Investigation of proteome changes in osteoclastogenesis in low serum culture system using quantitative proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27034619", "kind": "science-record", "revision": 6, "content_hash": "sha256:d329237e8915fb4a5a5fc764209981fd5101f630ae544b3a5bf95887becf997b", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:20:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of proteome changes in osteoclastogenesis in low serum culture system using quantitative proteomics.", "doi": "10.1186/s12953-016-0097-6", "pmid": "27034619", "authors": ["Qi Xiong", "Lihai Zhang", "Shaohua Zhan", "Wei Ge", "Peifu Tang"], "journal": "Proteome science", "year": 2016, "abstract": "BACKGROUND: RAW 264.7 cells can differentiate into osteoclasts when cultured in medium supplemented with 1 % FBS. However, the proteomic changes in the development of RAW 264.7 cells into osteoclasts in low serum culture system have not been elucidated. Therefore, we conducted quantitative proteomics analysis to investigate proteomic changes during osteoclastogenesis in low serum culture system.\nRESULTS: Our study confirmed that mature multinucleated osteoclasts were generated in a low serum culture system, validated by upregulated expression of 15 characteristic marker proteins, including TRAP, CTSK, MMP9, V-ATPase and ITGAV. Proteomics results demonstrated that 549 proteins expressed differentially in osteoclastogenesis in low serum culture system. In-depth bioinformatics analysis suggested that the differentially expressed proteins were mainly involved in mitochondrial activities and energy metabolism, including the electron transport chain pathway, TCA cycle pathway, mitochondrial LC-fatty acid beta-oxidation pathway and fatty acid biosynthesis pathway. The data have been deposited to the ProteomeXchange with identifier PXD001935.\nCONCLUSION: Osteoclast formation is an ATP consuming procedure, whether occurring in a low serum culture system or a conventional culture system. In contrast to osteoclasts formed in conventional culture system, the fatty acid biosynthesis pathway was upregulated in osteoclasts cultured in low serum condition.", "claims": [{"id": "claim-method", "statement": "Two-sided hypergeometric tests with Benjamini-Hochberg correction method were performed to minimize the false discovery rate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27034619", "locator": "sections[18] \"Data analysis\" paragraph 3", "quote": "Two-sided hypergeometric tests with Benjamini-Hochberg correction method were performed to minimize the false discovery rate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data identifier PXD001935 [36].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27034619", "locator": "sections[18] \"Data analysis\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data identifier PXD001935 [36]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TMT-labeling quantitative proteomics identified 549 differentially expressed proteins during osteoclastogenesis, with the source data deposited in ProteomeXchange under identifier PXD001935.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "In the present study, we used TMT labeling to analyze the quantitative proteomic changes during osteoclastogenesis in medium supplemented with 1 % FBS."}, "evidence": [{"asset": "source:pmid:27034619", "locator": "sections[1] \"Background\" paragraph 4", "quote": "In the present study, we used TMT labeling to analyze the quantitative proteomic changes during osteoclastogenesis in medium supplemented with 1 % FBS."}, {"asset": "source:pmid:27034619", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Proteomics results demonstrated that 549 proteins expressed differentially in osteoclastogenesis in low serum culture system."}, {"asset": "source:pmid:27034619", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data have been deposited to the ProteomeXchange with identifier PXD001935."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TMT-labeling quantitative proteomics identified 549 differentially expressed proteins during osteoclastogenesis, with the source data deposited in ProteomeXchange under identifier PXD001935.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27034619"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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However, the proteomic changes in the development of RAW 264.7 cell", "luding TRAP, CTSK, MMP9, V-ATPase and ITGAV. Proteomics results demonstrated that 549 proteins expre", "to RAW 264.7 cells Quantitative analysis of proteomic changes during osteoclastogenesis in a low s"], "order_basis": "paper_text_order:59", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ells can differentiate into osteoclasts when cultured in medium supplemented with 1 % FBS. 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