Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30980500", "kind": "science-record", "revision": 3, "content_hash": "sha256:c2a552a2e4ba0daa6773eecfb784371f57c180c94921947e0694197df38e9595", "created_at": "2026-11-01T17:32:45Z", "updated_at": "2026-11-01T21:22:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model.", "doi": "10.1002/pmic.201800469", "pmid": "30980500", "authors": ["Jennifer Guergues", "Ping Zhang", "Bin Liu", "Stanley M Stevens"], "journal": "Proteomics", "year": 2019, "abstract": "Microglia, as the resident brain immune cells, can exhibit a broad range of activation phenotypes, which have been implicated in a multitude of central nervous system disorders. Current widely studied microglial cell lines are mainly derived from neonatal rodent brain that can limit their relevance to homeostatic function and disease-related neuroimmune responses in the adult brain. Recently, an adult mouse brain-derived microglial cell line has been established; however, a comprehensive proteome dataset remains lacking. Here, an optimization method for sensitive and rapid quantitative proteomic analysis of microglia is described that involves suspension trapping (S-Trap) for efficient and reproducible protein extraction from a limited number of microglial cells expected from an adult mouse brain (≈300 000). Using a 2-h gradient on a 75-cm UPLC column with a modified data dependent acquisition method on a hybrid quadrupole-Orbitrap mass spectrometer, 4855 total proteins have been identified where 4698 of which are quantifiable by label-free quantitation with a median and average coefficient of variation (CV) of 6.7% and 10.6%, respectively. This dataset highlights the high depth of proteome coverage and related quantitation precision of the adult-derived microglial proteome including proteins associated with several key pathways related to immune response. Data are available via ProteomeXchange with identifier PXD012006.", "claims": [{"id": "claim-method", "statement": "Filtered lists were uploaded to Ingenuity Pathway Analysis (IPA) in order to determine over-represented canonical pathways as well as other biological and disease functions (p<0.05, Fisher’s exact test).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30980500", "locator": "sections[5] \"p\" paragraph 1", "quote": "Filtered lists were uploaded to Ingenuity Pathway Analysis (IPA) in order to determine over-represented canonical pathways as well as other biological and disease functions (p<0.05, Fisher’s exact test)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD012006.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30980500", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD012006."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The optimized method identified 4,855 total proteins, of which 4,698 were quantifiable by label-free quantitation with a median and average CV of 6.7% and 10.6%, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30980500", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using a 2-hr gradient on a 75-cm UPLC column with a modified data dependent acquisition method on a hybrid quadrupole-Orbitrap mass spectrometer, 4,855 total proteins were identified where 4,698 of which were quantifiable by label-free quantitation with a median and average CV of 6.7% and 10.6%, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The optimized method identified 4,855 total proteins, of which 4,698 were quantifiable by label-free quantitation with a median and average CV of 6.7% and 10.6%, respectively.", "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:30980500"], "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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