Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26870755", "kind": "science-record", "revision": 7, "content_hash": "sha256:d5c1d1044bca5baf0849b7f10f35cb0aca5af73d27a3e2c022c56e6ffb5f0bce", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.", "doi": "10.1016/j.dib.2015.11.062", "pmid": "26870755", "authors": ["Sadhna Phanse", "Cuihong Wan", "Blake Borgeson", "Fan Tu", "Kevin Drew", "Greg Clark", "Xuejian Xiong", "Olga Kagan", "Julian Kwan", "Alexandr Bezginov", "Kyle Chessman", "Swati Pal", "Graham Cromar", "Ophelia Papoulas", "Zuyao Ni", "Daniel R Boutz", "Snejana Stoilova", "Pierre C Havugimana", "Xinghua Guo", "Ramy H Malty", "Mihail Sarov", "Jack Greenblatt", "Mohan Babu", "W Brent Derry", "Elisabeth R Tillier", "John B Wallingford", "John Parkinson", "Edward M Marcotte", "Andrew Emili"], "journal": "Data in brief", "year": 2016, "abstract": "Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae) and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1].", "claims": [{"id": "claim-method", "statement": "To improve peptide-spectral matching sensitivity and accuracy in obtaining MS2 peptide identification and spectral count quantitation mass spectra were searched using 3 search engines: Tide, INSPECT and MSGFDB each employing a different search methodology, and the spectral counts were integrated probabilistically using MSblender [3].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26870755", "locator": "sections[17] \"Data processing protocol\" paragraph 3", "quote": "To improve peptide-spectral matching sensitivity and accuracy in obtaining MS2 peptide identification and spectral count quantitation mass spectra were searched using 3 search engines: Tide, INSPECT and MSGFDB each employing a different search methodology, and the spectral counts were integrated probabilistically using MSblender [3]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data accessibility•Biochemical fractionations – ProteomeXchange (PXD002319-PXD002328)•PPIs – BioGRID (185267)•Complexes and interaction network projections – http://metazoa.med.utoronto.ca•MS1 and MS2 elution profiles, correlation scores and ortholog mappings – http://metazoa.med.utoronto.ca•Supplementary data with research article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26870755", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data accessibility•Biochemical fractionations – ProteomeXchange (PXD002319-PXD002328)•PPIs – BioGRID (185267)•Complexes and interaction network projections – http://metazoa.med.utoronto.ca•MS1 and MS2 elution profiles, correlation scores and ortholog mappings – http://metazoa.med.utoronto.ca•Supplementary data with research article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "By applying a human-centric approach to merged fractionation and mass-spectrometry data from five species and performing subsequent computational analysis, the study identified 16,655 high-confidence protein–protein interactions and 981 putative functional modules encompassing 2,153 broadly conserved proteins; machine learning was used to predict conserved interactions and complex co-memberships, and the supporting data are accessible through ProteomeXchange (PXD002319–PXD002328), BioGRID (185267), and http://metazoa.med.utoronto.ca.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26870755", "locator": "sections[4] \"list\" paragraph 1", "quote": "By applying a human-centric approach on the merged data for 5 species obtained through fractionation and mass spectrometry, and subsequent computational analysis we identified 16,655 high confidence protein–protein interactions and 981 putative functional modules encompassing 2153 broadly-conserved proteins found in virtually all multicellular eukaryotes."}, {"asset": "source:pmid:26870755", "locator": "sections[18] \"MS1 and MS2 protein identification and quantitation\" paragraph 3", "quote": "These scores along with external biochemical [9], [10] and functional evidence [11] were used as input for machine learning to predict conserved protein–protein interactions and complex co-memberships."}, {"asset": "source:pmid:26870755", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "By applying a human-centric approach to merged fractionation and mass-spectrometry data from five species and performing subsequent computational analysis, the study identified 16,655 high-confidence protein–protein interactions and 981 putative functional modules encompassing 2,153 broadly conserved proteins; machine learning was used to predict conserved interactions and complex co-memberships, and the supporting data are accessible through ProteomeXchange (PXD002319–PXD002328), BioGRID (185267), and http://metazoa.med.utoronto.ca.", "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:26870755"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26870755", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.11.062", "sha256": "sha256:7e292d0679102b6cc4368f9c0dabaa02ef798e4ff4fdc4ff75a9498b89b478fb", "bytes": 20439, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.11.062", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4738005", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "MSblender probabilistic integration", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To improve peptide-spectral matching sensitivity and accuracy in obtaining MS2 peptide identification and spectral count quantitation mass spectra were searched using 3 search engines: Tide, INSPECT and MSGFDB each employing a different search methodology, and the spectral counts were integrated probabilistically using MSblender [3]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD002319-PXD002328"], "resolved_accessions": [], "statements": ["Data accessibility•Biochemical fractionations – ProteomeXchange (PXD002319-PXD002328)•PPIs – BioGRID (185267)•Complexes and interaction network projections – http://metazoa.med.utoronto.ca•MS1 and MS2 elution profiles, correlation scores and ortholog mappings – http://metazoa.med.utoronto.ca•Supplementary data with research article."], "basis": "The paper names PXD002319-PXD002328, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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