Table III

Functional classification of proteins identified by MS

Classification was performed according to the Swiss-Prot database. Abbreviations used for annotation of the proteomic map in Fig. 3 are listed. The General Identifier (GI) from the National Center for Biotechnology Information (NCBI) and full name of the corresponding protein are indicated as well as its theoretical molecular weight/pI. Also the number of peptide masses isolated from the corresponding spot that match the reference sequence and their coverage of the sequence are annotated. ER, endoplasmic reticulum; EGF, epidermal growth factor; HBsAg, hepatitis B surface antigen; TGFβ, transforming growth factor β; HS, heparan sulfate.

AbbreviationNCBI GIaFull name of closest identified proteinTheor. molecular weight/pIaPept. no./seq. cov. (%)b
Metabolism and energy
    ADK13097732Adenosine kinase, isoform a39,112/6.23c16/52
    ADH24497577Aldo-keto reductase family 1, member A136,761/6.34c15/54
    AR7A239645003Aldo-keto reductase family 7 member A239,889/6.7412/37
    ALDR113596Aldose reductase, aldehyde reductase36,028/6.51c10/47
    ENOA1167843α-Enolase47,350/6.9914/49
11/35
20/56
    CADH515147Carbonic anhydrase I28,408/6.9012/59
    ALAD248839δ-Aminolevulinate dehydratase36,758/6.1614/38
    LDHb126041l-Lactate dehydrogenase B chain36,769/5.7214/40
    NNMT730163Nicotinamide N-methyltransferase30,011/5.56c11/47
    PGAM-1130348Phosphoglycerate mutase isozyme B28,769/6.7515/70
14/66
    PNP55925942Purine-nucleoside phosphorylase32,325/6.4515/58
    PYK20178296Pyruvate kinase, isozymes M1/M258,339/7.9519/47
    TPIS39932641Triose-phosphate isomerase26,807/6.5110/61
13/75
13/75
Protein synthesis
    ACP12134737α-Complex protein 137,987/6.6616/57
    EF1B119163Elongation factor 1-β24,788/4.509/41
    LAMB34234Laminin-binding protein31,888/4.84c13/50
    BAT12500529Nuclear RNA helicase (DEAD family) BAT149,416/5.4416/46
    EF1g39644794Translation elongation factor 1γ50,156/6.2713/37
Protein fate (maturation, degradation, and trafficking)
    Grp9411936094-kDa glucose-regulated protein92,696/4.7621/25
    AHC20141702Adenosylhomocysteinase48,255/5.9212/28
    CALR1905911Calreticulin48,283/4.2910/31
    CALU14718453Calumenin37,198/4.4711/40
    GroEL107086Chaperonin GroEL precursor61,187/5.7014/41
    HSCP7087625dnaK-type molecular chaperone, HSCP7071,082/5.3722/41
    ELI266344Elastase inhibitor42,829/5.90c11/41
    ER4629839560Endoplasmic reticulum protein of 46 kDa48,283/5.6311/32
    ER287512406Endoplasmic reticulum luminal protein 2829,032/6.7711/51
    Grp786470150ER Ca2+-binding protein grp7871,002/5.2326/44
    HSP9020149594Heat shock 90-kDa protein 1, β83,423/4.9718/31
    APG24579909HSP110 family, member apg-295,096/5.1814/24
    PA2G433879698PAG2G4 metallopeptidase41,996/7.1417/53
    CATB181192Preprocathepsin B, fragment38,752/5.88c10/30
    P4HA220455169Prolyl 4-hydroxylase α2 subunit precursor60,994/5.5015/36
    PSD1320978558Proteasome 26 S subunit 13, non-ATPase43,175/5.4412/38
    PSA5P28066Proteasome subunit α type 526,565/4.7411/56
    PDI860986Protein-disulfide isomerase57,480/4.7611/31
19/43
18/44
18/42
    PI91709896Proteinase inhibitor 943,004/5.61c11/37
    RCN330316268Reticulocalbin-3 precursor, RLP4937,470/4.749/35
    RBPS2460318RNA-binding protein regulatory subunit20,050/6.3311/65
    S13L50403748SEC13-related protein, SEC13-like protein 135,900/5.227/35
    STIP1400042Stress-induced-phosphoprotein 163,227/6.4013/24
    TCP1t9988062T-complex protein 1, θ subunit60,022/5.4215/34
    TERA2984586Transitional ER ATPase89,819/5.1425/32
    OTUB144888286Ubiquitin thioesterase protein31,493/4.858/43
Cytoskeleton and cell structure
    gACT12653055Actin, γ142,108/5.3121/68
    ACTN146397817α-Actinin cytoskeletal isoform103,480/5.22c25/35
    CAPa7448799Capping protein α subunit isoform 133,073/5.4512/61
9/49
    EZR21614499Ezrin69,313/5.9418/32
    FASN2498357Fascin, 55-kDa actin-bundling protein54,992/6.8116/37
    GELS4504165Gelsolin isoform a85,925/5.7713/25
    LASP12135552Lasp-1 protein30,185/6.1111/32
11/36
    TPM88926Tropomyosin26,618/4.7710/37
    TPM315929959Tropomyosin 327,386/4.7712/41
    TPM4a54039751Tropomyosin α4 chain28,487/4.6711/42
8/32
    TUBA117921989Tubulin, α150,626/4.9711/36
    TUBB29788785Tubulin, β polypeptide48,135/4.70c9/28
    VIM57471646Vimentin49,680/5.1913/24
13/34
13/27
12/27
27/55
9/27
28/55
28/56
28/56
25/55
9/25
17/32
26/53
20/40
    VCN340237Vinculin117,220/5.8328/28
Cell defense
    eSODM134635Extracellular superoxide dismutase precursor26,321/6.14c7/36
    GST284131Glutathione transferase23,569/5.43c11/55
    GSTO16016173Glutathione transferase Omega 127,704/6.77c10/34
    HSP27662841Heat shock protein 2722,427/7.83c8/42
    PRDX61718024Peroxiredoxin 625,002/6.02c13/74
    PGTP404108Plasma glutathione peroxidase16,760/8.93c9/54
    SODM134665Superoxide dismutase mitochondrial22,705/7.537/42
Signal transduction
    1433e349333614-3-3 ε29,326/4.6314/50
    1433g4842872114-3-3 protein γ28,325/4.8013/50
    1433t11269014-3-3 protein θ28,032/4.6814/55
    1433z5200088714-3-3 protein ζ/δ27,899/4.7313/64
    40PK2387940-kDa protein kinase40,794/6.6710/32
    ANX14502101Annexin I38,918/6.5713/52
8/35
17/60
    ANX250845386Annexin II38,808/7.5717/57
19/62
9/31
10/31
    ANX44502105Annexin IV36,290/5.8424/68
17/51
    ANX5468888Annexin V35,971/4.9421/66
8/29
19/61
    CP9s438373690COP9 signalosome subunit 446,525/5.5710/30
    DRP23122051Dihydropyrimidinase-related protein 262,711/5.95c25/62
    GDI256410846GDP dissociation inhibitor 251,087/6.1113/43
    KRap12643951Serine-threonine kinase receptor-associated protein38,756/4.9810/46
    SPD152783472Spondin-1 precursor93,537/5.8513/23
    TCTP136479Translationally controlled tumor protein19,697/4.849/44
Unknown intracellular functions
    TRP1433415057Transformation-related protein 1443,248/5.4917/41
    WDRP62897353WD repeat-containing protein 1 isoform 1 variant66,822/6.1715/35
Extracellular matrix
    ACTR177933α1-Antichymotrypsin precursor45,567/5.3214/41
    a2PG4502005α2-HS-glycoprotein40,098/5.438/23
    CACP147777317Cartilage acidic protein 170,404/5.0911/23
    COL2825645Pro-α (II) collagen31,919/6.3511/44
    COMP27530066Cartilage oligomeric matrix protein85,403/4.3424/41
11/26
    LUM20141464Keratan sulfate proteoglycan lumican precursor38,747/6.16c9/34
9/31
    KNG28932976Kininogen48,936/6.29c13/34
13/37
13/29
    MAT32326547Matrilin-334,944/5.55c9/50
12/70
    MMP34505217Matrix metalloproteinase 3 preproprotein54,229/5.6113/24
    OIF107244Osteoinductive factor34,243/5.469/40
9/40
9/40
9/45
8/42
    PRELP1709586Proline-arginine-rich end leucine-rich repeat protein44,181/9.47c9/27
14/37
    PGLP14585875Proteoglycan link protein40,767/7.1010/38
    HTRA118202620Serine protease HTRA1 precursor52,167/8.0911/27
    BIGH32498193TGFβ-induced protein BIGH3 precursor75,261/7.62c24/39
    TGFi6862897225TGFβ-induced, 68-kDa variant75,231/7.6214/22
    PCPE6919941Type 1 procollagen C-proteinase enhancer protein48,797/7.4113/34
15/44
Complement components
    C1r115204Complement C1r subcomponent precursor81,661/5.8920/42
    C1s115205Complement C1s subcomponent precursor78,174/4.8617/26
21/37
    C3p116594Complement C3 precursor188,585/6.0221/15
16/13
39/24
    C6p105741Complement C6 precursor108,367/6.3916/21
    C8p29575Complement C8-β propeptide63,605/8.2418/39
    CFB584908Complement factor B precursor86,847/6.6720/36
    CFH62739186Complement factor H isoform a precursor143,710/6.2844/40
Synovial fluid components (classically known as plasma components)
    aFP178236α-Fetoprotein68,354/5.6723/47
    IgKF3721651Anti-HBsAg immunoglobulin Fab κ chain23,783/8.30c7/55
    ATHR28907Antithrombin47,415/6.25c14/35
    ATHR3179130Antithrombin III53,025/6.32c19/40
9/24
    APOA1490098Apolipoprotein AI28,061/5.2715/61
14/55
11/51
    APOA4178779Apolipoprotein A-IV precursor43,358/5.2221/58
    APOH6573461β2-Glycoprotein-I, apolipoprotein H37,499/8.37c9/45
9/45
    EFEM115072400EGF-containing fibulin-like extracellular matrix protein 156,885/4.9521/51
    EDIL321410823EGF-like and discoidin I-like domains protein 355,128/7.0811/30
11/30
13/34
    FBGb399492Fibrinogen β chain precursor49,768/7.02c29/61
    FBGd2781208Fibrinogen fragment d36,331/7.6629/81
    HPX1335098Hemopexin49,948/6.43c16/53
14/39
    HP47124562Haptoglobin protein31,647/8.48c15/45
14/42
14/43
14/43
    ZAG7246026Human zinc-α2-glycoprotein30,775/6.03c14/55
    IgKL21669345Immunoglobulin κ light chain28,918/6.15c8/51
    PEDF15217079Pigment epithelium-derived factor46,484/5.9717/44
19/51
18/50
    CPM180256Preceruloplasmin122,983/5.4418/23
    ATRY15080499Serine proteinase inhibitor, antitrypsin46,864/5.3618/51
    ALB3212625Serum albumin67,931/5.6912/22
22/45
15/35
12/28
18/36
15/30
    TTN37409Tetranectin20,480/5.80c5/37
    TFR339453Transferrin precursor79,280/6.8132/51
28/44
    VDBP32483410Vitamin D-binding protein precursor54,526/5.4017/55
  • a NCBI GI and molecular weight/pI are given for the closest isoform of the identified protein.

  • b Peptide number and sequence coverage were calculated based on the reference sequence.

  • c Indicates that none of the spots from which the reference protein was found has the corresponding molecular weight/pI coordinates on the map.