Table I

Chondrocytic proteins identified by 2-D DIGE-MS as differentially expressed in osteoarthritis grouped according to their predicted biological function

ECM, extracellular matrix; PM, plasma membrane; Exc, extracellular, secreted; Cyt, cytoplasmic; Nuc, nuclear; ER, endoplasmic reticulum; Mit, mitochondria; Lys, lysosomes; Pex, peroxisomes; Vac, vacuoles; Ves, vesicles; Mem, membrane-associated. The first column (No.) gives the protein spot number according to Fig. 2. TCA, tricarboxylic acid; PI3K, phosphatidylinositol 3-kinase; EGF, epidermal growth factor.

No.Protein IDaSwiss-ProtaProtein nameAv. ratiobt testCellular roleLoc.cPredicteddExp.eScorefNo. pept.gCov.hApp.i
Molecular weightpIMolecular weightpI
%
Structural and cytoskeleton-related
    1CO1A2 P08123 Collagen α-2(I) chain (precursor)−1.940.013ECM componentExc129.79.08126.56.1814220/412412
    2CO6A2 P12110 Collagen α-2(VI) chain (precursor)1.360.034ECM organizationExc/Mem108.65.85107.15.6449YGGLHFSDQVEVFSPPGSDRj18
    12TGM2 P21980 Protein-glutamine γ-glutamyltransferase 21.440.011Regulation of cell adhesionER78.45.1186.25.1510914/362818
    13ACTB P60709 Actin, cytoplasmic 11.680.0082Cytoskeleton componentCyt42.15.2983.45.2718121/295318
    14TGM2 P21980 Protein-glutamine γ-glutamyltransferase 21.660.028Regulation of cell adhesionER78.45.1181.15.0216620/303712
    18EZRI P15311 Ezrin (cytovillin)−1.310.015Cytoskeletal anchoring to PMCyt/Mem69.05.9477.36.3422126/244618
    19EZRI P15311 Ezrin (cytovillin)−1.390.0051Cytoskeletal anchoring to PMCyt/Mem69.05.9477.26.4411112/382018
96IGFPWSEIRAPDFVFYAPR
    23MOES P26038 Moesin−1.320.0058Cytoskeletal anchoring to PMCyt/Mem67.86.0873.86.3818824/264118
    26PSLT3 P13797 Plastin-3−1.350.028Actin-bundling proteinCyt70.95.5267.05.808614/362118
    34VIM P08670 Vimentin−1.390.013Cytoskeleton componentCyt53.75.0654.35.0219419/315318
    36VIM P08670 Vimentin−1.380.042Cytoskeleton componentCyt53.75.0653.75.0725830/206718
    39SCRN1 Q12765 Secernin-11.830.0025Exocytosis regulationCyt/Mem46.44.6646.74.859110/404215
    43VIM P08670 Vimentin1.620.039Cytoskeleton componentCyt53.75.0643.24.3936132/186515
    49CH3L1 P36222 Chitinase-3-like protein 1 (precursor)−1.630.0001Tissue remodelingExc43.08.6940.48.6610011/393418
    54SDCB1 O00560 Syntenin-1−1.710.038Cytoskeleton organization, signal transductionMem32.67.0534.77.079610/404518
    55MYH13 O95252 Myosin-131.590.024Microfilament formationCyt224.75.5632.46.786413/37918
    64EDIL3 O43854 EGF-like repeat and discoidin I-like domain-containing protein 3 (precursor)−1.780.0073Cell adhesionExc55.17.0825.98.006812/382012
Transcription, protein synthesis, and turnover
    5P3H3 Q8IVL6 Prolyl 3-hydroxylase 3 (precursor)1.460.0098Collagen synthesisER82.65.9389.66.2414516/343415
    6P3H3 Q8IVL6 Prolyl 3-hydroxylase 3 (precursor)1.370.0053Collagen synthesisER82.65.9389.96.3118220/303818
    7P3H3 Q8IVL6 Prolyl 3-hydroxylase 3 (precursor)1.370.04Collagen synthesisER82.65.9389.96.3512413/372918
    9EF2 P13639 Elongation factor 2−1.760.039Protein synthesisCyt96.26.4187.36.8020526/243315
    10EF2 P13639 Elongation factor 2−1.350.031Protein synthesisCyt96.26.4187.16.8813819/313118
    11IREB1 P21399 Iron-responsive element-binding protein 1−1.360.014Regulates ferritin transcriptionCyt98.96.2387.16.6219323/273118
    11PLOD2 O00469 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (precursor)−1.360.014Collagen synthesisER/Mem85.46.2487.16.6212815/352918
    22DDX3X O00571 ATP-dependent RNA helicase DDX3X−1.440.0033TranscriptionNuc/Cyt73.66.7373.66.957012/382218
    58CATD P07339 Cathepsin D (precursor)−1.310.0079Acid proteaseLys45.06.1026.95.5517719/314218
    66PSB1 P20618 Proteasome subunit β type 1 (precursor)−1.430.015ProteolysisNuc/Cyt26.78.2723.08.7610811/395618
%
Transport
    3AT1A3 P13637 Sodium/potassium-transporting ATPase subunit α-31.340.042Na+/K+ exchangeMem113.15.22106.95.67607/43918
    22SC23A Q15436 Protein transport protein Sec23A−1.440.0033ER to Golgi protein transportER/Mem87.06.6473.66.957111/392318
    33VATB2 P21281 Vacuolar ATP synthase subunit B, brain isoform1.380.021Proton transportVac56.85.5756.05.8018120/304518
    35VATB2 P21281 Vacuolar ATP synthase subunit B, brain isoform−1.30.0024Proton transportVac56.85.5753.95.8912315/353718
    47VDAC2 P45880 Voltage-dependent anion-selective channel protein 2−1.360.049Anion channelMit38.66.3241.26.919210/404018
    56CLIC1 O00299 Chloride intracellular channel protein 1−1.50.023Chloride ion channelNuc/Mem27.25.0930.95.1026020/308618
    57CLIC1 O00299 Chloride intracellular channel protein 1−1.550.011Chloride ion channelNuc/Mem27.25.0929.65.35969/415018
    61CLIC4 Q9Y696 Chloride intracellular channel protein 4−1.450.0043Chloride ion channelCyt/Ves29.05.4526.65.559010/405015
    72FRIL P02792 Ferritin light chain−1.590.047Cellular iron homeostasisCyt20.15.5113.85.95706/444118
Signal transduction
    4MVP Q14764 Major vault protein−1.430.039Nucleocytoplasmic transportNuc/Cyt99.67.3492.45.526527/234718
    8PCD6I Q8WUM4 Programmed cell death 6-interacting protein−1.320.0058Protein concentration and sortingCyt/Vac96.66.1389.16.4712718/322715
71MVPVSVQQSLAAYNQRFYNELTEILVR15
    15IMMT Q16891 Mitochondrial inner membrane protein (mitofilin)1.50.038Protein bindingMit83.76.0877.86.2127827/234412
    16IMMT Q16891 Mitochondrial inner membrane protein (mitofilin)−1.670.021Protein bindingMit83.76.0877.76.1623324/263718
    17IMMT Q16891 Mitochondrial inner membrane protein (mitofilin)−1.390.0066Protein bindingMit83.76.0877.66.2826326/244118
    21OPA1 O60313 Dynamin-like 120-kDa protein, mitochondrial (precursor)−1.340.0038Mitochondrial membrane organization, antiapoptoticMit112.27.8877.36.737615/351615
    28DPYL2 Q16555 Dihydropyrimidinase-related protein 2−1.370.015Nucleic acid metabolism, signal transductionCyt62.75.9563.16.3132829/216718
    30TRXR1 Q16881 Thioredoxin reductase 1, cytoplasmic (precursor)−1.340.0012Signal transductionCyt55.06.0757.76.367010/402518
    322AAA P30153 Serine/threonine-protein phosphatase 2A 65-kDa regulatory subunit A α isoform (PP2A, subunit A)−1.510.0082Assembly of catalytic and regulatory subunits of PP2ACyt66.05.0056.24.9914317/333218
    38DAPP1 Q9UN19 Dual adapter for phosphotyrosine, 3-phosphotyrosine, and 3-phosphoinositide1.460.012Signal transduction downstream of PI3KCyt/Mem32.07.6646.94.81737/432118
    41RCN3 Q96D15 Reticulocalbin-3 (precursor)1.580.0076Protein bindingER37.54.7446.44.5610211/394518
    45RCN3 Q96D15 Reticulocalbin-3 (precursor)1.890.026Protein bindingER37.54.7442.14.5614414/365018
    46RCN3 Q96D15 Reticulocalbin-3 (precursor)1.640.018Protein bindingER37.54.7441.34.5810211/394518
    621433T P27348 14-3-3 protein θ−1.370.0016Signaling pathway regulationCyt28.04.6828.44.6113013/375618
    63RAN P62826 GTP-binding nuclear protein Ran1.340.032Nucleocytoplasmic transportNuc/Cyt24.67.0126.87.17929/414718
    73NDKB P22392 Nucleoside-diphosphate kinase B1.360.012Nucleoside triphosphate synthesisNuc/Cyt17.48.529.58.629610/406518
%
Metabolism
    20PLCD1 P51178 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase δ 1−1.390.005Phospholipid metabolismCyt/Ves86.56.1776.16.5010914/362518
    25ECHA P40939 Trifunctional enzyme subunit α, mitochondrial (precursor)−1.40.036Fatty acid β oxidationMit83.79.1669.25.1113819/312618
42VIIVVKDGPGFYTTR
    27CLUS P10909 Clusterin (precursor) (apolipoprotein J)−1.450.0049Lipid metabolismExc53.05.8963.76.28588/421915
    31GLSK O94925 Glutaminase kidney isoform, mitochondrial (precursor)1.410.035Glutamine catabolismMit56.27.1357.16.527312/382515
    40ENOA P06733 α-Enolase−1.330.0061GlycolysisCyt47.57.0147.46.9927627/236718
    42THIM P42765 3-Ketoacyl-CoA thiolase, mitochondrial1.610.0015Lipid and fatty acid metabolismMit42.48.3245.88.8535929/218018
    47HIBCH Q6NVY1 3-Hydroxyisobutyryl-CoA hydrolase, mitochondrial (precursor)−1.360.049Valine catabolismMit43.88.3841.26.9115920/304318
    48G3P P04406 Glyceraldehyde-3-phosphate dehydrogenase1.590.041GlycolysisCyt36.28.5740.48.74689/413418
47LISWYDNEFGYSNR
    49AK1C1 Q04828 Aldo-keto reductase family 1 member C1−1.630.0001Cholesterol homeostasisCyt37.28.0240.48.6619718/326918
    52AK1C2 P52895 Aldo-keto reductase family 1 member C2−1.320.046Prostaglandin and steroid metabolic processCyt37.17.1339.47.2222521/297118
    53ESTD P10768 S-Formylglutathione hydrolase (esterase D)−1.580.0093Formaldehyde detoxificationCyt/Ves32.06.5437.16.7715614/366918
Energy production
    29DHSA P31040 Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (precursor)−1.560.007Electron transport, subunit of complex IIMit73.77.0663.16.4527628/225418
    37NDUV1 P49821 NADH dehydrogenase (ubiquinone) flavoprotein 1, mitochondrial (precursor)1.360.029Electron transport, subunit of complex IMit51.58.5152.17.9932627/236015
    44ODPA P08559 Pyruvate dehydrogenase E1 component α subunit, somatic form, mitochondrial (precursor)−1.520.017Oxidative decarboxylation of pyruvate and TCA cycleMit44.08.3544.56.2515118/324018
    50IDH3A P50213 Isocitrate dehydrogenase (NAD) subunit α, mitochondrial (precursor)−1.690.015Oxidative decarboxylation of pyruvate and TCA cycleMit40.06.4740.06.0819319/314118
    51IDH3A P50213 Isocitrate dehydrogenase (NAD) subunit α, mitochondrial (precursor)−1.90.038Oxidative decarboxylation of pyruvate and TCA cycleMit40.06.4740.25.9211714/363812
    54ETFA P13804 Electron transfer flavoprotein subunit α, mitochondrial (precursor)−1.710.038Electron carrierMit35.48.6234.77.07859/413618
    59KAD4 P27144 Adenylate kinase isoenzyme 4, mitochondrial1.520.014ATP productionMit25.48.4727.48.8017712/385815
    60IDHP P48735 Isocitrate dehydrogenase (NADP), mitochondrial (precursor)−1.530.0074Oxidative decarboxylation of pyruvate and TCA cycleMit51.38.8826.75.487511/392718
    67NDUS8 O00217 NADH dehydrogenase (ubiquinone) iron-sulfur protein 8, mitochondrial (precursor)1.320.031Electron transport, subunit of complex IMit24.26.0022.15.09737/434118
    71ISOC2 Q96AB3 Isochorismatase domain-containing protein 2, mitochondrial (precursor)1.480.03Pyruvate metabolismMit22.67.6719.58.0316814/367812
%
Chaperones and stress
    24TRAP1 Q12931 Tumor necrosis factor type 1 receptor-associated protein (Hsp75)1.470.041Chaperone, ROS antagonistMit80.38.3071.66.6112419/313518
    65GSTK1 Q9Y2Q3 Glutathione S-transferase Kappa 11.410.025Glutathione conjugationPex25.68.5024.08.819810/404518
    68SODM P04179 Superoxide dismutase (manganese), mitochondrial (precursor)−1.520.011Superoxide destructionMit24.98.3522.47.32586/443118
    69SODM P04179 Superoxide dismutase (manganese), mitochondrial (precursor)−1.560.0024Superoxide destructionMit24.98.3522.37.1911410/405518
    70SODM P04179 Superoxide dismutase (manganese), mitochondrial (precursor)−1.650.018Superoxide destructionMit24.98.3521.26.69777/434018
  • a Protein identity and accession number according to Swiss-Prot and TrEMBL databases.

  • b Average volume ratio OA/N quantified by DeCyder BVA module.

  • c Subcellular localization according to database and PSORT information.

  • d Predicted molecular weight (×103) and pI according to protein sequence and Swiss-2DPAGE database.

  • e Experimental molecular weight (×103) and pI calculated by analysis of the gel images with PDQuest 7.3.1 software.

  • f Mascot MS protein score, or MS/MS ion score, obtained from MALDI-TOF/TOF spectra. In all cases, a probability score <0.01 was obtained.

  • g Number of peptide masses matching/not matching the top hit from MS-Fit PMF. On each spot, the 50 most intense peaks were launched for search.

  • h Amino acid sequence coverage for the identified proteins.

  • i Number of gel images (from a total of 18) where each spot appears.

  • j Amino acid sequence identified by tandem mass spectrometry using MALDI-TOF/TOF MS/MS.