Table I

Proteins with different abundance levels in supernatants of control versus MMP-9 siRNA- or BB-94-treated PC-3ML cells identified by tandem mass spectrometry

ND, not detected; ECM, extracellular matrix; Ctrl, control; Seq. cov., sequence coverage. — indicates that a p value could not be calculated because the indicated protein was not detected in one of the paired samples.

Protein nameRef.Accession no. (Swiss-Prot)aScoreb (PLGS)Seq. cov.No. of MS/MS spectraMMP-9 siRNA:Ctrlp valuecBB-94:Ctrlp valuecScored (Mascot)
Known substrates
    Alzheimer disease amyloid A4 protein (APP)e47–49 P05067 222f17101.10.360.3<0.0179f
    Galectin 3-binding protein precursor 45 Q08380 102g2211ND0.8<0.0153f
    Fibronectin 64 Q28275 128f740.7<0.010.6<0.01152g
    Collagen α1 XI chain precursor 58 Q61245 h 79f13.4240.24<0.01NDND
    Collagen α4 IV chain precursor1, 2 P53420 93f6.380.30.02NDND
    Collagen α1 II chain precursor 4 P02458 79f8.28CtrlND0f
    Integrin β1 precursor 44 P05556 42f12CtrlNDND
    TIMP-1 P01033 135f3050.7<0.010.6<0.0158f
    TIMP-2 P16035 62g357ND0.7<0.01ND
Novel substrate candidates
    Cell surface
        CD166 Q13740 96f7.463.2<0.01ND34f
        Neuropilin-1 precursor vascular endothelial celle O14786 123f1291.9<0.01NDND
        Galectin 1 β-galactoside-binding lectin L 14 P09382 65f1321.750.160.8<0.01ND
        Saposin-A P07602 254f21111.5<0.010.5<0.01260f
        Semaphorin 7A O75326 111g630.90.1Ctrl35f
        Integrin α3 galactoprotein B3 P26006 64f7.78MMP-9 KDNDND
        Angiopoietin 1 receptor precursor Tie-2 Q02763 49f22MMP-9 KDNDND
        Clathrin heavy chain CLH17 Q00610 72f6.57MMP-9 KDNDND
        Laminin β1 chain precursor, laminin B1 chain P07942 76f5.47MMP-9 KDNDND
        Nexin-1 (PN-1)e P07093 81g197>10<0.012.0<0.0140f
        LIFe P09056 h 55f2452.6<0.01NDND
        Granulins precursor acrogranin (PCDGF)e P28799 185f8.651.4<0.01ND54f
        HSP-90 P08238 357g27191.2<0.011.3<0.0167f
        Urokinase type plasminogen activator precursor P00749 254g35120.6<0.010.8<0.01135f
        Tissue type plasminogen activator precursor P00750 142f29.813Ctrl<0.010.7<0.01ND
        Collagenase 3 MMP-13 P33435 h 33f5.13CtrlNDND
        Collagen α1 VI chain precursore P12109 854g37341.5<0.010.9<0.01582f
        Collagen α2 VI chain precursor P12110 252f13131.5<0.010.8<0.0134f
        Procollagen-lysine 2-oxoglutarate 5-dioxygenase 1 Q02809 107f3.321.5<0.011.2<0.01ND
  • a Accession number from Swiss-Prot.

  • b Scores based on the software PLGS 2.2.5.

  • c p values calculated from individual peak intensities derived from all tryptic peptides detected per protein (see “Experimental Procedures”).

  • d As a comparison, Mascot scores are included where applicable (Mascot version 2.2, MudPIT protein score).

  • e Confirmed by immunoblotting (Fig. 4).

  • f PLGS score, sequence coverage, and number of MS/MS spectra derived from the MMP-9 siRNA experiment.

  • g PLGS score, sequence coverage, and number of MS/MS spectra derived from the BB-94 inhibitor experiment.

  • h Accession number for the mouse protein sequence.