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Home , Ribosomal protein SA, Tropomyosin 3

ELECTROPHORESIS

Supporting Information for Electrophoresis DOI 10.1002/elps.200600696

Jinfeng Liu, Yun Cai, Jinglan Wang, Qi Zhou, Bing Yang, Zhuang Lu, Liyan Jiao, Dongyang Zhang, Shaohui Sui, Ying Jiang, Wantao Ying and Xiaohong Qian

Phosphoproteome profile of human liver Chang’s cell based on 2-DE with fluorescence staining and MALDI-TOF/TOF MS

ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.electrophoresis-journal.com

Figures S1:The distribution of the spots selected for MALDI-TOF/TOF-MS identification.

Table S1: Cellular location and functional classification of phosphoproteins in Chang’s cells Protein name Protein ID Subcellular Protein function

location

HS9B_ Heat shock P08238 positive regulation of nitric oxide

protein HSP90-beta biosynthesis；nitric-oxide synthase

(HSP 84) regulator activity；binding

G3BP_ Ras-GTPase- Q13283 nucleus transport； Ras protein signal

activating protein cytoplasm transduction；catalytic activity binding protein 1

VIME_ P08670 cytoplasm structural constituent of

cytoskeleton protein binding

cell motility

RLA0_ 60S acidic P05388 binding；protein

ribosomal proteinP0 biosynthesis；translational

elongation；structural constituent of

ribosome

HS27_Heat shock 27 P04792 cytoplasm protein binding；regulation of

kDa protein(HSP 27) cytoskeleton translational initiation；protein cell surface folding；anti-apoptosis；cell

motility；response to unfolded

protein

NDKA_Nucleoside P15531 nucleus binding; biosynthesis; catalytic

diphosphatekinase A cytoplasm activity; cell cycle; regulation of

apoptosis EF1B_Elongation P24534 eukaryotic factor 1-beta translation activity；protein binding；protein

elongation factor biosynthesis；translational 1 complex elongation

PSA5_ Proteasome P28066 proteasome core threonine endopeptidase activity subunit alpha type 5 complex ubiquitin-dependent protein

catabolism

TCTP_Translationally P13693 cytoplasm;multiv calcium ion controlletumor protein esicular body; transport、homeostasis、binding；

anti-apoptosis；regulation of

apoptosis

RLA2_ 60S acidic P05387 ribosome binding；protein ribosomal proteinP2 biosynthesis；translational

elongation；structural constituent of

ribosome

Z255_ Zinc finger Q9UID9 nucleus binding； protein 255

Table S2: The list of identified by MALDI-TOF/TOF-MS in Chang’s cells

Spot Protein Name Accession Position Number 1 NCL protein IPI00183526.4 CDNA FLJ45706 fis, clone FEBRA2028457, highly similar to Nucleolin IPI00444262.1 Hypothetical protein FLJ34423 IPI00604517.1 Hypothetical protein NCL IPI00604620.1 2 Nucleolin IPI00217506.4 3 Endoplasmin precursor IPI00027230.3 4 GARS protein IPI00465260.1 5 Splice Isoform A of Ras-GTPase-activating protein binding p IPI00009057.1 Ras-GTPase-activating prot IPI00012442.1 Splice Isoform B of Ras-GTPase-activating protein binding protein 2 IPI00179890.2 6 CDNA FLJ26493 fis, clone KDN06317, highly similar to Ras-GTPase- activating protein bin IPI00442863.1 7 Cytoskeleton associated protein 2 IPI00071824.2 Clusterin precursor IPI00291262.3 Clusterin isoform 1 IPI00400826.1 8 Similar to A/C IPI00514320.2 Lamin A\/C IPI00514817.3 Chaperonin Containing TCP1, subunit 3 isoform C IPI00552715.1 T-complex protein 1, gamma subunit IPI00553185.2 9 Hypothetical protein DKFZp761K0511 IPI00334775.3 10 Splice Isoform 1 of Mitochondrial inner membrane protein IPI00009960.6 Splice Isoform 3 of Mitochondrial inner membrane protein IPI00470829.2 Splice Isoform 2 of Mitochondrial inner membrane protein IPI00554469.1 11 Heat shock protein 90Ad IPI00555957.1 12 Heat shock protein HSP 90-alpha 2 IPI00382470.2 Tax_Id IPI00414676.5 Heat shock protein 90Bc IPI00555614.1 Heat shock protein HSP 90-alp IPI00604607.1 13 Splice Isoform A of Lami IPI00021405.3 Splice Isoform C of Lamin A/C IPI00216952.1 Splice Isoform ADelta10 of Lamin A/C IPI00216953.1 Bifunctional purine biosynthesis protein PURH IPI00289499.3 14 Nucleosome assembly protein 1-like IPI00023860.1 Synapse associated protein 1 IPI00059242.3 15 Splice Isoform 1 of Calumenin precursor IPI00014537.1 Splice Isoform 2 of Calumenin precursor IPI00045396.1 16 Splice Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049.1 Splice Isoform 2 of Heterogeneous nucl IPI00216746.1 PREDICTED: similar to heterogeneous nuclear ribonucleoprotein K IPI00398052.2 Heterogeneous nuclear ribonucleoprotein K IPI00514561.1 17 Vimentin IPI00418471.5 Ribonuclease/angiogenin inhibitor IPI00465081.2 Hypothetical protein FLJ36605 IPI00477807.3 Placental ribonuclease inhibitor IPI00550069.2 Ribonuclease/angiogenin inhibitor IPI00550654.2 Placental ribonuclease inhibitor IPI00550874.1 Vimentin IPI00552689.1 18 , type I cytoskeletal 17 IPI00450768.4 19 78 kDa glucose-regulated protein precursor IPI00003362.1 20 T-complex protein 1, epsilon subunit IPI00010720.1 21 Protein disulfide-isomerase A3 precursor IPI00025252.1 22 Keratin, type II cytoskeletal 1 IPI00220327.2 Keratin, type II cytoskele IPI00290078.2 Keratin, type II cytoskeletal 7 IPI00306959.7 48 kDa protein IPI00332128.1 Hypothetical protein DKFZp566O224 IPI00383815.3 variant IPI00418411.4 Keratin b20 IPI00431749.1 Hypothetical protein FLJ45472 IPI00443478.1

Keratin, type II cytoskeletal 8 IPI00554648.1

Keratin 1 IPI00556624.1 23 Pyruvate kinase 3 isoform 2 IPI00220644.6 Pyruvate kinase M2 IPI00383237.3 Pyruvate kinase 3 isoform 1 variant IPI00479186.2 Hypothetical protein IPI00604528.1 24 Tryptophanyl-tRNA synthetase IPI00295400.1 TrypTophanyl-TRNA synTheTase isoform b IPI00412737.1 25 Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial precursor IPI00026516.1 26 Heat shock 70kDa protein 1A IPI00514377.3 27 Tubulin beta-? chain IPI00007752.1 Tubulin beta-2 chain IPI00011654.2 Tubulin beta-3 chain IPI00013683.2 Tubulin beta-4 chain IPI00023598.1 Tubulin, beta polypeptide paralog IPI00031370.3 Similar to Tubulin beta-4 chain IPI00034283.2 Tubulin, beta, 4 IPI00152453.1 Tubulin, beta 4 IPI00160897.3 Class IVb beta tubulin IPI00549172.2 TUBB protein IPI00549853.2 28 Tubulin alpha-1 chain IPI00007750.1 TUBA6 protein IPI00166768.1 Tubulin alpha-3 chain IPI00180675.4 Tubulin alpha-8 chain IPI00216005.5 Tubulin alpha-6 chain IPI00218343.4 K-ALPHA-1 protein IPI00328163.1 Tubulin alpha-ubiquitous chain IPI00387144.4 Similar to alpha tubulin IPI00410402.1

46 kDa protein IPI00414274.2 29 50 kDa protein IPI00174849.4 30 Nucleoporin 54kDa variant IPI00172580.4 Hypothetical protein DKFZp434L1613 IPI00385666.1 Splice Isoform 2 of Nucleoporin p54 IPI00386702.1 31 26S protease regulatory subunit 7 IPI00021435.2 PREDICTED: similar to proteasome (prosome, macropain) 26S subunit, ATPase 2 IPI00454870.1 32 Glutathione synthetase IPI00010706.1 33 -like protein 3 IPI00028091.1 34 Actin, alpha 1, skeletal muscle IPI00514530.3 35 Sorting nexin 6, isoform a IPI00258833.1 Sorting nexin 6 IPI00298111.5 45 kDa protein IPI00513753.1 36 D-3-phosphoglycerate dehydrogenase IPI00011200.4 37 Rab GDP dissociation inhibitor alpha IPI00010154.3 Rab GDP dissociation inhibitor beta IPI00031461.1 GDP dissociation inhibitor 2 IPI00513829.1 GDP dissociation inhibitor 2 IPI00513929.1 GDP dissociation inhibitor 2 IPI00514395.1 38 Alpha enolase, lung specific IPI00013769.1 Gamma enolase IPI00216171.2 Beta enolase IPI00218474.4 Alpha enolase IPI00465248.4 39 Splice Isoform Long of Glucose-6-phosphate 1-dehydrogenase IPI00216008.2 Glucose-6-phosphate dehydroGenase IPI00289800.6 40 Splice Isoform 1 of SET protein IPI00072377.1 Splice Isoform 2 of SET protein IPI00301311.1 PREDICTED: similar to SET protein (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template IPI00397984.2 41 Septin-2 IPI00014177.1 42 Splice Isoform C2 of Heterogeneous nuclear ribonucleoproteins C1/C2 IPI00013944.2 Heterogeneous nuclear ribonucleoprotein C-like dJ845O24.4 IPI00027569.1 Splice Isoform C1 of Heterogeneous nuclear IPI00216592.1 ATPase family, AAA domain containing 3A IPI00295992.2 Hypothetical protein FLJ10709 IPI00396219.4 Full-length cDNA clone CS0DA009YK08 of Neuroblastoma of Homo sapiens IPI00477313.1 HNRPC protein IPI00552125.1 24 kDa protein IPI00556280.2 43 Splice Isoform 2 of Nucleophosmin IPI00220740.1 PREDICTED: similar to nucleophosmin 1 IPI00455423.1 06 PREDICTED: similar to nucleophosmin 1 IPI00457100.1 Nucleophosmin IPI00549248.3 Nucleophosmin IPI00554482.1 44 Splice Isoform 1 of RNA-binding protein 4 IPI00003704.2 45 COP9 sig IPI00171844.3 COP9 signalosome subunit 4 variant IPI00604797.1 46 Macrophage capping protein IPI00027341.1 47 Splice Isoform 1 of 3'(2'),5'-bisphosphate nucleotidase 1 IPI00410214.1 Splice Isoform 2 of 3'(2'),5'-bisphosphate nucleotidase 1 IPI00410215.4 3'(2'), 5'-bisphosphate nucleotidase 1 IPI00479394.2 48 Maspin precursor IPI00472082.1 49 DnaJ homolog subfamily B member 11 precursor IPI00008454.1 50 HypotHetical protein LOC345651 IPI00003269.1 Actin, aortic smooth muscle IPI00008603.1 Actin, alpha skeletal muscle IPI00021428.1 Actin, cytoplasmic 1 IPI00021439.1 Actin, cytoplasmic 2 IPI00021440.1 Actin, alpha cardiac IPI00023006.1 Actin, gamma-enteric smooth muscle IPI00025416.1 Actin, alpha 1, skeletal muscle IPI00515047.1

Actin, cytoplasmic 1 IPI00550724.3

FKSG30 IPI00555900.1 51 Galactokinase IPI00019383.1 Hypothetical protein FLJ26554 IPI00442827.1 52 Proliferating cell nuclear antigen IPI00021700.1 53 F-actin capping protein alpha-1 subunit IPI00005969.1 F-actin capping protein alpha-2 subunit IPI00026182.4 MGC14151 protein IPI00304922.1 PREDICTED: similar to SERTA domain containing 4 IPI00402160.2 54 60S acidic P0 IPI00008530.1 BLOCK 23 IPI00396373.1 RPLP0 protein IPI00556485.1 55 4 IPI00010779.3 Splice Isoform 1 of Tropomyosin beta chain IPI00013991.1 Splice Isoform 2 of Tropomyosin alpha 4 chain IPI00216975.1 Splice Isoform 3 of Tropomyosin beta chain IPI00218820.1 PREDICTED: similar to tropomyosin 4 IPI00374397.2 Tropomyosin 2 IPI00513698.1 Tropomyosin 2 IPI00604605.1 56 Tropomyosin 3 IPI00382894.2 Tropomyosin 3 IPI00477649.1 Tropomyosin 3 IPI00478716.3 Tropomyosin 3 IPI00479185.1 57 Tropomyosin isoform IPI00018853.1 29 kDa protein IPI00178083.2 Hypothetical protein FLJ35393 IPI00218320.2 58 Tropomyosin IPI00218319.2 29 kDa protein IPI00377005.1 59 Chloride intracellular channel protein 1 IPI00010896.2 PREDICTED: similar to Chloride intracellular channel protein 1 (Nuclear chloride ion ch IPI00456966.1 Chloride intracellular channel 1 IPI00554767.1 60 Isocitrate dehydrogenase [NAD] subunit alpha, mitocho IPI00030702.1 61 Rho GDP-dissociation inhibitor 1 IPI00003815.1 Protein IPI00411463.2 Protein IPI00414489.1 62 Protein IPI00412473.1 63 Annexin V IPI00329801.10 64 Splice Isoform Gamma-1 of Serine/threonine protein phosphatase PP1-gamm IPI00005705.1 Protein phosphatase type 1 catalytic subunit IPI00027423.2 Splice Isoform Gamma-2 of Serine/threonine protein phosphatase PP1-gamma catalytic subu IPI00218187.1 Serine/threonine protein ph IPI00218236.4 Protein PhosPhatase 1, catalytic subunit, alPha isoform 2 IPI00410128.1 Serine/threonine protein phosphatase PP1-alpha catalytic subu IPI00550451.1 65 Proteasome subunit alpha type 6 IPI00029623.1 66 ECH1 protein IPI00550041.1 67 PREDICTED: similar to Triosephosphate isomerase (TIM) IPI00383071.1 Splice Isoform 2 of Triosephosphate isomerase IPI00451401.2 Tax_Id=9606 IPI00465028.5 68 Peroxiredoxin 2 IPI00027350.1 Peroxiredoxin 2 isoform b IPI00375400.2 69 Endoplasmic reticulum protein ERp29 precursor IPI00024911.1 70 Splicing factor, arginine/serine-rich 3 IPI00010204.1 Splicing factor, arginine\/serine-rich 3 IPI00215802.1 71 Cofilin-1 IPI00012011.3 72 Transaldolase IPI00024102.3 TALDO1 protein IPI00550488.2 73 Peroxiredoxin 4 IPI00011937.1 74 HSPC220 IPI00009402.3 20 kDa protein IPI00180248.1 Hepatocellular -associated antigen 59 IPI00433576.1 Hepatocellular carcinoma-associated antigen 59 IPI00550191.2 75 Heat-shock protein beta-1 IPI00025512.2 Heat shock 27kDa protein 1 IPI00551023.2 76 PREDICTED: similar to RIKEN cDNA 1700012G19 IPI00177008.1 77 Peroxiredoxin 6 IPI00220301.4 26 kDa protein IPI00396482.3 78 isoform b IPI00031045.3 Destrin IPI00473014.2 79 PREDICTED: similar to 40S ribosomal protein SA (p40) (34/67 kDa receptor) (Colo IPI00399036.1 PREDICTED: similar to 40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (Colo IPI00456929.1 80 Ubiquitin carboxyl-terminal hydrolase isozyme L3 IPI00011250.3 81 PREDICTED: similar to 40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (Colo IPI00397774.1 PREDICTED: similar to 40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (Colo IPI00397881.2 PREDICTED: similar to Laminin receptor 1 IPI00399077.2 Laminin receptor-like protein LAMRL5 IPI00411639.1 82 Elongation factor 1-beta IPI00178440.2 83 Tumor protein, translationally-controlled 1 IPI00009943.2 Translationally controlled tumor protein IPI00550900.1 84 14-3-3 protein epsilon IPI00000816.1 PREDICTED: similar to epsilon isoform of 14-3-3 protein IPI00086909.4 24 kDa protein IPI00396452.3 PREDICTED: similar to hypothetical protein FLJ90430 IPI00455865.1 85 14-3-3 protein tau IPI00018146.1 86 60S acidic ribosomal protein P2 IPI00008529.1 87 14-3-3 protein sigma IPI00013890.1 SFN protein IPI00411765.2 88 14-3-3 protein gamma IPI00220642.4 Splice Isoform 3 of Centrosomal protein 4 IPI00470741.2 Splice Isoform 1 of Centrosomal protein 4 IPI00550987.1 89 Smooth muScle and non-muScle alkali light chain iSoform 4 IPI00066374.1 Similar to Zinc finger protein 62 IPI00410357.2 Splice Isoform 2 of Zinc finger protein 62 homolog IPI00410359.3 Hypothetical protein IPI00413922.2 Smooth muScle and non-muScle myoSin alkali light chain iSoform 3 IPI00473069.1 90 Nucleoside diphosphate kinase A IPI00012048.1 Nucleoside diphosphate kinase B IPI00026260.1 Putative nucleoside diphosphate kinase IPI00029091.1 NM23-H1 IPI00375531.1 Nucleoside-diphosphate kiNase 2 isoform 1 IPI00604590.1 91 14-3-3 protein zeta/delta IPI00021263.3 29 kDa protein IPI00180776.2 14-3-3 protein eta IPI00216319.2 24 kDa protein IPI00396479.1 92 14-3-3 protein beta/alpha IPI00216318.4 93 Proteasome subunit alpha type 5 IPI00291922.2 94 PREDICTED: similar to 40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (Colo IPI00398958.1 29 kDa protein IPI00413108.2 Similar to Laminin receptor 1 IPI00456731.1 Ribosomal protein SA, 67kDa IPI00553164.2 95 5AII IPI00006935.1 PREDICTED: similar to Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D) (Re IPI00069363.3 PREDICTED: similar to Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D) (Re IPI00218084.4 Eukaryotic initiation factor 5A isoform I variant A IPI00376005.1 Eukaryotic translation initiati IPI00411704.4 96 Adenine phosphoribosyltransferase IPI00218693.7 97 Interleukin-18 precursor IPI00290198.2 Similar to IPI00414553.1 98 Splice Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049.1 99 Splice Isoform 2 of Heterogeneous nuclear ribonucleoprotein K IPI00216746.1 163 40S ribosomal protein S7 IPI00013415.1 172 Splice Isoform 2 of Tropomyosin beta chain IPI00220709.3 176 Splice Isoform 1 of Pyridoxal kinase IPI00013004.1 Splice Isoform 2 of Pyridoxal kinase IPI00216320.1 Splice Isoform 3 of Pyridoxal kinase IPI00418202.1