Extracting histones for the specific purpose of label-free MS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27718312", "kind": "science-record", "revision": 8, "content_hash": "sha256:9f9d6411eb0a2f5d08869d35ff2b5a1bcb6c4aeaa86e51a715d4921ff8638c47", "created_at": "2026-11-01T15:40:20Z", "updated_at": "2026-11-01T22:42:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Extracting histones for the specific purpose of label-free MS.", "doi": "10.1002/pmic.201600341", "pmid": "27718312", "authors": ["Elisabeth Govaert", "Katleen Van Steendam", "Ellen Scheerlinck", "Liesbeth Vossaert", "Paulien Meert", "Martina Stella", "Sander Willems", "Laura De Clerck", "Maarten Dhaenens", "Dieter Deforce"], "journal": "Proteomics", "year": 2016, "abstract": "Extracting histones from cells is the first step in studies that aim to characterize histones and their post-translational modifications (hPTMs) with MS. In the last decade, label-free quantification is more frequently being used for MS-based histone characterization. However, many histone extraction protocols were not specifically designed for label-free MS. While label-free quantification has its advantages, it is also very susceptible to technical variation. Here, we adjust an established histone extraction protocol according to general label-free MS guidelines with a specific focus on minimizing sample handling. These protocols are first evaluated using SDS-PAGE. Hereafter, a selection of extraction protocols was used in a complete histone workflow for label-free MS. All protocols display nearly identical relative quantification of hPTMs. We thus show that, depending on the cell type under investigation and at the cost of some additional contaminating proteins, minimizing sample handling can be done during histone isolation. This allows analyzing bigger sample batches, leads to reduced technical variation and minimizes the chance of in vitro alterations to the hPTM snapshot. Overall, these results allow researchers to determine the best protocol depending on the resources and goal of their specific study. Data are available via ProteomeXchange with identifier PXD002885.", "claims": [{"id": "claim-method", "statement": "Eight variants were significantly different between the selected protocols at the 0.01 significance level (ANOVA q‐value), but only two showed a maximum fold enrichment >2, Histone H1.1 and macroH2A (Fig. 4A).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27718312", "locator": "sections[13] \"Label‐free quantification of histones and their PTMs in the different protocols\" paragraph 3", "quote": "Eight variants were significantly different between the selected protocols at the 0.01 significance level (ANOVA q‐value), but only two showed a maximum fold enrichment >2, Histone H1.1 and macroH2A (Fig. 4A)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD002885.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27718312", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002885."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used MS-precursor-intensity-based principal component analysis (PCA) to assess clustering and outliers across extraction protocols; the source data are available through ProteomeXchange under identifier PXD002885.", "kind": "quantitative", "target": {"value": 18.0, "unit": "per cent", "tolerance": null, "source": "Using this PCA three of 32 extractions appeared to have failed and these outliers were removed. Figure 3A shows that the multiply‐charged MS precursors aggregate the four protocols into two clusters along PC 1, explaining 18% of the variation: detergent‐based (Protocol C‐fresh, Cluster 1) versus detergent‐free (Protocols A‐fresh/frozen and B‐frozen, Cluster 2)."}, "evidence": [{"asset": "source:pmid:27718312", "locator": "sections[12] \"Evaluation of quality and repeatability using label‐free MS\" paragraph 3", "quote": "Using this PCA three of 32 extractions appeared to have failed and these outliers were removed. Figure 3A shows that the multiply‐charged MS precursors aggregate the four protocols into two clusters along PC 1, explaining 18% of the variation: detergent‐based (Protocol C‐fresh, Cluster 1) versus detergent‐free (Protocols A‐fresh/frozen and B‐frozen, Cluster 2)."}, {"asset": "source:pmid:27718312", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All protocols display nearly identical relative quantification of hPTMs."}, {"asset": "source:pmid:27718312", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002885."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used MS-precursor-intensity-based principal component analysis (PCA) to assess clustering and outliers across extraction protocols; the source data are available through ProteomeXchange under identifier PXD002885.", "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:27718312"], "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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