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

Hulme, Charlotte H.; Wilson, Emma L.; Fuller, Heidi R.; Roberts, Sally; Richardson, James B.; Gallacher, Pete; Peffers, Mandy J.; Shirran, Sally L.; Botting, Catherine H.; Wright, Karina T.

doi:10.1186/s13075-018-1573-4

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	Fold change	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		+

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

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