Table 1

Summary of proteins identified in untreated control and IL-1β-stimulated samples with qualitative nanoLC-MS/MS
Protein Accession number Mascot scores
Individual animal Untreated control Pooled untreated control Individual animal IL-1β stimulated Pooled IL-1β stimulated
ECM proteins
Cartilage oligomeric matrix protein COMP_BOVIN 4090 4763 7555 10590
Fibronectin FINC_BOVIN 4422 6222 3786 3492
Chondroadherin CHAD_HUMAN 1022 3069 1978 3689
Thrombospondin 1 TSP1_BOVIN 741 1256 3456 2782
Aggrecan core protein PGCA_HUMAN 1815 3389 2258 6412
Decorin PGS2_HORSE 665 802 513 1130
Biglycan PGS1_HORSE 1099 1062 2047 1720
Fibromodulin FMOD_HUMAN 1307 3200 1381 1930
Collagen alpha-1(II) chain CO2A1_BOVIN 137 59 133 82
Collagen alpha-2(VI) chain CO6A2_HUMAN 190 79
Collagen alpha-1(X) chain COAA1_MOUSE 77 102
Prolargin PRELP_MOUSE 124 147 311 301
Cartilage intermediate-layer protein 1 (CILP-1) CILP1_MOUSE 201 789 423 264
Proteoglycan 4 (Lubricin) PRG4_HUMAN 139 49 59
SPARC (secreted protein acidic, cysteine rich) SPRC_PIG 108 96
Non-ECM secreted proteins
Clusterin CLUS_HORSE 2767 4723 1785 4876
Chitinase-3-like protein 1 (YKL-40) CH3L1_BOVIN 574 1178 414 2018
Serum amyloid A protein SAA_CANFA 43
SAA_HORSE 55 219 436
Metalloproteinase inhibitor 1 TIMP1_HORSE 83 312 457 146
Alpha-1-antiproteinase 2 A1AT2_HORSE 99 342 50
MMP-1 MMP1_HORSE 1678 1586
MMP-3 MMP3_HORSE 653 956 5441 4580
MMP-13 MMP13_HORSE 1700 699
TNF-R superfamily, member 11b (Osteoprotegerin) TR11B_RAT 252 319 388 638
Procollagen C-endopeptidase enhancer 2 PCOC2_HUMAN 163 171
Lysozyme C LYSM_BOVIN 72 168 179 148
Secreted frizzled-related protein 3 SFRP3_BOVIN 74 98
Lactadherin MFGM_PIG 83 63 54
Extracellular superoxide dismutase [Cu-Zn] SODE_HUMAN 67 72
Macrophage migration inhibitory factor MIF_HUMAN 91 86
Ribonuclease 4 RNAS4_HUMAN 48 46 59
Intracellular proteins
Vimentin VIME_PANTR 84
VIME_PIG 2361 3837
Alpha-enolase ENOA_BOVIN 506 686
Phosphoglycerate mutase 1 PGAM1_MOUSE 149 104
Phosphatidylethanolamine-binding protein 1 PEBP1_HUMAN 423 148
Phosphoglycerate kinase 1 PGK1_HORSE 792 651
Pyruvate kinase isoforms M1/M2 KPYM_HUMAN 488 245
Purine nucleoside phosphorylase PNPH_HUMAN 175 134
Glyceraldehyde 3-phosphate dehydrogenase G3P_PIG 208 115
Thioredoxin THIO_HORSE 145 143
Other
Serum albumin ALBU_BOVIN 283 86
Pancreatic trypsin inhibitor BPT1_BOVIN 283 477 281 703
Trypsin TRYP_PIG 111 106 746
Keratin, type II cytoskeletal 3 K2C3_RABIT 151 277 110

MMPs (-1, -3, and -13) were identified from this high-throughput proteomic analysis and investigated further in this study. Identifications were attained by using Mascot Daemon to search the Swiss-Prot database (All mammals). Only peptide identifications with a probability-based protein family mascot MOWSE score above the significant threshold of >42 (with a statistical significance level of P < 0.05) were included. MMPs (-1, -3, and -13) were identified from this high-throughput proteomic analysis and investigated further in this study.

Williams et al.

Williams et al. Arthritis Research & Therapy 2013 15:R223   doi:10.1186/ar4424

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