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Table 5 Fold change of proteins that are differentially abundant in the synovial fluid of clinical non-responders at stage II compared with stage I

From: Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation

Protein Fold change Identification method
Description Accession LF LC-MS/MS iTRAQ nLC-MS/MS
Protein S100-A6 P06703 − 4.49   +
Annexin A1 P04083 − 4.13   +
Haemoglobin subunit beta P68871 − 4.09   +
Complement factor D P00746 − 3.87   +
Perilipin-4 Q96Q06 − 3.87 +  
Gelsolin P06396 − 3.31   +
Gelsolin P06396 − 1.68 +  
Syntaxin 7 O15400 − 3.31 +  
Fermitin family homolog 3 Q86UX7 − 3.29 +  
Histone H1.2 P16403 − 3.13   +
Transaldolase P37837 − 3.08   +
Neuroblast differentiation-associated protein AHNAK Q09666 − 2.78 +  
Heterogeneous nuclear ribonucleoprotein K P61978 − 2.69 +  
Hyaluronan and proteoglycan link protein 3 Q96S86 − 2.65 +  
Alpha-enolase P06733 − 2.63   +
ATP-citrate synthase P53396 − 2.63 +  
Annexin A2 P07355 − 2.56   +
Fatty acid-binding protein, epidermal Q01469 − 2.43 +  
Peroxiredoxin-1 Q06830 − 2.20 +  
Tripeptidyl-peptidase 1 O14773 − 2.19 +  
Insulin-like growth factor-binding protein 6 P24592 − 2.13 +  
Na+/H+ exchange regulatory cofactor NHE-RF1 O14745 − 2.11 +  
Peroxiredoxin-6 P30041 − 2.08 +  
Histamine N-methyltransferase P50135 − 2.07 +  
Mortality factor 4-like protein 1 Q9UBU8 − 2.06 +  
Transcription elongation factor A protein 1 P23193 − 2.06 +  
Cartilage acidic protein 1 Q9NQ79 − 2.03   +
2′,3′-cyclic-nucleotide 3′-phosphodiesterase P09543 − 1.20 +  
Fructose-bisphosphate aldolase A P04075 − 1.97 +  
Leucine zipper transcription factor-like protein 1 Q9NQ48 − 1.94 +  
Protein S100-A13 Q99584 − 1.94 +  
40S Ribosomal protein S3 P23396 − 1.93 +  
Filamin-A P21333 − 1.92 +  
Microtubule-associated protein RP/EB family member 1 Q15691 − 1.92 +  
Nuclear migration protein nudC Q9Y266 − 1.90 +  
Prostaglandin E synthase 3 Q15185 − 1.85 +  
Stress-induced phosphoprotein 1 P31948 − 1.85 +  
Cytokine-like protein 1 Q9NRR1 − 1.81 +  
Plastin-2 P13796 − 1.81 +  
Coronin-1C Q9ULV4 − 1.80 +  
Vinculin P18206 − 1.80 +  
Cathepsin K P43235 − 1.79 +  
Hsc70-interacting protein P50502;Q8IZP2 − 1.76 +  
Putative phospholipase B-like 2 Q8NHP8 − 1.74 +  
Spectrin beta chain, erythrocytic P11277 − 1.73 +  
Complement factor I P05156 2.11   +
Alpha-1-antichymotrypsin P01011 2.22   +
Titin Q8WZ42 2.23   +
Cytoplasmic dynein 1 heavy chain 1 Q14204 2.23 +  
F-actin-capping protein subunit beta P47756 2.25 +  
Mannan-binding lectin serine protease 1 P48740 2.26 +  
Serum amyloid P-component P02743 2.27   +
Complement component C6 P13671 2.29   +
Thrombospondin-3 P49746 2.36 +  
Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D A1L4H1 2.39 +  
Plasma kallikrein P03952 2.42   +
Complement factor B P00751 2.47   +
Afamin P43652 2.47   +
Vitamin K-dependent protein S P07225 2.49 +  
Vitamin K-dependent protein S P07225 3.08   +
Integrin beta-like protein 1 O95965 2.51 +  
C4b-binding protein beta chain P20851 2.55 +  
Fibronectin P02751 2.58 +  
Clusterin P10909 2.65   +
Vitronectin P04004 2.68   +
Bifunctional glutamate/proline-transfer RNA ligase P07814 2.70   +
Nucleobindin 1 Q02818 2.71 +  
Complement component C9 P02748 2.75   +
Zinc-alpha-2-glycoprotein P25311 2.75   +
Complement C1r subcomponent P00736 2.83   +
Heparin cofactor 2 P05546 2.83   +
Ferritin light chain P02792 2.84 +  
Proteoglycan 4 Q92954 2.88   +
C4b-binding protein alpha chain P04003 2.91 +  
C4b-binding protein alpha chain P04003 10.38   +
Matrix metalloproteinase 3 P08254 2.91   +
Attractin O75882 2.94   +
Insulin-like growth factor-binding protein complex acid labile subunit P35858 3.02   +
Alpha-1B-glycoprotein P04217 3.05   +
Fibrinogen alpha chain P02671 3.10 +  
Fibrinogen alpha chain P02671 11.91   +
Lumican P51884 3.13   +
Chondroitin sulphate proteoglycan 4 Q6UVK1 3.16 +  
Collagen alpha-2(V) chain P05997 3.19 +  
Complement C2 P06681 3.22   +
Fibrinogen beta chain P02675 3.25 +  
Fibrinogen beta chain P02675 18.37   +
Secreted phosphoprotein 24 Q13103 3.26 +  
Matrix metalloproteinase 1 P03956 3.33 +  
Latent-transforming growth factor beta-binding protein 1 Q14766 3.45 +  
Phospholipid transfer protein P55058 3.47   +
Inter-alpha-trypsin inhibitor heavy chain H3 Q06033 3.47   +
Complement C1q tumour necrosis factor-related protein 3 Q9BXJ4 3.50 +  
Adipocyte enhancer-binding protein 1 Q8IUX7;Q8N436 3.51 +  
Adiponectin Q15848 3.52 +  
Fibrinogen gamma chain P02679 3.79 +  
Fibrinogen gamma chain P02679 18.37   +
Plasminogen P00747 3.84   +
Apolipoprotein C-II P02655 3.94   +
CD5 antigen-like O43866 4.17   +
Collagen alpha-1(V) chain P20908 4.26 +  
Complement factor H P08603 4.57   +
Inter-alpha-trypsin inhibitor heavy chain H4 Q14624 4.61   +
Complement C5 P01031 4.74   +
Collagen alpha-1(I) chain P02452 4.84 +  
Ceruloplasmin P00450 5.01   +
Histidine-rich glycoprotein P04196 5.11   +
Target of Nesh-SH3 Q7Z7G0 5.25   +
Plasma protease C1 inhibitor P05155 5.30   +
Apolipoprotein M O95445 5.65   +
Inter-alpha-trypsin inhibitor heavy chain H2 P19823 5.70   +
Periostin Q15063 5.81 +  
Apolipoprotein C-III P02656 5.92   +
Kinectin Q86UP2 6.02   +
Carboxypeptidase N subunit 2 P22792 7.73   +
Serum paraoxonase/arylesterase 1 P27169 8.02   +
Apolipoprotein L1 O14791 8.95   +
Ig mu chain C region P01871 13.30   +
Apolipoprotein E P02649 13.80   +
Inter-alpha-trypsin inhibitor heavy chain H1 P19827 15.56   +
  1. Footnote: Differential abundance was denoted by greater than or equal to ± 2.0-fold change; p ≤ 0.05; protein identified by at least two unique peptides. Positive numbers denote higher abundance at stage II compared with stage I of autologous chondrocyte implantation (ACI). Proteins were identified using either protein dynamic compression coupled with label free quantitation LC-MS/MS or no protein dynamic compression with isobaric tags for absolute and relative quantitation (iTRAQ) LC-MS/MS. Proteins identified by both proteomic techniques are underlined and in italics