubiquitin-activating enzyme E1 R.KPLLESGTLGTK.G ubiquitin-conjugating enzyme E2L 3 gi 4507789 K.TDQVIQSLIALVNDPQPEHPLR.A ubiquitin-conjugating enzyme E2L 3 R.IEINFPAEYPFKPPK.I ubiquitin-conjugating enzyme E2L 3 K.GQVC*LPVISAENWKPATK.T ubiquitin-conjugating enzyme E2N gi 4507793 K.TNEAQAIETAR.A Ubiquitin-like protein SMT3B gi 19111164 K.VAGQDGSVVQFK.I Ubiquitin-like protein SMT3B K.TENNDHINLK.V UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 1 gi 731050 R.NENTFLDLTVQQIEHLNK.S valosin-containing protein gi 6005942 K.NAPAIIFIDELDAIAPK.R valosin-containing protein R.AHVIVMAATNRPNSIDPALR.R valosin-containing protein K.AIGVKPPR.G vesicle docking protein p115 gi 4505541 R.NQELLQSQLTEK.D vesicle docking protein p115 K.SSQTSGTNEQSSAIVSAR.D Vinculin (Metavinculin) gi 7669550 K.AIPDLTAPVAAVQAAVSNLVR.V voltage-dependent anion channel 1 gi 4507879 K.VNNSSLIGLGYTQTLKPGIK.L voltage-dependent anion channel 2 gi 4507881 K.VNNSSLIGVGYTQTLRPGVK.L

Supplemental Table 2, "Sample preparation and digestion for proteomic analyses using spin filters", Manza et al. Nuclear protein identifications Protein Accession # Peptide 14-3-3 epsilon gi 5803225 K.AAFDDAIAELDTLSEESYK.D 5.34 14-3-3 epsilon K.EAAENSLVAYK.A 2.27 14-3-3 epsilon K.AASDIAMTELPPTHPIR.L 3.3 14-3-3 epsilon K.HLIPAANTGESK.V 3.29 14-3-3 protein beta/alpha gi 4507949 K.EMQPTHPIR.L 2.03 14-3-3 protein eta chain gi 486669 K.AVTELNEPLSNEDR.N 3.37 14-3-3 protein tau gi 5803227 K.AVTEQGAELSNEER.N 3.55 28S ribosomal protein S31, mitochondrial precursor (S31mt) gi 24212378 R.IEPLSPELVAAASAVADSLPFDK.Q 3.61 28S ribosomal protein S31, mitochondrial precursor (S31mt) K.EAPETDTSPSLWDVEFAK.Q 2.82 40S ribosomal protein S10 gi 4506679 K.HPELADK.N 2.01 40S ribosomal protein S12 gi 133742 K.TALIHDGLAR.G 2.74 40S ribosomal protein S16 gi 4506691 K.LLEPVLLLGK.E 2.58 40S ribosomal protein S17 gi 4506693 R.DNYVPEVSALDQEIIEVDPDTK.E 4.66 40S ribosomal protein S17 K.LLDFGSLSNLQVTQPTVGMNFK.T 4.09 40S ribosomal protein S2, cytosolic gi 88570 K.SLEEIYLFSLPIK.E 4.29 40S ribosomal protein S3 gi 15718687 K.KPLPDHVSIVEPK.D 3.7 40S ribosomal protein S3a gi 4506723 R.EVQTNDLK.E 2.11 40S ribosomal protein S3a K.LITEDVQGK.N 2.21 40S ribosomal protein S3a K.AC*QSIYPLHDVFVR.K 3.71 40S ribosomal protein S4 gi 4506725 K.FDTGNLC*MVTGGANLGR.I 3.73 40S ribosomal protein S4 R.LSNIFVIGK.G 2.38 40S ribosomal protein S4 K.GIPHLVTHDAR.T 2.43 40S ribosomal protein S5, cytosolic gi 1362935 K.TIAEC*LADELINAAK.G 4.31 40S ribosomal protein S5, cytosolic R.VNQAIWLLC*TGAR.E 3.6 40S ribosomal protein S6 gi 6677809 K.LIEVDDER.K 2.58 40S ribosomal protein S7 gi 4506741 K.DVNFEFPEFQL.- 2.07 40S ribosomal protein S8 gi 4506743 R.LDVGNFSWGSEC*C*TR.K 3.2 40S ribosomal protein S8 R.ADGYVLEGK.E 2.11 40S ribosomal protein S9 gi 14141193 R.IGVLDEGK.M 2.05 60 kda heat shock protein (Hsp60) gi 129379 K.LVQDVANNTNEEAGDGTTTATVLAR.S 6.47 60 kda heat shock protein (Hsp60) K.IMQSSSEVGYDAMAGDFVNMVEK.G 5.62

60 kda heat shock protein (Hsp60) R.ALMLQGVDLLADAVAVTMGPK.G 2.75 60 kda heat shock protein (Hsp60) K.VGGTSDVEVNEK.K 3.04 60 kda heat shock protein (Hsp60) K.VGEVIVTK.D 2.44 60 kda heat shock protein (Hsp60) R.GYISPYFINTSK.G 2.57 60 kda heat shock protein (Hsp60) K.VGLQVVAVK.A 2.11 60S acidic ribosomal protein P0 gi 4506667 K.AFLADPSAFVAAAPVAAATTAAPAAAAAPAK.V 4.56 60S acidic ribosomal protein P0 R.AGAIAPC*EVTVPAQNTGLGPEK.T 3.32 60S acidic ribosomal protein P0 K.IIQLLDDYPK.C 3 60S acidic ribosomal protein P1 gi 4506669 K.ALANVNIGSLIC*NVGAGGPAPAAGAAPAGGPAPST AAAPAEEK.K 3.43 60S acidic ribosomal protein P1 K.AAGVNVEPFWPGLFAK.A 3.74 60S acidic ribosomal protein P2 gi 4506671 K.LASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEK.K 3.03 60S acidic ribosomal protein P2 R.YVASYLLAALGGNSSPSAK.D 4.96 60S ribosomal protein L10a gi 13592009 K.FSVC*VLGDQQHC*DEAK.A 3.22 60S ribosomal protein L13a gi 6912634 R.LAHEVGWK.Y 2.25 60S ribosomal protein L14 gi 1710488 K.LVAIVDVIDQNR.A 3.29 60S ribosomal protein L15 gi 13385036 R.NPDTQWITKPVHK.H 3.51 60S ribosomal protein L18 gi 4506607 K.ILTFDQLALDSPK.G 3.69 60S ribosomal protein L18a gi 11415026 R.IFAPNHVVAK.S 2.51 60S ribosomal protein L19 K.TAVVVGTITDDVR.V 4.57 60S ribosomal protein L21 gi 18104948 R.VYNVTQHAVGIVVNK.Q 5.41 60S ribosomal protein L21 K.HGVVPLATYMR.I 3.11 60S ribosomal protein L23a gi 17105394 K.VNTLIRPDGEK.K 3.11 60S ribosomal protein L27 gi 4506623 K.VYNYNHLMPTR.Y 3.71 60S ribosomal protein L29 gi 4506629 K.AQAAAPASVPAQAPK.R 3.4 60S ribosomal protein L3 gi 4506649 R.LEQQVPVNQVFGQDEMIDVIGVTK.G 4.97 60S ribosomal protein L3 K.NNASTDYDLSDK.S 3.34 60S ribosomal protein L31 gi 4506633 K.NLQTVNVDEN.- 2.44 60S ribosomal protein L32 gi 4506635 K.SYC*AEIAHNVSSK.N 3.73 60S ribosomal protein L4 gi 16579885 R.YAIC*SALAASALPALVMSK.G 3.89 60S ribosomal protein L4 R.NIPGITLLNVSK.L 2.36 60S ribosomal protein L4 K.APIRPDIVNFVHTNLR.K 3.23 60S ribosomal protein L5 gi 1173054 K.GAVDGGLSIPHSTK.R 3.77 60S ribosomal protein L7a gi 4506661 K.VAPAPAVVK.K 2.29 60S ribosomal protein L8 gi 4506663 R.ASGNYATVISHNPETK.K 3.16 acetyl-coenzyme A acetyltransferase 1 gi 4557237 K.EAYMGNVLQGGEGQAPTR.Q 4.22

acetyl-coenzyme A acetyltransferase 1 R.TPIGSFLGSLSLLPATK.L 4.34 acetyl-coenzyme A acetyltransferase 1 K.VNINGGAVSLGHPIGMSGAR.I 4.69 Actin gi 71611 R.DLTDYLMK.I 2.32 Actin K.EITALAPSTMK.I 2.75 Actin K.YPIEHGIITNWDDMEK.I 4.2 Actin R.VAPEEHPTLLTEAPLNPK.A 3.52 Actin R.HQGVMVGMGQK.D 2.61 Adapter-related protein complex gi 1703167 R.QVGSISMDLQLTNK.A 2.66 Adenosylhomocysteinase gi 9951915 R.GISEETTTGVHNLYK.M 3.9 ADP,ATP carrier protein T2 gi 86755 K.DFLAGGVAAAISK.T 3.1 ADP,ATP carrier protein T2 R.YFPTQALNFAFK.D 2.43 ADP,ATP carrier protein T2 R.LAADVGK.A 2.09 ADP,ATP carrier protein T2 K.LLLQVQHASK.Q 2.24 alternative splicing factor ASF-3 gi 105295 R.GGPPFAFVEFEDPR.D 3.98 Annexin V (Lipocortin V) gi 4502107 R.GTVTDFPGFDER.A 3.6 Arsenite-resistance protein 2 gi 20137457 R.ISHGEVLEWQK.T 2.47 ATP synthase gi 4502297 K.AQAELVGTADEATR.A 3.97 ATP synthase oligomycin sensitivity conferral protein gi 4502303 R.GEVPC*TVTSASPLEEATLSELK.T 3.38 ATP synthase oligomycin sensitivity conferral protein R.FSPLTTNLINLLAENGR.L 4.52 ATP synthase, alpha subunit gi 4757810 R.EVAAFAQFGSDLDAATQQLLSR.G 5.95 ATP synthase, H+ transporting, mitochondrial F0 complex gi 5453559 R.LAALPENPPAIDWAYYK.A 2.58 ATPB_HUMAN ATP synthase beta chain, mitochondrial precursor gi 114549 K.TVLIMELINNVAK.A 4.68 ATPB_HUMAN ATP synthase beta chain, mitochondrial precursor K.VLDSGAPIK.I 2.19 ATPB_HUMAN ATP synthase beta chain, mitochondrial precursor R.LVLEVAQHLGESTVR.T 4.06 ATP-binding cassette gi 4506559 R.LKPDEGGEVPVLNVSYKPQK.I 2.7 ATP-citrate (pro-s-)-lyase (Citrate cleavage enzyme) gi 20141248 K.GVTIIGPATVGGIKPGC*FK.I 4.2 ATP-dependant DNA helicase II gi 10863945 K.YAPTEAQLNAVDALIDSMSLAK.K 4.66 ATP-dependant DNA helicase II K.EEASGSSVTAEEAK.K 4.03 ATP-dependant DNA helicase II K.VDEEQMK.Y 2.04 ATP-dependant DNA helicase II K.SQLDIIIHSLK.K 3.6

ATP-dependant DNA helicase II R.ANPQVGVAFPHIK.H 2.85 ATP-dependant DNA helicase II R.LGGHGPSFPLK.G 2.67 ATP-dependent RNA helicase A gi 3915658 K.AIEPPPLDAVIEAEHTLR.E 3.63 ATP-dependent RNA helicase A R.TPLHEIALSIK.L 2.56 ATP-dependent RNA helicase A R.YQILPLHSQIPR.E 3.33 beta actin gi 4501885 R.TTGIVMDSGDGVTHTVPIYEGYALPHAILR.L 5.49 beta-fodrin gi 476928 R.QNLLSQSHAYQQFLR.D 4.02 beta-tubulin gi 2119276 K.EVDEQMLNVQNK.N 3.74 beta-tubulin K.NSSYFVEWIPNNVK.T 2.73 beta-tubulin R.SGPFGQIFRPDNFVFGQSGAGNNWAK.G 6.29 beta-tubulin K.GHYTEGAELVDSVLDVVR.K 6.29 Brain acid soluble protein 1 gi 6686256 K.ETPAATEAPSSTPK.A 3.24 Calponin Homology (Ch) Domain From Human Beta-Spectrin gi 2914153 K.TAGYPNVNIHNFTTSWR.D 4.03 capsid protein gi 9629419 R.DAADAVR.A 2.32 catenin gi 461853 K.AHVLAASVEQATENFLEK.G 3.91 cell division cycle 2 protein, isoform 1 gi 4502709 R.LESEEEGVPSTAIR.E 3.17 chaperonin containing TCP1, subunit 4 (delta) gi 5453605 R.AFADAMEVIPSTLAENAGLNPISTVTELR.N 4.91 chaperonin containing TCP1, subunit 4 (delta) K.GIHPTIISESFQK.A 3.4 chaperonin containing TCP1, subunit 6A gi 4502643 K.NAIDDGC*VVPGAGAVEVAMAEALIK.H 4.33 chaperonin containing TCP1, subunit 6A K.VATAQDDITGDGTTSNVLIIGELLK.Q 3.91 chaperonin containing TCP1, subunit 6A K.ALQFLEEVK.V 2.26 chaperonin containing TCP1, subunit 7 (eta) gi 5453607 K.LPIGDVATQYFADR.D 3.63 chromosome 17 open reading frame 31 gi 8922132 R.LLESR.K 2.06 clathrin heavy chain gi 4758012 R.GQFSTDELVAEVEK.R 3.49 clathrin heavy chain R.NLQNLLILTAIK.A 4.41 clathrin heavy chain R.LAELEEFINGPNNAHIQQVGDR.C 3.41 clathrin heavy chain R.IHEGC*EEPATHNALAK.I 4.48 clathrin heavy chain K.LHIIEVGTPPTGNQPFPK.K 4.23 cleavage and polyadenylation specific factor 6 gi 5901928 R.AVSDASAGDYGSAIETLVTAISLIK.Q 6.38 cleavage stimulation factor subunit 3 gi 4557495 R.GC*VNPMINIEQLWR.D 3.73 cofilin 1 (non-muscle) gi 5031635 K.MIYASSK.D 2.2

Contactin associated protein-like 4 precursor gi 17433039 R.LISISGK.V 2.03 creatine kinase-b gi 21536286 K.TDLNPDNLQGGDDLDPNYVLSSR.V 4.5 creatine kinase-b R.FC*TGLTQIETLFK.S 3.74 Cyclophilin A gi 2981731 K.FEDENFILK.H 2.93 cytochrome c gi 11128019 K.TGPNLHGLFGR.K 2.7 cytochrome c oxidase subunit IV gi 4502981 R.DHPLPEVAHVK.H 2.42 cytochrome c oxidase subunit VIb gi 4502985 R.NC*WQNYLDFHR.C 3.87 d(ttaggg)n-binding protein B39 gi 477766 -.GFGFVLFK.E 2.04 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 isoform 1 gi 5453840 R.ELAQQVQQVADDYGK.C 4.17 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 isoform 1 K.NFYVEHPEVAR.L 3.02 DEAD/H box-5 (RNA helicase, 68kD) gi 4758138 R.ELAQQVQQVAAEYC*R.A 4.25 DEAD/H box-5 (RNA helicase, 68kD) R.TTYLVLDEADR.M 3.9 DEAD/H box-5 (RNA helicase, 68kD) K.APILIATDVASR.G 3.56 DEAD/H box-5 (RNA helicase, 68kD) R.GLDVEDVK.F 2.36 DEAD/H box-5 (RNA helicase, 68kD) K.NFYQEHPDLAR.R 3.55 DEAD-box protein 3 gi 3023628 K.HVINFDLPSDIEEYVHR.I 5.22 DEAD-box protein 3 R.YTRPTPVQK.H 2.22 DEK oncogene (DNA binding) gi 4503249 K.VYENYPTYDLTER.K 4.11 DEK oncogene (DNA binding) K.NVGQFSGFPFEK.G 3.15 DEK oncogene (DNA binding) K.LLYNRPGTVSSLK.K 3.81 Diff6,H5,CDC10 homologue gi 1040689 K.STLINSLFLTDLYPER.V 3.6 Dihydrolipoamide acetyltransferase component of pyruvate de gi 3915777 K.GVETIANDVVSLATK.A 3.67 dihydrolipoamide dehydrogenase precursor gi 4557525 K.ADGGTQVIDTK.N 3.63 Dihydrolipoamide succinyltransferase component of 2-oxoglut gi 1709442 K.AKPAEAPAAAAPK.A 2.7 DNA topoisomerase I gi 11225260 K.GPVFAPPYEPLPENVK.F 3.3 DNA topoisomerase II, alpha isozyme gi 19913406 K.ELILFSNSDNER.S 3.44 DNA-activated protein kinase gi 7512396 K.TVSLLDENNVSSYLSK.N 3.6 DNA-activated protein kinase, catalytic subunit gi 1362789 R.VEQLFQVMNGILAQDSAC*SQR.A 5.79 DNA-activated protein kinase, catalytic subunit R.NELEIPGQYDGR.G 3.39

DNA-activated protein kinase, catalytic subunit R.DYVAVAR.G 2.13 DNA-activated protein kinase, catalytic subunit R.AQEPESGLSEETQVK.C 3.61 DNA-activated protein kinase, catalytic subunit R.SLGPPQGEEDSVPR.D 3.26 DNA-activated protein kinase, catalytic subunit K.ATQMPEGGQGAPPMYQLYK.R 4.67 DNA-activated protein kinase, catalytic subunit K.AALSALESFLK.Q 3.26 DNA-activated protein kinase, catalytic subunit R.ELLNPVVEFVSHPSTTC*R.E 3.94 DNA-activated protein kinase, catalytic subunit K.INQVFHGSC*ITEGNELTK.T 4.72 DNA-activated protein kinase, catalytic subunit R.NC*ISTVVHQGLIR.I 4.45 DNA-activated protein kinase, catalytic subunit K.HSSLITPLQAVAQR.D 4.06 dnak-type molecular chaperone HSP70-2 gi 2119728 K.SINPDEAVAYGAAVQAAILMGDK.S 6.18 dnak-type molecular chaperone HSPA1L gi 2119712 K.ELEQVC*NPIISGLYQGAGGPGPGGFGAQGPK.G 4.96 dnak-type molecular chaperone HSPA1L K.QTQIFTTYSDNQPGVLIQVYEGER.A 4.66 dnak-type molecular chaperone HSPA1L K.DAGVIAGLNVLR.I 4.51 dnak-type molecular chaperone HSPA1L K.EIAEAYLGYPVTNAVITVPAYFNDSQR.Q 3.69 dnak-type molecular chaperone HSPA1L K.AFYPEEISSMVLTK.M 3.58 dnak-type molecular chaperone HSPA1L K.FGDPVVQSDMK.H 3.68 dnak-type molecular chaperone HSPA1L K.SAVEDEGLK.G 2.07 dnak-type molecular chaperone HSPA1L K.NALESYAFNMK.S 3.74 dnak-type molecular chaperone HSPA1L K.LLQDFFNGR.D 2.78 dnak-type molecular chaperone HSPA1L K.AQIHDLVLVGGSTR.I 3.06 dnak-type molecular chaperone HSPA1L R.LVNHFVEEFK.R 2.4 dnak-type molecular chaperone HSPA1L K.HWPFQVINDGDKPK.V 2.76 Dolichyl-diphosphooligosaccharide gi 9297108 K.NFESLSEAFSVASAAAVLSHNR.Y 4.84 Double-stranded RNA-specific adenosine deaminase gi 1706532 R.NAEFLTC*NIPTSNASNNMVTTEK.V 3.95 dyskerin gi 4503337 R.ALETLTGALFQRPPLIAAVK.R 5.17 E1B PROTEIN, LARGE T-ANTIGEN gi 119030 K.YSIEQLTTYWLQPGDDFEEAIR.V 3.84

E1B PROTEIN, LARGE T-ANTIGEN R.AEFGSSDEDTD.- 2.22 E1B PROTEIN, LARGE T-ANTIGEN K.ILLEPESMSK.V 2.35 E1B PROTEIN, LARGE T-ANTIGEN R.NQPVMLDVTEELRPDHLVLAC*TR.A 3.19 E1B PROTEIN, LARGE T-ANTIGEN R.HRPEC*ITFQQIK.D 3.5 E1B PROTEIN, LARGE T-ANTIGEN K.AWPVFEHNILTR.C 2.44 E1B PROTEIN, LARGE T-ANTIGEN K.HNMVC*GNC*EDR.A 2.7 E1B PROTEIN, LARGE T-ANTIGEN R.ASQMLTC*SDGNC*HLLK.T 3.64 E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K) gi 119040 K.SC*GELFDSLNLGHQALFQEK.V 4.35 early-pregnancy factor, EPF=chaperonin 10 gi 565169 R.DGDILGK.Y 2.02 EBNA-2 co-activator (100kD) gi 7657431 R.VADISGDTQK.A 2.85 EBNA-2 co-activator (100kD) K.LRPLYDIPYMFEAR.E 2.74 ELAV-like protein 1 (Hu-antigen R) gi 20981691 R.TNLIVNYLPQNMTQDELR.S 4.02 ELAV-like protein 1 (Hu-antigen R) R.SEAEEAITSFNGHKPPGSSEPITVK.F 3.6 ELAV-like protein 1 (Hu-antigen R) K.NVALLSQLYHSPAR.R 4.25 Elongation factor 1-alpha 1 gi 4503471 K.SGDAAIVDMVPGKPMC*VESFSDYPPLGR.F 3.17 Elongation factor 1-alpha 1 K.IGGIGTVPVGR.V 2.8 Elongation factor 1-alpha 1 R.YEEIVK.E 2.11 Elongation factor 1-alpha 1 R.LPLQDVYK.I 2.02 Elongation factor 1-alpha 1 K.DGNASGTTLLEALDC*ILPPTRPTDKPLR.L 4.22 Elongation factor 1-alpha 1 R.VETGVLKPGMVVTFAPVNVTTEVK.S 4.39 Elongation factor 1-alpha 1 K.QLIVGVNK.M 2.13 Elongation factor 1-alpha 1 K.YYVTIIDAPGHR.D 3.14 Elongation factor 1-alpha 1 R.EHALLAYTLGVK.Q 3.21 Elongation factor 1-alpha 1 K.STTTGHLIYK.C 2.85 Elongation factor 1-alpha 1 K.YYVTIIDAPGHR.D 3.48 Elongation factor 1-beta (EF-1-beta) gi 4503477 K.SPAGLQVLNDYLADK.S 5.25 Elongation factor 1-beta (EF-1-beta) K.SSILLDVKPWDDETDMAK.L 3.58 Elongation factor 2 (EF-2) gi 4503483 R.YVEPIEDVPC*GNIVGLVGVDQFLVK.T 4.07 Elongation factor 2 (EF-2) K.NPADLPK.L 2.3 Elongation factor 2 (EF-2) R.GHVFEESQVAGTPMFVVK.A 5.1 emerin gi 4557553 R.YNIPHGPVVGSTR.R 2.57 enhancer of rudimentary homolog gi 4758302 R.TYADYESVNECMEGVCK.M 2.87 enhancer of rudimentary homolog R.ADTQTYQPYNK.D 3.53 enolase 1; phosphopyruvate hydratase gi 4503571 K.DYPVVSIEDPFDQDDWGAWQK.F 5.52 enolase 1; phosphopyruvate hydratase K.LAMQEFMILPVGAANFR.E 4.34 enolase 1; phosphopyruvate hydratase R.GNPTVEVDLFTSK.G 2.59 enolase 1; phosphopyruvate hydratase R.HIADLAGNSEVILPVPAFNVINGGSHAGNK.L 6.76

enolase alpha gi 7657062 R.YISPDQLADLYK.G 3.91 enolase alpha R.IGAEVYHNLK.N 4.01 enoyl-coa hydratase alpha gi 543064 K.TVLGTPEVLLGALPGAGGTQR.L 3.14 eukaryotic translation elongation factor 1 gi 4503481 R.ILGLLDAYLK.T 2.03 eukaryotic translation elongation factor 1 R.WFLTC*INQPQFR.A 3.77 eukaryotic translation initiation factor 3, subunit 5 gi 4503519 R.LHPVILASIVDSYER.R 4.4 eukaryotic translation initiation factor 3, subunit 8 gi 4503525 K.SEQDQAENEGEDSAVLMER.L 6.14 Eukaryotic translation initiation factor 4 gamma gi 1170510 R.LQGINC*GPDFTPSFANLGR.T 4.24 eukaryotic translation initiation factor 4A1 (eif- 4A-I) gi 4503529 R.GIYAYGFEKPSAIQQR.A 4.18 eukaryotic translation initiation factor 5A; eif5a gi 4503545 K.VHLVGIDIFTGK.K 3.27 Ewing sarcoma breakpoint region gi 4885225 R.AGDWQC*PNPGC*GNQNFAWR.T 4.07 Familial Als Mutant G37r Cuznsod gi 2982080 K.GDGPVQGIINFEQK.E 3.47 FBRL gi 4321126 K.LAAAILGGVDQIHIKPGAK.V 3.83 GAP-associated tyrosine phosphoprotein p62 (Sam68) gi 5730027 K.DSLDPSFTHAMQLLTAEIEK.I 3.98 GAP-associated tyrosine phosphoprotein p62 (Sam68) K.YLPELMAEK.D 2.42 GAP-associated tyrosine phosphoprotein p62 (Sam68) R.SGSMDPSGAHPSVR.Q 3.43 GDP dissociation inhibitor 1 gi 4503971 K.NTNDANSC*QIIIPQNQVNR.K 3.88 glioblastoma amplified sequence gi 4503937 K.LQFHNVKPEC*LEAYNK.I 3.99 glucose-regulated protein precursor (GRP 78) gi 16507237 R.IINEPTAAAIAYGLDK.R 4.8 glucose-regulated protein precursor (GRP 78) R.TWNDPSVQQDIK.F 3.68 glucose-regulated protein precursor (GRP 78) K.VTHAVVTVPAYFNDAQR.Q 4.02 Glutathione S-transferase P (GSTP1-1) gi 4504183 K.ALPGQLKPFETLLSQNQGGK.T 3.26 Glyceraldehyde 3-phosphate dehydrogenase gi 120643 K.IISNASC*TTNC*LAPLAK.V 3.55 glyceraldehyde-3-phosphate dehydrogenase gi 7669492 R.VPTANVSVVDLTC*R.L 4

glyceraldehyde-3-phosphate dehydrogenase K.LVINGNPITIFQER.D 4.02 glyceraldehyde-3-phosphate dehydrogenase K.LISWYDNEFGYSNR.V 3.81 glyceraldehyde-3-phosphate dehydrogenase R.GALQNIIPASTGAAK.A 3.17 glyceraldehyde-3-phosphate dehydrogenase R.VIISAPSADAPMFVMGVNHEK.Y 3.88 GTP-binding nuclear protein RAN (TC4) (Ran GTPase) gi 5453555 K.NLQYYDISAK.S 3.11 GTP-binding nuclear protein RAN (TC4) (Ran GTPase) K.LVLVGDGGTGK.T 2.26 GTP-BINDING NUCLEAR PROTEIN RAN/TC4 gi 23508374 R.SNYNFEKPFLWLAR.R 3.78 GTP-binding protein Rab2 gi 106185 K.IQEGVFDINNEANGIK.I 3.75 guanine nucleotide-binding protein, beta-2 subunit gi 13937391 R.AGVLAGHDNR.V 2.14 H1 histone family gi 5174449 R.GAPAAATAPAPTAHK.A 3.29 H1 histone family, member 1 gi 4885373 K.ALAAAGYDVEK.N 3.03 H2A histone family, member A gi 10645195 R.VTIAQGGVLPNIQAVLLPK.K 4.28 H2A histone family, member A R.NDEELNK.L 2.29 ha1225 gene product (related to human alphaglucosidase) gi 577295 R.FGAVWTGDNTAEWDHLK.I 3.08 Heat shock 70 kda protein 1 (HSP70.1) gi 462325 K.AAAIGIDLGTTYSC*VGVFQHGK.V 4.09 heat shock 70kDa protein 2 gi 13676857 K.DNNLLGK.F 2.05 heat shock 70kDa protein 6 (HSP70B') gi 4504515 R.IINEPTAAAIAYGLDR.R 4.78 heat shock 70kDa protein 6 (HSP70B') K.DNNLLGR.F 2.47 heat shock 70kDa protein 6 (HSP70B') R.FEELC*SDLFR.S 2.84 heat shock 70kDa protein 6 (HSP70B') R.VEILANDQGNR.T 3.58 heat shock 70kDa protein 6 (HSP70B') R.TTPSYVAFTDTER.L 2.49 heat shock 70kDa protein 6 (HSP70B') K.ATAGDTHLGGEDFDNR.L 3.94 heat shock 70kDa protein 6 (HSP70B') R.IINEPTAAAIAYGLDR.R 2.83 heat shock 70kDa protein 6 (HSP70B') K.ATAGDTHLGGEDFDNR.L 3.4 heat shock 70kDa protein 8 gi 5729877 K.TVTNAVVTVPAYFNDSQR.Q 3.31 heat shock 70kDa protein 8 K.SFYPEEVSSMVLTK.M 3.52 heat shock 70kDa protein 9B precursor gi 24234688 K.STNGDTFLGGEDFDQALLR.H 4.57 heat shock 70kDa protein 9B precursor R.VINEPTAAALAYGLDK.S 4.8 heat shock 70kDa protein 9B precursor K.NAVITVPAYFNDSQR.Q 2.76

heat shock protein 90-beta gi 72222 R.NPDDITQEEYGEFYK.S 4.83 heat shock protein 90-beta K.YIDQEELNK.T 2.9 heat shock protein 90-beta R.YHTSQSGDEMTSLSEYVSR.M 5.48 heat shock protein 90-beta K.HSQFIGYPITLYLEK.E 5 Heat shock protein HSP 90-alpha gi 123678 R.NPDDITNEEYGEFYK.S 4.35 Heat shock protein HSP 90-alpha K.FYEQFSK.N 2.08 Heat shock protein HSP 90-alpha K.HSQFIGYPITLFVEK.E 4.43 Heat shock protein HSP 90-alpha K.HIYYITGETK.D 2.99 high density lipoprotein binding protein gi 4885409 K.VATLNSEEESDPPTYK.D 3.82 high mobility group AT-hook 1 isoform a gi 22208967 K.EEEEGISQESSEEEQ.- 3.41 Histone H1.2 gi 4885375 K.KPAAATVTK.K 2.28 Histone H2B.l gi 7387740 K.AMGIMNSFVNDIFER.I 4.17 Histone H2B.l K.QVHPDTGISSK.A 2.83 HLA-B associated transcript-1; DEAD-box protein gi 4758112 K.FMQDPMEIFVDDETK.L 4.42 HLA-B associated transcript-1; DEAD-box protein K.GLAITFVSDENDAK.I 3.95 HLA-B associated transcript-1; DEAD-box protein R.VNIAFNYDMPEDSDTYLHR.V 4.08 HLA-B associated transcript-1; DEAD-box protein R.AIVDC*GFEHPSEVQHEC*IPQAILGMDVLC*QAK.S 5.74 HLA-B associated transcript-1; DEAD-box protein K.LTLHGLQQYYVK.L 3.23 HLA-B associated transcript-1; DEAD-box protein K.NC*PHIVVGTPGR.I 3.75 HLA-B associated transcript-1; DEAD-box protein K.GSYVSIHSSGFR.D 2.99 hnrna-binding protein M4 gi 479852 K.AAEVLNK.H 2.12 hnrna-binding protein M4 R.GNFGGSFAGSFGGAGGHAPGVAR.K 4.88 hnrnp A0 gi 5803036 K.EDIYSGGGGGGSR.S 3.08 hnrnp A0 K.AEIIADK.Q 2.07 hnrnp A0 K.GDVAEGDLIEHFSQFGTVEK.A 4.36 hnrnp A0 R.GFGFVYFQNHDAADK.A 4.16 hnrnp A1 gi 133254 R.DYFEQYGK.I 2.49 hnrnp A1 K.IEVIEIMTDR.G 3.89 hnrnp A1 R.GFAFVTFDDHDSVDK.I 4.3 hnrnp A1 R.NQGGYGGSSSSSSYGSGR.R 4.7

hnrnp A1 R.SSGPYGGGGQYFAKPR.N 4.07 hnrnp A2/B1, isoform B1 gi 14043072 R.GFGDGYNGYGGGPGGGNFGGSPGYGGGR.G 5.53 hnrnp A2/B1, isoform B1 K.IDTIEIITDR.Q 3.68 hnrnp A2/B1, isoform B1 R.DYFEEYGK.I 2.35 hnrnp A2/B1, isoform B1 K.LFIGGLSFETTEESLR.N 4.52 hnrnp A2/B1, isoform B1 R.QEMQEVQSSR.S 2.94 hnrnp A2/B1, isoform B1 R.NMGGPYGGGNYGPGGSGGSGGYGGR.S 5.01 hnrnp A2/B1, isoform B1 R.QEMQEVQSSR.S 3.07 hnrnp A2/B1, isoform B1 R.GGNFGFGDSR.G 2.58 hnrnp A2/B1, isoform B1 R.GGGGNFGPGPGSNFR.G 2.65 hnrnp A2/B1, isoform B1 R.EESGKPGAHVTVK.K 3.38 hnrnp A3 gi 1710627 K.IETIEVMEDR.Q 3.62 hnrnp A3 R.SSGSPYGGGYGSGGGSGGYGSR.R 4.75 hnrnp A3 R.EDSVKPGAHLTVK.K 2.49 hnrnp AB isoform b gi 4758542 R.EYFGEFGEIEAIELPMDPK.L 3.76 hnrnp AB isoform b K.FGEVVDC*TIK.M 3.13 hnrnp AB isoform b K.FHTVSGSK.C 2.06 hnrnp C-like gi 20455218 R.MIASQVVDINLAAEPK.V 2.98 hnrnp C-like protein gi 420052 R.EYFGGFGEVESIELPMDNK.T 4.31 hnrnp C-like protein K.IFVGGLSPDTPEEK.I 4.33 hnrnp C-like protein K.YHNVGLSK.C 2.66 hnrnp F gi 4826760 K.ATENDIYNFFSPLNPVR.V 4.73 hnrnp F K.ITGEAFVQFASQELAEK.A 3.16 hnrnp F K.ATENDIYNFFSPLNPVR.V 4.23 hnrnp F K.HSGPNSADSANDGFVR.L 3.63 hnrnp F R.YGDSEFTVQSTTGHC*VHMR.G 3.17 hnrnp G gi 23503093 R.DVYLSPR.D 2.07 hnrnp G R.GFAFVTFESPADAK.D 4.73 hnrnp G K.LFIGGLNTETNEK.A 3.95 hnrnp G R.IVEVLLMK.D 2.38 hnrnp G K.ALEAVFGK.Y 2.22 hnrnp G K.VEQATKPSFESGR.R 3.47 hnrnp H1 gi 5031753 R.GAYGGGYGGYDDYNGYNDGYGFGSDR.F 4.95 hnrnp H1 R.YGDGGSTFQSTTGHC*VHMR.G 4.06 hnrnp H2 gi 9624998 R.STGEAFVQFASQEIAEK.A 4.2 hnrnp H2 R.DLNYC*FSGMSDHR.Y 3.2 hnrnp H2 R.YVEVFK.S 2.02

hnrnp H2 K.HTGPNSPDTANDGFVR.L 4 hnrnp H2 R.VHIEIGPDGR.V 2.6 hnrnp H2 K.HTGPNSPDTANDGFVR.L 3.92 hnrnp homolog JKTBP gi 7446333 R.YHQIGSGK.C 2.54 hnrnp K isoform b gi 13384620 R.IITITGTQDQIQNAQYLLQNSVK.Q 5.18 hnrnp K isoform b R.GSYGDLGGPIITTQVTIPK.D 4.69 hnrnp K isoform b R.TDYNASVSVPDSSGPER.I 3.88 hnrnp K isoform b K.IDEPLEGSEDR.I 3.54 hnrnp K isoform b R.DYDDMSPR.R 2.18 hnrnp K isoform b K.IILDLISESPIK.G 3.13 hnrnp K isoform b K.GSDFDC*ELR.L 3.12 hnrnp K isoform b R.NTDEMVELR.I 3 hnrnp K isoform b K.RPAEDMEEEQAFK.R 3.83 hnrnp K isoform b R.VVLIGGKPDR.V 2.33 hnrnp K isoform b R.LLIHQSLAGGIIGVK.G 4.56 hnrnp L gi 4557645 K.QPAIMPGQSYGLEDGSC*SYK.D 3.05 hnrnp L R.SSSGLLEWESK.S 2.26 hnrnp L R.YGPQYGHPPPPPPPPEYGPHADSPVLMVYGLDQS K.M 6.49 hnrnp L K.SDALETLGFLNHYQMK.N 4.34 hnrnp L K.SKPGAAMVEMADGYAVDR.A 4.38 hnrnp L K.IEYAKPTR.L 2.19 hnrnp L R.AITHLNNNFMFGQK.L 3.27 hnrnp L K.TPASPVVHIR.G 2.77 hnrnp L R.MGPPVGGHR.R 2.73 hnrnp M gi 1710636 K.MEEESGAPGVPSGNGAPGPK.G 2.96 hnrnp R gi 5031755 K.YGGPPPDSVYSGVQPGIGTEVFVGK.I 3.65 hnrnp R R.NLATTVTEEILEK.S 4.16 hnrnp R K.VTEGLVDVILYHQPDDK.K 4.1 hnrnp R R.STAYEDYYYHPPPR.M 3.58 hnrnp R K.LC*DSYEIRPGK.H 3.38 hnrnp U gi 284156 K.SSGPTSLFAVTVAPPGAR.Q 3.08 hnrnp U R.NFILDQTNVSAAAQR.R 5.21 hnrnp U K.YNILGTNTIMDK.M 3.52 hnrnp U R.GYFEYIEENK.Y 2.66 hnrnp U K.EKPYFPIPEEYTFIQNVPLEDR.V 5.2 hnrnp U K.NGQDLGVAFK.I 2.67

hnrnp U K.FIEIAAR.K 2.16 hnrnp U K.HAAENPGK.Y 2.08 HUMAN 7-dehydrocholesterol reductase gi 20138066 K.FLPGYVGGIQEGAVTPAGVVNK.Y 3.64 Human DEAD-box protein p72 gi 13787204 R.TTSSANNPNLMYQDEC*DR.R 3.85 HUMAN Elongation factor 1-delta (EF-1-delta) gi 25453472 K.KPALVAK.S 2.15 Human Heart L-Lactate Dehydrogenase gi 13786847 K.LIAPVAEEEATVPNNK.I 3.03 Human P32, Acidic Mitochondrial Matrix Protein gi 4930073 K.VEEQEPELTSTPNFVVEVIK.N 4.9 Human Platelet Profilin gi 3891601 K.TFVNITPAEVGVLVGK.D 4.28 Human Platelet Profilin K.TLVLLMGK.E 2.15 HUMAN Putative pre-mrna splicing factor RNA helicase gi 13124667 K.IAPQYYDMSNFPQC*EAK.R 3.14 HUMAN Putative pre-mrna splicing factor RNA helicase R.TLATDILMGVLK.E 2.6 HUMAN T-complex protein 1, epsilon subunit gi 24307939 R.AFADALEVIPMALSENSGMNPIQTMTEVR.A 4.18 HUMAN T-complex protein 1, epsilon subunit R.FSELTAEK.L 2.26 HUMAN T-complex protein 1, epsilon subunit K.IAILTC*PFEPPKPK.T 3.03 hydroxysteroid (17-beta) dehydrogenase gi 4504505 R.FAKPVYPGQTLQTEMWK.E 2.41 HYPOTHETICAL PROTEIN KIAA0179 gi 2833254 K.SSTATHPPGPAVQLNK.T 3.61 hypothetical protein KIAA0324 gi 7512967 K.SEEPAGQILSHLSSELK.E 4.33 Integrin alpha-8 gi 1708570 R.LEGGESAVLK.V 2.13 Interleukin enhancer-binding factor 3 gi 20138587 K.AVSDWIDEQEK.G 3.32 karyopherin (importin) beta 1 gi 19923142 R.AAVENLPTFLVELSR.V 2.26 karyopherin (importin) beta 1 K.GALQYLVPILTQTLTK.Q 2.88 KIAA0111 gene product gi 7661920 R.DVIAQSQSGTGK.T 2.13 laminin receptor 1 gi 9845502 R.ADHQPLTEASYVNLPTIALC*NTDSPLR.Y 3.5 leucine-rich protein - human gi 284289 R.DAGIEPGPDTYLALLNAYAEK.G 4.23 leucine-rich protein - human K.GDVENIEVVQK.M 3.53 MAGUK p55 subfamily member 6 gi 27764857 K.EGGSAGLIPSQFLEEK.R 2.76 Malate dehydrogenase gi 6648067 K.VAVLGASGGIGQPLSLLLK.N 5.84 matrin 3 gi 21626466 R.DLSAAGIGLLAAATQSLSMPASLGR.M 4.54 matrin 3 R.IGPYQPNVPVGIDYVIPK.T 3.72 matrin 3 R.GNLGAGNGNLQGPR.H 2.33

matrin 3 K.ITPENLPQILLQLK.R 3.12 matrin 3 R.VIHLSNLPHSGYSDSAVLK.L 3.9 matrin 3 K.GYPHLC*SIC*DLPVHSNK.E 3.61 MCM6 minichromosome maintenance deficient 6 gi 7427519 R.TSILAAANPISGHYDR.S 2.37 microtubule-associated protein gi 19114435 R.INEAEK.E 2.01 mitochondrial short-chain enoyl-coenzyme A hydratase gi 12707570 K.AQFAQPEILIGTIPGAGGTQR.L 3.88 mitochondrial short-chain enoyl-coenzyme A hydratase K.IC*PVETLVEEAIQC*AEK.I 3.48 Muscle Aldolase gi 229674 K.DGADFAK.W 2.11 Muscle Aldolase K.GILAADESTGSIAK.R 3.49 myomesin (M-protein) 2 gi 4505315 K.ATGIIEMVMDR.F 2.1 myosin heavy chain nonmuscle form A gi 625305 K.DFSALESQLQDTQELLQEENR.Q 4.98 myosin IXB gi 4758750 K.YLDEFLLNK.I 2.45 Nascent polypeptide associated complex alpha subunit gi 5031931 K.NILFVITKPDVYK.S 4.45 nicotinamide nucleotide transhydrogenase gi 6912536 K.TSGTLISFIYPAQNPELLNK.L 3.67 nicotinamide nucleotide transhydrogenase K.AVVLAANHFGR.F 3.14 nonhistone chromosomal protein HMG-2B gi 422864 K.SEHPGLSIGDTAK.K 3.45 nuclear mitotic apparatus protein 1 gi 5453820 R.VEFATLQEALAHALTEK.E 5.8 Nuclear protein Hcc-1 (HSPC316) gi 18202440 R.FGIVTSSAGTGTTEDTEAK.K 4.31 nuclear ribonucleoprotein particle C2 protein gi 14110428 R.MIAGQVLDINLAAEPK.V 3.22 nuclear ribonucleoprotein particle C2 protein K.SDVEAIFSK.Y 2.08 nuclease sensitive element-binding protein 1 gi 423015 R.RPQYSNPPVQGEVMEGADNQGAGEQGRPVR.Q 3.85 nucleolar and coiled-body phosphoprotein 1 gi 4758860 R.DNQLSEVANK.F 2.46 nucleolar and coiled-body phosphoprotein 1 K.AAVVVSK.S 2.19 nucleolar and coiled-body phosphoprotein 1 K.SPAVKPAAAPK.Q 2.27 nucleolar protein NOP5/NOP58 gi 7706254 R.LIAHAGSLLNLAK.H 3.29 Nucleolar protein Nop56 gi 20141472 K.EEPVSSGPEEAVGK.S 2.45 nucleolin gi 4885511 K.TLVLSNLSYSATEETLQEVFEK.A 4.7 nucleolin K.VEGTEPTTAFNLFVGNLNFNK.S 4.41 nucleolin K.EAMEDGEIDGNK.V 3.16 nucleolin K.EVFEDAAEIR.L 3.49