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Table 4 Fold change of proteins that are differentially abundant in the synovial fluid of clinical responders at stage II compared with stage I of autologous chondrocyte implantation (ACI)

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 no.   LF LC-MS/MS iTRAQ nLC-MS/MS
Microtubule-associated protein 1B P46821 − 20.65 +  
40S Ribosomal protein S14 P62263 − 16.75   +
Protein disulphide-isomerase A6 Q15084 − 7.59   +
Nucleolin P19338 − 5.11   +
Histone H1.2 P16403 − 3.84   +
Stress-induced-phosphoprotein 1 P31948 − 3.63   +
Complement factor D P00746 − 3.44   +
SH3 domain-binding glutamic acid-rich-like protein O75368 − 3.44   +
Heterogeneous nuclear ribonucleoprotein U Q00839 − 3.40   +
78 kDa Glucose-regulated protein P11021 − 3.25   +
Cartilage oligomeric matrix protein P49747 − 3.10   +
Annexin A2 P07335 − 2.96   +
Mesencephalic astrocyte-derived neurotrophic factor P55145 − 2.86   +
Kinectin Q86UP2 − 2.81   +
Complement factor H-related protein 3 Q02985 − 2.77 +  
Phosphatidylethanolamine-binding protein 1 P30086 − 2.51   +
Peroxiredoxin-4 Q13162 − 2.49 +  
Regucalcin Q15493 − 2.44   +
Malate dehydrogenase, mitochondrial P40926 − 2.44   +
N-acetylglucosamine-6-sulphatase P15586 − 2.31   +
Gelsolin P06396 − 2.27   +
Alpha-endosulfine O43768 − 2.25   +
Peptidyl-prolyl cis-trans isomerase FKBP3 Q00688 − 2.11   +
Hemopexin P02790 2.05   +
Serum paraoxonase/arylesterase 1 P27169 2.07   +
Secreted phosphoprotein 24 Q13103 2.10 +  
Heparin cofactor 2 P05546 2.13   +
Ferritin light chain P02792 2.21 +  
Attractin O75882 2.21   +
Ig gamma-2 chain C region P01859 2.23   +
Plasma kallikrein P03952 2.24   +
Chondroitin sulphate proteoglycan 4 Q6UVK1 2.35 +  
Collagen alpha-2(I) chain P08123 2.37 +  
Collagen alpha-1(V) chain P20908 2.54 +  
CD5 antigen-like O43866 2.58   +
Phospholipid transfer protein P55058 2.63   +
Insulin-like growth factor-binding protein complex acid labile subunit P35858 2.68   +
Prothrombin P00734 2.68   +
Beta-2-glycoprotein 1 P02749 2.78   +
Collagen alpha-2(V) chain P05997 2.84 +  
Plasma protease C1 inhibitor P05155 2.91   +
Serum amyloid P component P02743 2.91   +
Complement C1q subcomponent subunit B P02746 3.01   +
Collagen alpha-1(I) chain P02452 3.05 +  
Alpha-2-antiplasmin P08697 3.10   +
Alpha-1B-glycoprotein P04217 3.19   +
Complement factor B P00751 3.25   +
Complement component C7 P10643 3.40   +
Vitamin K-dependent protein S P07225 3.42   +
Apolipoprotein E P02649 3.44   +
Alpha-1-antichymotrypsin P01011 3.44   +
Carboxypeptidase N subunit 2 P22792 3.53   +
Vitronectin P04004 3.63   +
Inter-alpha-trypsin inhibitor heavy chain H3 Q06033 3.66   +
Complement C5 O P01031 4.00   +
Plasminogen P00747 4.06   +
Kininogen 1 P01042 4.17   +
Platelet factor 4 P02776 4.26 +  
Inter-alpha-trypsin inhibitor heavy chain H2 P19823 4.49   +
Periostin Q15063 4.57 +  
Apolipoprotein L1 O14791 4.61   +
Protein 4.1 P11171 4.66 +  
26S Proteasome non-ATPase regulatory subunit 13 Q9UNM6 4.78 +  
Inter-alpha-trypsin inhibitor heavy chain H1 P19827 5.01   +
Inter-alpha-trypsin inhibitor heavy chain H4 Q14624 5.06   +
Complement C1r subcomponent P00736 5.15   +
Complement component C6 P13671 5.45   +
Complement factor H P08603 5.50   +
Catalase P04040 5.60   +
Ficolin-3 O75636 6.43   +
C4b-binding protein alpha chain P04003 7.05   +
Ceruloplasmin P00450 7.51   +
Pregnancy zone protein P20742 8.09   +
Fibrinogen alpha chain P02671 8.40   +
Apolipoprotein M O95445 9.04   +
Protein S100-A6 P06703 9.82   +
Haemoglobin subunit alpha P69905 9.82   +
Complement C1s subcomponent P09871 10.00   +
Ig mu chain C region P01871 12.13   +
Haptoglobin P00738 13.68   +
Fibrinogen beta chain P02675 16.90   +
Haemoglobin subunit beta P68871 19.41   +
Fibrinogen gamma chain P02679 23.55   +
  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 than at stage I. 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