A possible approach for gel-based proteomic studies in recalcitrant woody plants.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23724367", "kind": "science-record", "revision": 3, "content_hash": "sha256:c7fb0b125985ca40e8f3a2806168a083e74bb3b0ef66e479e6d89281e4c63a3f", "created_at": "2026-11-01T15:40:03Z", "updated_at": "2026-11-01T18:46:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A possible approach for gel-based proteomic studies in recalcitrant woody plants.", "doi": "10.1186/2193-1801-2-210", "pmid": "23724367", "authors": ["Mónica Sebastiana", "Andreia Figueiredo", "Filipa Monteiro", "Joana Martins", "Catarina Franco", "Ana Varela Coelho", "Fátima Vaz", "Tânia Simões", "Deborah Penque", "Maria Salomé Pais", "Sílvia Ferreira"], "journal": "SpringerPlus", "year": 2013, "abstract": "Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more efficient for woody recalcitrant plant gel-based proteomics. Grapevine leaves, pine needles and cork oak ectomycorrhizal roots were used to represent woody plant species and tissues. The phenol protocol produced higher quality 2-DE gels, with increased number of resolved spots, better spot focusing and representation of all molecular mass and isoelectric point ranges tested. In order to test the compatibility of the phenol extracted proteomes with protein identification several spots were excised from the phenol gels and analyzed by mass spectrometry (MALDI-TOF/TOF). Regardless the incomplete genome/protein databases for the plant species under analysis, 49 proteins were identified by Peptide Mass Fingerprint (PMF). Proteomic data have been deposited to the ProteomeXchange with identifier PXD000224. Our results demonstrate the complexity of protein extraction from woody plant tissues and the suitability of the phenol protocol for obtaining high quality protein extracts for efficient 2-DE separation and downstream applications such as protein identification by mass spectrometry.", "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 (Vizcaíno et al., 2013) with the dataset identifier PXD000224.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23724367", "locator": "sections[16] \"MS analysis and protein identification\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaíno et al., 2013) with the dataset identifier PXD000224."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The phenol extraction protocol produced the highest-quality 2-DE separation and was compatible with downstream MALDI-TOF/TOF protein identification; the study does not name a statistical method for comparing protocols. The source proteomics data were deposited in ProteomeXchange under identifier PXD000224.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23724367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The phenol protocol produced higher quality 2-DE gels, with increased number of resolved spots, better spot focusing and representation of all molecular mass and isoelectric point ranges tested."}, {"asset": "source:pmid:23724367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteomic data have been deposited to the ProteomeXchange with identifier PXD000224."}, {"asset": "source:pmid:23724367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results demonstrate the complexity of protein extraction from woody plant tissues and the suitability of the phenol protocol for obtaining high quality protein extracts for efficient 2-DE separation and downstream applications such as protein identification by mass spectrometry."}, {"asset": "source:pmid:23724367", "locator": "sections[2] \"Results\" paragraph 2", "quote": "In ECM oak roots, both TCA-acetone and ethanol produced a significantly lower amount of spots when compared with the phenol protocol (904), with ethanol producing 111 spots and TCA-acetone only 36 spots."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The phenol extraction protocol produced the highest-quality 2-DE separation and was compatible with downstream MALDI-TOF/TOF protein identification; the study does not name a statistical method for comparing protocols. The source proteomics data were deposited in ProteomeXchange under identifier PXD000224.", "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:23724367"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000224"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000224"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:23724367", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/2193-1801-2-210", "sha256": 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(http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaíno et al., 2013) with the dataset identifier PXD000224.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaíno et al., 2013) with the dataset identifier PXD000224.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Protein extraction in recalcitrant plant species", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:23724367:1", "role": "table", "format": "jats-table", "media_type": 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"21.88 ± 4.00", "392"], ["TCA-acetone", "13.86 ± 1.14", "657"], ["Grapevine", "Phenol", "3.78 ± 0.61", "532"], ["Ethanol", "20.55 ± 1.79", "166"], ["TCA-acetone", "16.57 ± 1.31", "362"], ["Oak", "Phenol", "0.61 ± 0.14", "904"], ["Ethanol", "3.57 ± 0.20", "111"], ["", "TCA-acetone", "2.77 ± 0.14", "36"]], "row_count": 10, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[2]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:23724367:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5350cdff8fa9dd229edabc680ea3027db3eeebaf1c5f792d35c7533bada20b1e", "bytes": 8918, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[2]#Tab2", "version": null, "note": "Protein annotation in the grapevine fully developed leaves (V1-V15), cork oak ectomycorrhizal roots (S1-S20) and pine needles (P1-P14) spots excised from 2-DE gels and trypsin-digested", "structure": {"pmcid": "PMC3663981", "section_index": 2, "section_title": "Results", "row_count": 194, "column_count": 7}, "table": {"label": "Table 2", "caption": "Protein annotation in the grapevine fully developed leaves (V1-V15), cork oak ectomycorrhizal roots (S1-S20) and pine needles (P1-P14) spots excised from 2-DE gels and trypsin-digested", "rows": [["Spot", "Protein ID", "Annotation", "Score", "Search engine", "Protein score", "Sequence of the distinct fragmented peptides (p < 0,05)"], ["V1", "8615601", "cyclase [Vitis pseudoreticulata]", "532", "ProteinPilot", "14", "EFESDYAGFTEDGAR"], ["EVILVESLK"], ["KEFESDYAGFTEDGAR"], ["LDDVPAGMYNVHCLHLR"], ["LPGAEGAPIR"], ["SEAYPSAYGSGSCNVELIPVKR"], ["WLVENTDIK"], ["EFESDYAGFTEDGAR"], ["GPALLVDAPR"], ["LPGAEGAPIR"], ["V2", "49388156", "putative chlorophyll a/b-binding protein type III precursor [Oryza sativa Japonica Group]", "270", "ProteinPilot", "10.67", "FQDWANPGSMGK"], ["QGADRPLWFASK"], 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"30687535", "Quinone reductase family protein [Arabidopsis thaliana]", "393", "MASCOT", "62.96", "AFLDATGGLWR"], ["V13", "225456238", "PREDICTED: glutamine synthetase cytosolic isozyme 1[Vitis vinifera]", "", "MASCOT", "183.79", "VIVEYIWVGGSGMDLR"], ["GNNILVMCDTYTPAGEPIPTNKR"], ["V14", "359473178", "Quinone oxidoreductase-like protein At1g23740, chloroplastic-like [Vitis vinifera]", "612", "MASCOT", "460.41", "VKPVVDPK"], ["LNPYLESGK"], ["KLNPYLESGK"], ["VVAAALNPVDAK"], ["AWVYGDYGGVDVLK"], ["QFGSFAEYTAVEEK"], ["EGGSVVALTGAVTPPGFR"], ["ELKEGDEVYGDINEK"], ["ATDSPLPTVPGYDVAGVVVK"], ["V15", "225432496", "PREDICTED: glutamine synthetase leaf isozyme, chloroplastic [Vitis vinifera]", "", "MASCOT", "349.06", "DISDAHYK"], ["AAEIFGNKK"], ["EHISAYGEGNER"], ["TISKPVEHPSELPK"], ["HKEHISAYGEGNER"], ["HETANINTFSWGVANR"], ["GGNNILVICDSYTPAGEPIPTNKR"], ["S1", "4838443", "symbiosis regulated acidic polypeptide SRAP32-3 [Pisolithus tinctorius]", "", "Protein Pilot", "4", "DKLEAKLDKAAGDYIDGVDI"], ["TDVANSLEFASR"], ["S2", "160897637", "hypothetical protein Daci_2194 [Delftia acidovorans SPH-1]", "", "MASCOT", "59.58", "ERAQSAAAIER"], ["S3", "71659717", "hypothetical protein [Trypanosoma cruzi strain CL Brener]", "", "MASCOT", "58.93", "KDIAEEVLER"], ["S4", "20162432", "AF493154_1 32 kDa-cell wall symbiosis regulated acidic polypeptide [Pisolithus microcarpus]", "", "MASCOT", "80.35", "NDPLYSEAEK"], ["S5", "71659717", "hypothetical protein [Trypanosoma cruzi strain CL Brener]", "", "MASCOT", "57", "KDIAEEVLER"], ["S6", "20162434", "32 kDa-cell wall symbiosis regulated acidic polypeptide precursor [Pisolithus microcarpus]", "358", "MASCOT", "210.62", "ATGDDYAR"], ["NSLEFAAR"], ["FQLAVCSEK"], ["AADKATGDDYAR"], ["S7", "390601324", "cysteine peroxiredoxin [Punctularia strigosozonata HHB-11173SS5]", "391", "MASCOT", "334.84", "NFDEVLR"], ["TVFVIDPK"], ["LTISYPASTGR"], ["VVDSLQLGDKYR"], ["LGSIAPDFEAETTAGPIK"], ["ISTLYDMLDEQDATNR"], ["S8", "225461209", "PREDICTED: flavoprotein wrbA 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["SPPEKYYNIFK"], ["SATLIGVDGDIMQEYK"], ["GQAYHVPNAAPDHIQGVDVHEGDWETHGSVK"], ["S15", "3164115", "major latex-like protein [Rubus idaeus]", "", "MASCOT", "68.2", "EKVELDDVNK"], ["S16", "Q9S1X8", "Na(+)/H(+) antiporter NhaA 1/4[Streptomyces coelicolor strain ATCC BAA-471/A3(2)/M145]", "", "MASCOT", "483.67", "NDAYVIAK"], ["EEREEER"], ["GVGWVAPSPENK"], ["VGECTYVISAR"], ["SVTEPPTFNMEK"], ["KSVTEPPTFNMEK"], ["GVGWVAPSPENKEER"], ["S17", "375333787", "lectin 2 [Agrocybe aegerita]", "565", "MASCOT", "647.19", "FLGEATGDGR"], ["FVVDLTGDGR"], ["DFAYSAGGWR"], ["DGFSIQPFVAIK"], ["ADIVGFGDGGVLVSK"], ["SVIDNFTYSAGGWR"], ["FVLNNFGVQQGWQVNK"], ["NTGGGNFSPASLALNDFGYNAGGWR"], ["S18", "392590852", "phosphoglycerate mutase-like protein [Coniophora puteana]", "540", "MASCOT", "431.54", "VYASPEFK"], ["DIGGIGNLPGR"], ["TAQPFFGAIR"], ["LPPTLIEQAR"], ["GPAPEDRDFLR"], ["ADIPLTEFFYR"], ["SVYLSPSSPSYITNMK"], ["S19", "160184939", "Serine protease inhibitor [Lentinula edodes (Shiitake mushroom)]", "58.9", "MASCOT", "106.97", "WCIQYTER"], ["VGDCTYVISAR"], ["S20", "1001331", "jgi|Pisti1|1001331|fgenesh1_kg.33_#_73_#_Locus10529v3rpkm0.40_PRE", "", "MASCOT", "205.69", "YYINYLIER"], ["WIITFVPQPGR"], ["NNLLYEQVTAPQK"], ["P1", "332591479", "phosphoglycerate kinase 1 [Pinus pinaster]", "", "MASCOT", "260.9", "AHASTEGVTK"], ["LTELLGVNVVK"], ["ELDYLVGAVSNPK"], ["ADLNVPLDENQNITDDTR"], ["P2", "396547", "glutamate-ammonia ligase [Pinus sylvestris]", "", "MASCOT", "134.75", "SLSGPVSSVK"], ["VIAEYIWIGGSGMDMR"], ["P3", "218155", "chloroplastic aldolase [Oryza sativa Japonica Group]", "", "MASCOT", "129.98", "EAAWGLAR"], ["AKANSLAQLGK"], ["LASIGLENTEANR"], ["P4", "3415126", "phenylcoumaran benzylic ether reductase [Pinus taeda]", "", "MASCOT", "497.86", "VVILGDGNAR"], ["SLAQAGLTAPPR"], ["ILLIGATGYIGR"], ["DKVVILGDGNAR"], ["ASLDLGHPTFLLVR"], ["FFPSEFGNDVDNVHAVEPAK"], ["GDQTNFEIGPAGVEASQLYPDVK"], ["AIEAEGIPYTYVSSNCFAGYFLR"], ["P5", "413951269", "ferredoxin-NADP reductase, leaf isozyme [Zea mays]", "768", "MASCOT", "388.09", "KDNTYVYMCGLK"], ["RLVYTNDQGEIVK"], ["LYSIASSALGDFGDSK"], ["ITGDDAPGETWHMVFSTEGEIPYR"], ["P6", "359473184", "carbonic anhydrase, chloroplastic-like isoform 2 [Vitis vinifera]", "299", "MASCOT", "109.34", "FMVVACADSR"], ["QTAFIEDWIK"], ["P7", "359473184", "carbonic anhydrase, chloroplastic-like isoform 2 [Vitis vinifera]", "299", "MASCOT", "107.77", "FMVVACADSR"], ["QTAFIEDWIK"], ["P8", "14719331", "putative 3-beta hydroxysteroid dehydrogenase/isomerase protein [Oryza sativa]", "496", "MASCOT", "245.13", "MKPGFDPSK"], ["IGGGDDVFVGDIR"], ["AEQYLADSGLPYTIIR"], ["KAEQYLADSGLPYTIIR"], ["P9", "116790330", "unknown [Picea sitchensis]", "", "MASCOT", "104.32", "TTFLSDSEVK"], ["TTFLSDSEVKR"], ["P10", "116782111", "unknown [Picea sitchensis]", "", "MASCOT", "220.45", "EYYNISVLTR"], ["YEDNGDTVSNVSVMVIPTDKK"], ["P11", "16798638", "AF434186_1 Cu-Zn-superoxide dismutase precursor [Pinus pinaster]", "", "MASCOT", "234.71", "LTHGAPEDDVR"], ["KLTHGAPEDDVR"], ["GGHELSLTTGNAGGR"], ["GNSQVEGVVNLSQEDNGPTTVK"], ["P12", "2911276", "LMW heat shock protein [Fragaria x ananassa]", "103", "MASCOT", "105.95", "QPEPQPPQPK"], ["ASMEDGVLTVTVPK"], ["P13", "413946843", "Putative peptidyl-prolyl cis-trans isomerase family protein [Zea mays]", "307", "MASCOT", "138.86", "TFEDENFK"], ["KLESEETNR"], ["IVLGLFGEDVPK"], ["P14", "20794", "Type III chlorophyll a/b-binding protein [Pinus sylvestris]", "259", "MASCOT", "268.1", "LQDYRNPGSMGK"], ["YLGGSGNPAYPGGPLFNPLGFGK"], ["", "YLGGSGNPAYPGGPLFNPLGFGKDEK"]], "row_count": 194, "column_count": 7, "numeric_cells": 166, "header_rows": 1, "locator": "section[2]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:PXD000224 not downloaded", "asset:data:geo:PXD000224 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", 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