Supporting Information for Proteomics DOI /pmic

Transkript

1 Supporting Information for Proteomics DOI /pmic 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

2 Supplemental Table 1, "Sample preparation and digestion for proteomic analyses using spin filters", Manza et al. Cytosolic protein identifications Protein Accession # Peptide protein beta/alpha gi R.VISSIEQK.T protein beta/alpha K.AVTEQGHELSNEER.N protein tau gi K.TELIQK.A 26S proteinase chain 5a gi R.LQAQQDAVNIVC*HSK.T 40S ribosomal protein S10 gi K.HPELADK.N 40S ribosomal protein S12 gi K.LGEWVGLC*K.I 40S ribosomal protein S12 K.TALIHDGLAR.G 40S ribosomal protein S18 gi K.YSQVLANGLDNK.L 40S ribosomal protein S23 gi K.ANPFGGASHAK.G 40S ribosomal protein S3 gi K.GGKPEPPAMPQPVPTA.- 40S ribosomal protein S3 K.KPLPDHVSIVEPK.D 40S ribosomal protein S6 gi K.QGVLTHGR.V 40S ribosomal protein S7 gi R.TLTAVHDAILEDLVFPSEIVGK.R 40S ribosomal protein S8 gi K.ISSLLEEQFQQGK.L 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase gi R.YGMNPHQTPAQLYTLQPK.L 60 kda heat shock protein (Hsp60) gi 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 K.AFLADPSAFVAAAPVAAATTAAPAAAAAPAK.V 60S acidic ribosomal protein P1 R.GHLENNPALEK.L 60S acidic ribosomal protein P1 gi K.AAGVNVEPFWPGLFAK.A 60S acidic ribosomal protein P2 gi R.YVASYLLAALGGNSSPSAK.D 60S acidic ribosomal protein P2 K.VISELNGK.N

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

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

5 creatine kinase-b R.FC*TGLTQIETLFK.S creatine kinase-b K.SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR.D creatine kinase-b R.FPAEDEFPDLSAHNNHMAK.V cyclophilin A gi VNPTVFFDIAVDGEPLGR.X Cyclophilin A gi K.HTGPGILSMANAGPNTNGSQFFIC*TAK.T Cyclophilin B gi K.HVVFGK.V cystatin B gi R.VFQSLPHENKPLTLSNYQTNK.A cytosolic malate dehydrogenase gi K.NVIIWGNHSSTQYPDVNHAK.V D-3-phosphoglycerate dehydrogenase gi K.NAGNC*LSPAVIVGLLK.E D-3-phosphoglycerate dehydrogenase K.GTIQVITQGTSLK.N D-3-phosphoglycerate dehydrogenase R.ALVDHENVISC*PHLGASTK.E D-dopachrome tautomerase gi R.LC*AAAASILGKPADR.V desmoplakin (DPI, DPII) gi R.NNYDEEIISLK.N Dihydrolipoamide succinyltransferase gi K.AKPAEAPAAAAPK.A DnaJ (Hsp40) homolog, subfamily A, member 1 gi R.IHQIGPGMVQQIQSVC*MEC*QGHGER.I dnak-type molecular chaperone HSP70-2 gi K.SINPDEAVAYGAAVQAAILMGDK.S dnak-type molecular chaperone HSP70-2 K.SENVQDLLLLDVAPLSLGLETAGGVMTALIK.R dnak-type molecular chaperone HSPA1L gi 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 K.VQVEYK.G dystrophin gi R.LETELK.E E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K) gi K.SC*GELFDSLNLGHQALFQEK.V E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K) R.LLLLSSVRPAIIPTEEQQQQQEEAR.R electron-transfer-flavoprotein, beta polypeptide gi K.VETTEDLVAK.L electron-transfer-flavoprotein, beta polypeptide K.IEVIKPGDLGVDLTSK.L Elongation factor 1-alpha 1 (EF-1-alpha-1) gi K.IGGIGTVPVGR.V

6 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 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 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 K.DATNVGDEGGFAPNILENK.E enolase alpha, lung-specific K.VNQIGSVTESLQAC*K.L enolase alpha, lung-specific R.IGAEVYHNLK.N eukaryotic translation elongation factor 1 gi R.QIPVLQTNNGPSLTGLTTIAAHLVK.Q Eukaryotic translation initiation factor 4 gamma gi K.IHNAENIQPGEQK.Y eukaryotic translation initiation factor 5A; eif5a gi K.VHLVGIDIFTGK.K Ezrin (p81) (Cytovillin) gi K.FVIKPIDK.K F-actin capping protein alpha-1 subunit; Cap Z gi K.IIENAENEYQTAISENYQTMSDTTFK.A F-actin capping protein alpha-1 subunit; Cap Z R.EGAAHAFAQYNMDQFTPVK.I F-actin capping protein beta subunit gi K.NLSDLIDLVPSLC*EDLLSSVDQPLK.I Familial Als Mutant G37r Cuznsod gi R.HVGDLGNVTADK.D Familial Als Mutant G37r Cuznsod R.TLVVHEK.A filamin 1 (actin-binding protein-280) gi R.NGHVGISFVPK.E fructose-1,6-bisphosphate aldolase A gi PYQYPALTPEQK.K fumarate hydratase gi R.THTQDAVPLTLGQEFSGYVQQVK.Y fumarate hydratase K.LHDALDAK.S fumarate hydratase K.IPVHPNDHVNK.S Gamma enolase gi R.HIAQLAGNSDLILPVPAFNVINGGSHAGNK.L glioblastoma amplified sequence gi K.LQFHNVKPEC*LEAYNK.I glucose phosphate isomerase, GPI gi K.TLAQLNPESSLFIIASK.T glucose phosphate isomerase, GPI R.SNTPILVDGK.D

7 glucose phosphate isomerase, GPI R.VWYVSNIDGTHIAK.T glucose phosphate isomerase, GPI R.VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK.M glucose-regulated protein precursor gi 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 K.NPEVGLKPVWYSPK.V Glyceraldehyde 3-phosphate dehydrogenase gi K.IISNASC*TTNC*LAPLAK.V glyceraldehyde-3-phosphate dehydrogenase gi 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 K.ATLELTHNWGTEDDATQSYHNGNSDPR.G GTP-binding nuclear protein RAN (TC4) (Ran GTPase) gi K.LVLVGDGGTGK.T GTP-binding nuclear protein RAN (TC4) (Ran GTPase) K.NLQYYDISAK.S heat shock 10kD protein 1 (chaperonin 10) gi K.VLLPEYGGTK.V heat shock 10kD protein 1 (chaperonin 10) K.VLQATVVAVGSGSK.G Heat shock 70 kda protein 1 (HSP70.1) gi K.AAAIGIDLGTTYSC*VGVFQHGK.V HEAT SHOCK 70 KDA PROTEIN 4 gi K.LNLQNK.Q heat shock 70kDa protein 6 (HSP70B') gi 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 K.SINPDEAVAYGAAVQAAILSGDK.S heat shock 70kDa protein 9B precursor gi 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 K.YIDQEELNK.T heat shock protein 90-beta R.TLTLVDTGIGMTK.A heat shock protein 90-beta K.HLEINPDHPIVETLR.Q

8 Heat shock protein HSP 90-alpha (HSP 86) gi 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 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 K.HLVMGDIPAAVNAFQEAASLLGK.K hnrnp A2/B1, isoform B1 gi R.EESGKPGAHVTVK.K hnrnp C-like protein gi K.YHNVGLSK.C hnrnp K isoform b gi R.IITITGTQDQIQNAQYLLQNSVK.Q hnrnp U gi K.SSGPTSLFAVTVAPPGAR.Q Human Carbonic Anhydrase gi K.VGSAKPGLQK.V HUMAN Elongation factor 1-delta gi R.GVVQELQQAISK.L HUMAN Elongation factor 1-delta K.KPALVAK.S HUMAN Glutathione S-transferase P (GSTP1-1) gi K.ALPGQLKPFETLLSQNQGGK.T Human Heart L-Lactate Dehydrogenase gi 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 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 K.DYNVTANSK.L Human P32, Acidic Mitochondrial Matrix Protein gi K.VEEQEPELTSTPNFVVEVIK.N human PGP 9.5 homologue gi MQLKPMEXDPEMLNK.V Human Platelet Profilin gi K.TFVNITPAEVGVLVGK.D Human Platelet Profilin R.SSFYVNGLTLGGQK.C Human Platelet Profilin K.STGGAPTFNVTVTK.T HUMAN Putative GTP-binding protein gi K.IHTDFEK.G HUMAN Stress-induced-phosphoprotein 1 gi K.NPVIAQK.I HUMAN T-complex protein 1, epsilon subunit gi 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 R.AVAQALEVIPR.T

9 HUMAN T-complex protein 1, gamma subunit R.NVLLDPQLVPGGGASEMAVAHALTEK.S HUMAN T-complex protein 1, gamma subunit R.EIQVQHPAAK.S hypothetical protein DKFZp434K gi K.AIANEC*QANFISIK.G lactate dehydrogenase, LDH-A gi R.NVNIFK.F laminin receptor 1 (67kD, ribosomal protein SA) gi R.ADHQPLTEASYVNLPTIALC*NTDSPLR.Y macrophage myristoylated alanine-rich C kinase substrate gi R.GDVTAEEAAGASPAK.A malate dehydrogenase gi K.VIVVGNPANTNC*LTASK.S Malate dehydrogenase, mitochondrial precursor gi K.VAVLGASGGIGQPLSLLLK.N Malate dehydrogenase, mitochondrial precursor R.IQEAGTEVVK.A Malate dehydrogenase, mitochondrial precursor R.LTLYDIAHTPGVAADLSHIETK.A methionine adenosyltransferase II, alpha gi K.TC*NVLVALEQQSPDIAQGVHLDR.N methionine--trna ligase gi K.TSPKPAVVETVTTAKPQQIQALMDEVTK.Q mitochondrial short-chain enoyl-coenzyme A hydratase 1 gi K.IC*PVETLVEEAIQC*AEK.I mitochondrial short-chain enoyl-coenzyme A hydratase 2 K.NNTVGLIQLNRPK.A murine mammary tumor integration site 6 gi R.MLFDYLADK.H myc far upstream element-binding protein gi K.AGLVIGK.G myristoylated alanine-rich PKC substrate (MARCKS) gi K.GEPAAAAAPEAGASPVEK.E myristoylated alanine-rich PKC substrate (MARCKS) K.GEAAAERPGEAAVASSPSK.A N8 gene product long isoform gi K.ASAAFSSVGSVITK.K N-acetylglucosamine-specific receptor 1 precursor gi R.INEILSNALK.R nef protein [Human immunodeficiency virus 1] gi R.ENSSLLHPICQHGMDDEER.E neuropolypeptide h3 gi K.WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK.V NKEF-B homolog/thiol-dependent antioxidant protein gi IGKPAPDFK.A N-Terminal Actin-Crosslinking Domain From Human Fimbrin gi K.AYFHLLNQIAPK.G nuclease sensitive element-binding protein 1 gi K.GAEAANVTGPGGVPVQGSK.Y nucleolin gi K.VEGTEPTTAFNLFVGNLNFNK.S Nucleoside diphosphate kinase A (NDK A) gi R.VMLGETNPADSKPGTIR.G Nucleoside diphosphate kinase A (NDK A) R.NIIHGSDSVESAEK.E nucleosomal binding protein 1 gi K.ITEAPASEK.E

10 ORF 56 gi K.EQLLVSR.H ornithine aminotransferase, OAT gi R.WLAVDYENVRPDIVLLGK.A oxysterol binding protein gi R.GATVLPANTPGNVGSGK.D PAI-1 mrna-binding protein gi R.RPDQQLQGEGK.I PAI-1 mrna-binding protein R.KPNEGADGQWK.K PDZ and LIM domain 1 gi K.VAASIGNAQK.L peptidylprolyl cis-trans isomerase gi K.GEHSIVYLKPSYAFGSVGK.E peptidylprolyl isomerase F (cyclophilin F) gi R.VIPSFMC*QAGDFTNHNGTGGK.S peroxiredoxin 1 gi 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 R.GLFIIDGK.G Peroxiredoxin 2 K.ATAVVDGAFK.E peroxiredoxin 3 gi K.AFQYVETHGEVC*PANWTPDSPTIKPSPAASK.E peroxiredoxin 3 K.NGGLGHMNIALLSDLTK.Q Peroxiredoxin 4 (Prx-IV) (Thioredoxin peroxidase) gi R.GLFIIDDK.G peroxiredoxin 5 gi K.ALNVEPDGTGLTC*SLAPNIISQL.- peroxiredoxin 5 K.GVLFGVPGAFTPGC*SK.T Peroxisomal acyl-coenzyme A thioester hydrolase 2 gi R.GLAPEQPVTLR.A Phenylalanyl-tRNA synthetase beta chain gi K.AVHISNPK.T phosphoglycerate kinase 1 gi 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 K.LGDVYVNDAFGTAHR.A phosphoglycerate mutase 1 gi K.NLKPIKPMQFLGDEETVR.K Phosphoglycerate mutase 2 gi K.AMEAVAAQGK.A Phosphoglycerate mutase 2 R.VLIAAHGNSLR.G phosphoglycerate mutase processed protein gi R.ALPFWNEEIVPQIK.E phosphoglycerate mutase processed protein R.SYDVPPPPMEPDHPFYSNISK.D phosphopyruvate hydratase human gi R.AAVPSGASTGIYEALELR.D phosphopyruvate hydratase human K.VNQIGSVTESIQAC*K.L

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

12 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 K.LTPITYPQGLAMAK.E replication protein A1, 70kDa gi K.AAGPSLSHTSGGTQSK.V replication protein A3, 14kDa gi R.INAGMLAQFIDKPVC*FVGR.L ribosomal protein HL6, cytosolic gi K.VLATVTKPVGGDK.N ribosomal protein L13, cytosolic gi K.LATQLTGPVMPVR.N RNA-binding protein regulatory subunit gi K.EGPYDVVVLPGGNLGAQNLSESAAVK.E RNA-binding protein regulatory subunit K.VTTHPLAK.D SEB4B protein - human gi R.FVNVVPTFGK.K SECIS binding protein 2 gi K.NVSIPSSEALSSDPSYNK.E secretory carrier membrane protein 1 gi K.TVQTAAANAASTAASSAAQNAFK.G Ser/Thr protein phosphatase 2A (PP2A, subunit A, PR65-alpha) gi R.AISHEHSPSDLEAHFVPLVK.R similar to tubulin alpha 1 [Mus musculus] gi K.AYHEQLSVAEITNAC*FEPANQMVK.C spectrin alpha chain, nonerythroid gi R.ELELQK.E sperm surface protein gi K.ERPISLGIFPLPAGDGLLTPDAQK.G stromal cell-derived factor 2-like 1 gi R.LTHVLTGK.N Talin 1 gi 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 K.GANINEK.T T-complex protein 1, alpha subunit gi R.SLLVIPNTLAVNAAQDSTDLVAK.L T-complex protein 1, alpha subunit R.SQNVMAAASIANIVK.S T-complex protein 1, theta subunit (TCP-1-theta) gi K.ANEVISK.L template activating factor-i gi K.KPRPPPALGPEETSASAGLPK.K Thermostable Mutant Of Human Superoxide Dismutase gi K.GLTEGLHGFHVHEFGDNTAGC*TSAGPHFNPLSR.K Thioredoxin gi K.VGEFSGANK.E Threonyl-tRNA synthetase, cytoplasmic gi R.NELSGALTGLTR.V

13 transaldolase 1 gi K.IHLDEK.S Transcription factor BTF3 gi R.LAEALPK.Q transcription factor NF-AT 90K chain gi R.LNQLKPGLQYK.L transcription factor ZFM1 gi R.HNLITEMVALNPDFKPPADYKPPATR.V transketolase gi K.ILATPPQEDAPSVDIANIR.M transketolase R.TSRPENAIIYNNNEDFQVGQAK.V transketolase R.VLDPFTIKPLDR.K transketolase K.ISSDLDGHPVPK.Q translocase of inner mitochondrial membrane 9 gi K.VQIAVANAQELLQR.M triosephosphate isomerase 1 gi 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 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 R.EIVHIQAGQC*GNQIGAK.F tubulin, beta, 2 gi R.INVYYNEATGGK.Y tubulin, beta, 2 K.LTTPTYGDLNHLVSATMSGVTTC*LR.F tumor necrosis factor type 1 receptor associated protein gi R.AQLLQPTLEINPR.H Tumor rejection antigen-1 (gp96) gi 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 R.EQLVQK.A U5 snrnp-specific protein, 116 kd gi R.GGGQIIPTAR.R Ubiquitin C-terminal esterase L1 gi K.NEAIQAAHDAVAQEGQC*R.V Ubiquitin C-terminal esterase L1 K.QTIGNSC*GTIGLIHAVANNQDK.L

14 ubiquitin-activating enzyme E1 gi R.IYDDDFFQNLDGVANALDNVDAR.M ubiquitin-activating enzyme E1 R.AAVATFLQSVQVPEFTPK.S ubiquitin-activating enzyme E1 R.KPLLESGTLGTK.G ubiquitin-conjugating enzyme E2L 3 gi 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 K.TNEAQAIETAR.A Ubiquitin-like protein SMT3B gi K.VAGQDGSVVQFK.I Ubiquitin-like protein SMT3B K.TENNDHINLK.V UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 1 gi R.NENTFLDLTVQQIEHLNK.S valosin-containing protein gi K.NAPAIIFIDELDAIAPK.R valosin-containing protein R.AHVIVMAATNRPNSIDPALR.R valosin-containing protein K.AIGVKPPR.G vesicle docking protein p115 gi R.NQELLQSQLTEK.D vesicle docking protein p115 K.SSQTSGTNEQSSAIVSAR.D Vinculin (Metavinculin) gi K.AIPDLTAPVAAVQAAVSNLVR.V voltage-dependent anion channel 1 gi K.VNNSSLIGLGYTQTLKPGIK.L voltage-dependent anion channel 2 gi K.VNNSSLIGVGYTQTLRPGVK.L

15 Supplemental Table 2, "Sample preparation and digestion for proteomic analyses using spin filters", Manza et al. Nuclear protein identifications Protein Accession # Peptide epsilon gi K.AAFDDAIAELDTLSEESYK.D epsilon K.EAAENSLVAYK.A epsilon K.AASDIAMTELPPTHPIR.L epsilon K.HLIPAANTGESK.V protein beta/alpha gi K.EMQPTHPIR.L protein eta chain gi K.AVTELNEPLSNEDR.N protein tau gi K.AVTEQGAELSNEER.N S ribosomal protein S31, mitochondrial precursor (S31mt) gi R.IEPLSPELVAAASAVADSLPFDK.Q S ribosomal protein S31, mitochondrial precursor (S31mt) K.EAPETDTSPSLWDVEFAK.Q S ribosomal protein S10 gi K.HPELADK.N S ribosomal protein S12 gi K.TALIHDGLAR.G S ribosomal protein S16 gi K.LLEPVLLLGK.E S ribosomal protein S17 gi R.DNYVPEVSALDQEIIEVDPDTK.E S ribosomal protein S17 K.LLDFGSLSNLQVTQPTVGMNFK.T S ribosomal protein S2, cytosolic gi K.SLEEIYLFSLPIK.E S ribosomal protein S3 gi K.KPLPDHVSIVEPK.D S ribosomal protein S3a gi R.EVQTNDLK.E S ribosomal protein S3a K.LITEDVQGK.N S ribosomal protein S3a K.AC*QSIYPLHDVFVR.K S ribosomal protein S4 gi K.FDTGNLC*MVTGGANLGR.I S ribosomal protein S4 R.LSNIFVIGK.G S ribosomal protein S4 K.GIPHLVTHDAR.T S ribosomal protein S5, cytosolic gi K.TIAEC*LADELINAAK.G S ribosomal protein S5, cytosolic R.VNQAIWLLC*TGAR.E S ribosomal protein S6 gi K.LIEVDDER.K S ribosomal protein S7 gi K.DVNFEFPEFQL S ribosomal protein S8 gi R.LDVGNFSWGSEC*C*TR.K S ribosomal protein S8 R.ADGYVLEGK.E S ribosomal protein S9 gi R.IGVLDEGK.M kda heat shock protein (Hsp60) gi K.LVQDVANNTNEEAGDGTTTATVLAR.S kda heat shock protein (Hsp60) K.IMQSSSEVGYDAMAGDFVNMVEK.G 5.62

16 60 kda heat shock protein (Hsp60) R.ALMLQGVDLLADAVAVTMGPK.G kda heat shock protein (Hsp60) K.VGGTSDVEVNEK.K kda heat shock protein (Hsp60) K.VGEVIVTK.D kda heat shock protein (Hsp60) R.GYISPYFINTSK.G kda heat shock protein (Hsp60) K.VGLQVVAVK.A S acidic ribosomal protein P0 gi K.AFLADPSAFVAAAPVAAATTAAPAAAAAPAK.V S acidic ribosomal protein P0 R.AGAIAPC*EVTVPAQNTGLGPEK.T S acidic ribosomal protein P0 K.IIQLLDDYPK.C 3 60S acidic ribosomal protein P1 gi K.ALANVNIGSLIC*NVGAGGPAPAAGAAPAGGPAPST AAAPAEEK.K S acidic ribosomal protein P1 K.AAGVNVEPFWPGLFAK.A S acidic ribosomal protein P2 gi K.LASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEK.K S acidic ribosomal protein P2 R.YVASYLLAALGGNSSPSAK.D S ribosomal protein L10a gi K.FSVC*VLGDQQHC*DEAK.A S ribosomal protein L13a gi R.LAHEVGWK.Y S ribosomal protein L14 gi K.LVAIVDVIDQNR.A S ribosomal protein L15 gi R.NPDTQWITKPVHK.H S ribosomal protein L18 gi K.ILTFDQLALDSPK.G S ribosomal protein L18a gi R.IFAPNHVVAK.S S ribosomal protein L19 K.TAVVVGTITDDVR.V S ribosomal protein L21 gi R.VYNVTQHAVGIVVNK.Q S ribosomal protein L21 K.HGVVPLATYMR.I S ribosomal protein L23a gi K.VNTLIRPDGEK.K S ribosomal protein L27 gi K.VYNYNHLMPTR.Y S ribosomal protein L29 gi K.AQAAAPASVPAQAPK.R S ribosomal protein L3 gi R.LEQQVPVNQVFGQDEMIDVIGVTK.G S ribosomal protein L3 K.NNASTDYDLSDK.S S ribosomal protein L31 gi K.NLQTVNVDEN S ribosomal protein L32 gi K.SYC*AEIAHNVSSK.N S ribosomal protein L4 gi R.YAIC*SALAASALPALVMSK.G S ribosomal protein L4 R.NIPGITLLNVSK.L S ribosomal protein L4 K.APIRPDIVNFVHTNLR.K S ribosomal protein L5 gi K.GAVDGGLSIPHSTK.R S ribosomal protein L7a gi K.VAPAPAVVK.K S ribosomal protein L8 gi R.ASGNYATVISHNPETK.K 3.16 acetyl-coenzyme A acetyltransferase 1 gi K.EAYMGNVLQGGEGQAPTR.Q 4.22

17 acetyl-coenzyme A acetyltransferase 1 R.TPIGSFLGSLSLLPATK.L 4.34 acetyl-coenzyme A acetyltransferase 1 K.VNINGGAVSLGHPIGMSGAR.I 4.69 Actin gi 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 R.QVGSISMDLQLTNK.A 2.66 Adenosylhomocysteinase gi R.GISEETTTGVHNLYK.M 3.9 ADP,ATP carrier protein T2 gi 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 R.GGPPFAFVEFEDPR.D 3.98 Annexin V (Lipocortin V) gi R.GTVTDFPGFDER.A 3.6 Arsenite-resistance protein 2 gi R.ISHGEVLEWQK.T 2.47 ATP synthase gi K.AQAELVGTADEATR.A 3.97 ATP synthase oligomycin sensitivity conferral protein gi R.GEVPC*TVTSASPLEEATLSELK.T 3.38 ATP synthase oligomycin sensitivity conferral protein R.FSPLTTNLINLLAENGR.L 4.52 ATP synthase, alpha subunit gi R.EVAAFAQFGSDLDAATQQLLSR.G 5.95 ATP synthase, H+ transporting, mitochondrial F0 complex gi R.LAALPENPPAIDWAYYK.A 2.58 ATPB_HUMAN ATP synthase beta chain, mitochondrial precursor gi 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 R.LKPDEGGEVPVLNVSYKPQK.I 2.7 ATP-citrate (pro-s-)-lyase (Citrate cleavage enzyme) gi K.GVTIIGPATVGGIKPGC*FK.I 4.2 ATP-dependant DNA helicase II gi 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

18 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 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 R.TTGIVMDSGDGVTHTVPIYEGYALPHAILR.L 5.49 beta-fodrin gi R.QNLLSQSHAYQQFLR.D 4.02 beta-tubulin gi 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 K.ETPAATEAPSSTPK.A 3.24 Calponin Homology (Ch) Domain From Human Beta-Spectrin gi K.TAGYPNVNIHNFTTSWR.D 4.03 capsid protein gi R.DAADAVR.A 2.32 catenin gi K.AHVLAASVEQATENFLEK.G 3.91 cell division cycle 2 protein, isoform 1 gi R.LESEEEGVPSTAIR.E 3.17 chaperonin containing TCP1, subunit 4 (delta) gi R.AFADAMEVIPSTLAENAGLNPISTVTELR.N 4.91 chaperonin containing TCP1, subunit 4 (delta) K.GIHPTIISESFQK.A 3.4 chaperonin containing TCP1, subunit 6A gi 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 K.LPIGDVATQYFADR.D 3.63 chromosome 17 open reading frame 31 gi R.LLESR.K 2.06 clathrin heavy chain gi 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 R.AVSDASAGDYGSAIETLVTAISLIK.Q 6.38 cleavage stimulation factor subunit 3 gi R.GC*VNPMINIEQLWR.D 3.73 cofilin 1 (non-muscle) gi K.MIYASSK.D 2.2

19 Contactin associated protein-like 4 precursor gi R.LISISGK.V 2.03 creatine kinase-b gi K.TDLNPDNLQGGDDLDPNYVLSSR.V 4.5 creatine kinase-b R.FC*TGLTQIETLFK.S 3.74 Cyclophilin A gi K.FEDENFILK.H 2.93 cytochrome c gi K.TGPNLHGLFGR.K 2.7 cytochrome c oxidase subunit IV gi R.DHPLPEVAHVK.H 2.42 cytochrome c oxidase subunit VIb gi R.NC*WQNYLDFHR.C 3.87 d(ttaggg)n-binding protein B39 gi GFGFVLFK.E 2.04 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 isoform 1 gi 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 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 K.HVINFDLPSDIEEYVHR.I 5.22 DEAD-box protein 3 R.YTRPTPVQK.H 2.22 DEK oncogene (DNA binding) gi 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 K.STLINSLFLTDLYPER.V 3.6 Dihydrolipoamide acetyltransferase component of pyruvate de gi K.GVETIANDVVSLATK.A 3.67 dihydrolipoamide dehydrogenase precursor gi K.ADGGTQVIDTK.N 3.63 Dihydrolipoamide succinyltransferase component of 2-oxoglut gi K.AKPAEAPAAAAPK.A 2.7 DNA topoisomerase I gi K.GPVFAPPYEPLPENVK.F 3.3 DNA topoisomerase II, alpha isozyme gi K.ELILFSNSDNER.S 3.44 DNA-activated protein kinase gi K.TVSLLDENNVSSYLSK.N 3.6 DNA-activated protein kinase, catalytic subunit gi R.VEQLFQVMNGILAQDSAC*SQR.A 5.79 DNA-activated protein kinase, catalytic subunit R.NELEIPGQYDGR.G 3.39

20 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 K.SINPDEAVAYGAAVQAAILMGDK.S 6.18 dnak-type molecular chaperone HSPA1L gi 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 K.NFESLSEAFSVASAAAVLSHNR.Y 4.84 Double-stranded RNA-specific adenosine deaminase gi R.NAEFLTC*NIPTSNASNNMVTTEK.V 3.95 dyskerin gi R.ALETLTGALFQRPPLIAAVK.R 5.17 E1B PROTEIN, LARGE T-ANTIGEN gi K.YSIEQLTTYWLQPGDDFEEAIR.V 3.84

21 E1B PROTEIN, LARGE T-ANTIGEN R.AEFGSSDEDTD 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 K.SC*GELFDSLNLGHQALFQEK.V 4.35 early-pregnancy factor, EPF=chaperonin 10 gi R.DGDILGK.Y 2.02 EBNA-2 co-activator (100kD) gi R.VADISGDTQK.A 2.85 EBNA-2 co-activator (100kD) K.LRPLYDIPYMFEAR.E 2.74 ELAV-like protein 1 (Hu-antigen R) gi 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 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 K.SPAGLQVLNDYLADK.S 5.25 Elongation factor 1-beta (EF-1-beta) K.SSILLDVKPWDDETDMAK.L 3.58 Elongation factor 2 (EF-2) gi 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 R.YNIPHGPVVGSTR.R 2.57 enhancer of rudimentary homolog gi R.TYADYESVNECMEGVCK.M 2.87 enhancer of rudimentary homolog R.ADTQTYQPYNK.D 3.53 enolase 1; phosphopyruvate hydratase gi 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

22 enolase alpha gi R.YISPDQLADLYK.G 3.91 enolase alpha R.IGAEVYHNLK.N 4.01 enoyl-coa hydratase alpha gi K.TVLGTPEVLLGALPGAGGTQR.L 3.14 eukaryotic translation elongation factor 1 gi R.ILGLLDAYLK.T 2.03 eukaryotic translation elongation factor 1 R.WFLTC*INQPQFR.A 3.77 eukaryotic translation initiation factor 3, subunit 5 gi R.LHPVILASIVDSYER.R 4.4 eukaryotic translation initiation factor 3, subunit 8 gi K.SEQDQAENEGEDSAVLMER.L 6.14 Eukaryotic translation initiation factor 4 gamma gi R.LQGINC*GPDFTPSFANLGR.T 4.24 eukaryotic translation initiation factor 4A1 (eif- 4A-I) gi R.GIYAYGFEKPSAIQQR.A 4.18 eukaryotic translation initiation factor 5A; eif5a gi K.VHLVGIDIFTGK.K 3.27 Ewing sarcoma breakpoint region gi R.AGDWQC*PNPGC*GNQNFAWR.T 4.07 Familial Als Mutant G37r Cuznsod gi K.GDGPVQGIINFEQK.E 3.47 FBRL gi K.LAAAILGGVDQIHIKPGAK.V 3.83 GAP-associated tyrosine phosphoprotein p62 (Sam68) gi 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 K.NTNDANSC*QIIIPQNQVNR.K 3.88 glioblastoma amplified sequence gi K.LQFHNVKPEC*LEAYNK.I 3.99 glucose-regulated protein precursor (GRP 78) gi 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 K.ALPGQLKPFETLLSQNQGGK.T 3.26 Glyceraldehyde 3-phosphate dehydrogenase gi K.IISNASC*TTNC*LAPLAK.V 3.55 glyceraldehyde-3-phosphate dehydrogenase gi R.VPTANVSVVDLTC*R.L 4

23 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 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 R.SNYNFEKPFLWLAR.R 3.78 GTP-binding protein Rab2 gi K.IQEGVFDINNEANGIK.I 3.75 guanine nucleotide-binding protein, beta-2 subunit gi R.AGVLAGHDNR.V 2.14 H1 histone family gi R.GAPAAATAPAPTAHK.A 3.29 H1 histone family, member 1 gi K.ALAAAGYDVEK.N 3.03 H2A histone family, member A gi R.VTIAQGGVLPNIQAVLLPK.K 4.28 H2A histone family, member A R.NDEELNK.L 2.29 ha1225 gene product (related to human alphaglucosidase) gi R.FGAVWTGDNTAEWDHLK.I 3.08 Heat shock 70 kda protein 1 (HSP70.1) gi K.AAAIGIDLGTTYSC*VGVFQHGK.V 4.09 heat shock 70kDa protein 2 gi K.DNNLLGK.F 2.05 heat shock 70kDa protein 6 (HSP70B') gi 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 K.TVTNAVVTVPAYFNDSQR.Q 3.31 heat shock 70kDa protein 8 K.SFYPEEVSSMVLTK.M 3.52 heat shock 70kDa protein 9B precursor gi 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

24 heat shock protein 90-beta gi 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 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 K.VATLNSEEESDPPTYK.D 3.82 high mobility group AT-hook 1 isoform a gi K.EEEEGISQESSEEEQ Histone H1.2 gi K.KPAAATVTK.K 2.28 Histone H2B.l gi K.AMGIMNSFVNDIFER.I 4.17 Histone H2B.l K.QVHPDTGISSK.A 2.83 HLA-B associated transcript-1; DEAD-box protein gi 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 K.AAEVLNK.H 2.12 hnrna-binding protein M4 R.GNFGGSFAGSFGGAGGHAPGVAR.K 4.88 hnrnp A0 gi 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 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

25 hnrnp A1 R.SSGPYGGGGQYFAKPR.N 4.07 hnrnp A2/B1, isoform B1 gi 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 K.IETIEVMEDR.Q 3.62 hnrnp A3 R.SSGSPYGGGYGSGGGSGGYGSR.R 4.75 hnrnp A3 R.EDSVKPGAHLTVK.K 2.49 hnrnp AB isoform b gi 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 R.MIASQVVDINLAAEPK.V 2.98 hnrnp C-like protein gi 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 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 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 R.GAYGGGYGGYDDYNGYNDGYGFGSDR.F 4.95 hnrnp H1 R.YGDGGSTFQSTTGHC*VHMR.G 4.06 hnrnp H2 gi R.STGEAFVQFASQEIAEK.A 4.2 hnrnp H2 R.DLNYC*FSGMSDHR.Y 3.2 hnrnp H2 R.YVEVFK.S 2.02

26 hnrnp H2 K.HTGPNSPDTANDGFVR.L 4 hnrnp H2 R.VHIEIGPDGR.V 2.6 hnrnp H2 K.HTGPNSPDTANDGFVR.L 3.92 hnrnp homolog JKTBP gi R.YHQIGSGK.C 2.54 hnrnp K isoform b gi 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 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 K.MEEESGAPGVPSGNGAPGPK.G 2.96 hnrnp R gi 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 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

27 hnrnp U K.FIEIAAR.K 2.16 hnrnp U K.HAAENPGK.Y 2.08 HUMAN 7-dehydrocholesterol reductase gi K.FLPGYVGGIQEGAVTPAGVVNK.Y 3.64 Human DEAD-box protein p72 gi R.TTSSANNPNLMYQDEC*DR.R 3.85 HUMAN Elongation factor 1-delta (EF-1-delta) gi K.KPALVAK.S 2.15 Human Heart L-Lactate Dehydrogenase gi K.LIAPVAEEEATVPNNK.I 3.03 Human P32, Acidic Mitochondrial Matrix Protein gi K.VEEQEPELTSTPNFVVEVIK.N 4.9 Human Platelet Profilin gi K.TFVNITPAEVGVLVGK.D 4.28 Human Platelet Profilin K.TLVLLMGK.E 2.15 HUMAN Putative pre-mrna splicing factor RNA helicase gi 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 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 R.FAKPVYPGQTLQTEMWK.E 2.41 HYPOTHETICAL PROTEIN KIAA0179 gi K.SSTATHPPGPAVQLNK.T 3.61 hypothetical protein KIAA0324 gi K.SEEPAGQILSHLSSELK.E 4.33 Integrin alpha-8 gi R.LEGGESAVLK.V 2.13 Interleukin enhancer-binding factor 3 gi K.AVSDWIDEQEK.G 3.32 karyopherin (importin) beta 1 gi R.AAVENLPTFLVELSR.V 2.26 karyopherin (importin) beta 1 K.GALQYLVPILTQTLTK.Q 2.88 KIAA0111 gene product gi R.DVIAQSQSGTGK.T 2.13 laminin receptor 1 gi R.ADHQPLTEASYVNLPTIALC*NTDSPLR.Y 3.5 leucine-rich protein - human gi R.DAGIEPGPDTYLALLNAYAEK.G 4.23 leucine-rich protein - human K.GDVENIEVVQK.M 3.53 MAGUK p55 subfamily member 6 gi K.EGGSAGLIPSQFLEEK.R 2.76 Malate dehydrogenase gi K.VAVLGASGGIGQPLSLLLK.N 5.84 matrin 3 gi R.DLSAAGIGLLAAATQSLSMPASLGR.M 4.54 matrin 3 R.IGPYQPNVPVGIDYVIPK.T 3.72 matrin 3 R.GNLGAGNGNLQGPR.H 2.33

28 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 R.TSILAAANPISGHYDR.S 2.37 microtubule-associated protein gi R.INEAEK.E 2.01 mitochondrial short-chain enoyl-coenzyme A hydratase gi K.AQFAQPEILIGTIPGAGGTQR.L 3.88 mitochondrial short-chain enoyl-coenzyme A hydratase K.IC*PVETLVEEAIQC*AEK.I 3.48 Muscle Aldolase gi K.DGADFAK.W 2.11 Muscle Aldolase K.GILAADESTGSIAK.R 3.49 myomesin (M-protein) 2 gi K.ATGIIEMVMDR.F 2.1 myosin heavy chain nonmuscle form A gi K.DFSALESQLQDTQELLQEENR.Q 4.98 myosin IXB gi K.YLDEFLLNK.I 2.45 Nascent polypeptide associated complex alpha subunit gi K.NILFVITKPDVYK.S 4.45 nicotinamide nucleotide transhydrogenase gi K.TSGTLISFIYPAQNPELLNK.L 3.67 nicotinamide nucleotide transhydrogenase K.AVVLAANHFGR.F 3.14 nonhistone chromosomal protein HMG-2B gi K.SEHPGLSIGDTAK.K 3.45 nuclear mitotic apparatus protein 1 gi R.VEFATLQEALAHALTEK.E 5.8 Nuclear protein Hcc-1 (HSPC316) gi R.FGIVTSSAGTGTTEDTEAK.K 4.31 nuclear ribonucleoprotein particle C2 protein gi R.MIAGQVLDINLAAEPK.V 3.22 nuclear ribonucleoprotein particle C2 protein K.SDVEAIFSK.Y 2.08 nuclease sensitive element-binding protein 1 gi R.RPQYSNPPVQGEVMEGADNQGAGEQGRPVR.Q 3.85 nucleolar and coiled-body phosphoprotein 1 gi 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 R.LIAHAGSLLNLAK.H 3.29 Nucleolar protein Nop56 gi K.EEPVSSGPEEAVGK.S 2.45 nucleolin gi K.TLVLSNLSYSATEETLQEVFEK.A 4.7 nucleolin K.VEGTEPTTAFNLFVGNLNFNK.S 4.41 nucleolin K.EAMEDGEIDGNK.V 3.16 nucleolin K.EVFEDAAEIR.L 3.49