Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24416096", "kind": "science-record", "revision": 7, "content_hash": "sha256:24f549b5e3e44cd7c8edc0d71c4782123c47b59994e87e7407c028af929ed2f8", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:58:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis.", "doi": "10.1371/journal.pone.0084669", "pmid": "24416096", "authors": ["Harriet T Parsons", "Cristina S Weinberg", "Lucy J Macdonald", "Paul D Adams", "Christopher J Petzold", "Timothy J Strabala", "Armin Wagner", "Joshua L Heazlewood"], "journal": "PloS one", "year": 2013, "abstract": "Our understanding of the contribution of Golgi proteins to cell wall and wood formation in any woody plant species is limited. Currently, little Golgi proteomics data exists for wood-forming tissues. In this study, we attempted to address this issue by generating and analyzing Golgi-enriched membrane preparations from developing xylem of compression wood from the conifer Pinus radiata. Developing xylem samples from 3-year-old pine trees were harvested for this purpose at a time of active growth and subjected to a combination of density centrifugation followed by free flow electrophoresis, a surface charge separation technique used in the enrichment of Golgi membranes. This combination of techniques was successful in achieving an approximately 200-fold increase in the activity of the Golgi marker galactan synthase and represents a significant improvement for proteomic analyses of the Golgi from conifers. A total of thirty known Golgi proteins were identified by mass spectrometry including glycosyltransferases from gene families involved in glucomannan and glucuronoxylan biosynthesis. The free flow electrophoresis fractions of enriched Golgi were highly abundant in structural proteins (actin and tubulin) indicating a role for the cytoskeleton during compression wood formation. The mass spectrometry proteomics data associated with this study have been deposited to the ProteomeXchange with identifier PXD000557.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000557 and DOI 10.6019/PXD000557. The data comprises the raw data files (.wiff AB Sciex), the peak files (.mgf) and the search files for interrogation against Arabidopsis (Mascot .dat) for samples mCW-P2 (31966), mCW-P3 (31967), sCW-P2 (31968) and sCW-P3 (31969).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24416096", "locator": "sections[9] \"Tandem mass spectrometry data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000557 and DOI 10.6019/PXD000557. The data comprises the raw data files (.wiff AB Sciex), the peak files (.mgf) and the search files for interrogation against Arabidopsis (Mascot .dat) for samples mCW-P2 (31966), mCW-P3 (31967), sCW-P2 (31968) and sCW-P3 (31969)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Free-flow electrophoresis combined with density centrifugation produced approximately 200-fold enrichment of Golgi-marker activity, with peptide identifications controlled at a false discovery rate ≤5% (p<0.05) and source mass-spectrometry data deposited in ProteomeXchange/PRIDE under PXD000557.", "kind": "quantitative", "target": {"value": 200.0, "unit": "fold change", "tolerance": null, "source": "This combination of techniques was successful in achieving an approximately 200-fold increase in the activity of the Golgi marker galactan synthase and represents a significant improvement for proteomic analyses of the Golgi from conifers."}, "evidence": [{"asset": "source:pmid:24416096", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This combination of techniques was successful in achieving an approximately 200-fold increase in the activity of the Golgi marker galactan synthase and represents a significant improvement for proteomic analyses of the Golgi from conifers."}, {"asset": "source:pmid:24416096", "locator": "sections[8] \"Tandem mass spectrometry data analysis\" paragraph 2", "quote": "A significance threshold corresponding to a false discovery rate of ≤ 5% (p<0.05) was used to determine the ‘Ions score or expect cut-off’ for peptide matches."}, {"asset": "source:pmid:24416096", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data associated with this study have been deposited to the ProteomeXchange with identifier PXD000557."}, {"asset": "source:pmid:24416096", "locator": "sections[9] \"Tandem mass spectrometry data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000557 and DOI 10.6019/PXD000557."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Free-flow electrophoresis combined with density centrifugation produced approximately 200-fold enrichment of Golgi-marker activity, with peptide identifications controlled at a false discovery rate ≤5% (p<0.05) and source mass-spectrometry data deposited in ProteomeXchange/PRIDE under PXD000557.", "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:24416096"], "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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"X", "X", ""], ["UDP-arabinose 4-epimerase (UXE)", "X", "", "", "", ""], ["reversible glycosylated polypeptide (RGP)", "", "X", "", "", ""], ["SNARE family", "X", "X", "X", "X", ""], ["alpha/beta-hydrolases superfamily protein", "X", "X", "X", "X", ""], ["beta-1,2-N-acetylglucosaminyltransferase (CGL/GNT)", "X", "", "X", "", ""], ["alpha-mannosidase 1", "X", "", "", "", ""], ["O-fucosyltransferase family protein", "X", "X", "X", "", ""], ["O-glycosyl hydrolase (GH47)", "", "X", "", "", ""], ["Copper transporting ATPase", "", "X", "", "", ""], ["CASP CCAAT-displacement protein", "X", "X", "X", "", ""], ["cation-chloride co-transporter", "X", "X", "", "", ""], ["cation efflux family protein", "X", "", "X", "", ""], ["calcium ion binding", "", "", "X", "", ""]], "row_count": 30, "column_count": 6, "numeric_cells": 16, "header_rows": 1, "locator": "section[15]/table-wrap[2]#pone-0084669-t005"}}], "gaps": ["asset:data:geo:PXD000557 not downloaded", "asset:data:geo:PXD000557 licence not 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No tolerance is published because the paper states none."}, {"id": "target-published-estimate-per-cent", "claim_id": "claim-target-result", "operation": "alignment_identity", "expected_value": 5.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "alignment_identity", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD000557"], "resolved_accessions": ["PXD000557"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000557 and DOI 10.6019/PXD000557. The data comprises the raw data files (.wiff AB Sciex), the peak files (.mgf) and the search files for interrogation against Arabidopsis (Mascot .dat) for samples mCW-P2 (31966), mCW-P3 (31967), sCW-P2 (31968) and sCW-P3 (31969)."], "basis": "The paper names PXD000557 in ProteomeXchange Consortium and the accession resolves in the repository. 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