Dataset from proteomic analysis of rat, mouse, and human liver microsomes and S9 fractions.

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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 [1]) with the dataset identifiers PXD000717, PXD000720, PXD000721, PXD000731, PXD000733 and PXD000734. Data related to the peptides (trypsin digests only) were also uploaded to Peptide Atlas (Farrah et al., 2013 [2]) and are available with the dataset identifiers PASS00407, PASS00409, PASS00411, PASS00412, PASS00413 and PASS00414. The present dataset is associated with a research article published in EuPA Open Proteomics [3].", "claims": [{"id": "claim-method", "statement": "Proteins were identified with a 1% global false discovery rate (FDR) using a target-decoy database search algorithm [5] in ProteinPilot Descriptive Statistics Template (version 3.001p) (www.absciex.com/PDST).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26217725", "locator": "sections[5] \"Experimental design, materials and methods\" paragraph 4", "quote": "Proteins were identified with a 1% global false discovery rate (FDR) using a target-decoy database search algorithm [5] in ProteinPilot Descriptive Statistics Template (version 3.001p) (www.absciex.com/PDST)."}], "state": "complete"}, {"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 [1]) with the dataset identifiers PXD000717, PXD000720, PXD000721, PXD000731, PXD000733 and PXD000734. Data related to the peptides (trypsin digests only) were also uploaded to Peptide Atlas (Farrah et al., 2013 [2]) and are available with the dataset identifiers PASS00407, PASS00409, PASS00411, PASS00412, PASS00413 and PASS00414.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26217725", "locator": "sections[0] \"Abstract\" paragraph 1", "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 [1]) with the dataset identifiers PXD000717, PXD000720, PXD000721, PXD000731, PXD000733 and PXD000734. Data related to the peptides (trypsin digests only) were also uploaded to Peptide Atlas (Farrah et al., 2013 [2]) and are available with the dataset identifiers PASS00407, PASS00409, PASS00411, PASS00412, PASS00413 and PASS00414."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used a target-decoy database search to identify proteins at a 1% global false discovery rate, and the source mass-spectrometry data are accessible through ProteomeXchange via PRIDE, with peptide data also available through PeptideAtlas.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "Proteins were identified with a 1% global false discovery rate (FDR) using a target-decoy database search algorithm [5] in ProteinPilot Descriptive Statistics Template (version 3.001p) (www.absciex.com/PDST)."}, "evidence": [{"asset": "source:pmid:26217725", "locator": "sections[5] \"Experimental design, materials and methods\" paragraph 4", "quote": "Proteins were identified with a 1% global false discovery rate (FDR) using a target-decoy database search algorithm [5] in ProteinPilot Descriptive Statistics Template (version 3.001p) (www.absciex.com/PDST)."}, {"asset": "source:pmid:26217725", "locator": "sections[0] \"Abstract\" paragraph 1", "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 [1]) with the dataset identifiers PXD000717, PXD000720, PXD000721, PXD000731, PXD000733 and PXD000734."}, {"asset": "source:pmid:26217725", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data related to the peptides (trypsin digests only) were also uploaded to Peptide Atlas (Farrah et al., 2013 [2]) and are available with the dataset identifiers PASS00407, PASS00409, PASS00411, PASS00412, PASS00413 and PASS00414."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used a target-decoy database search to identify proteins at a 1% global false discovery rate, and the source mass-spectrometry data are accessible through ProteomeXchange via PRIDE, with peptide data also available through PeptideAtlas.", "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:26217725"], "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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No tolerance is published because the paper states none."}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Target-decoy database search algorithm), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R1", "reachable": true, "accessions": ["PXD000717", "PXD000720", "PXD000721", "PXD000731", "PXD000733", "PXD000734"], "resolved_accessions": ["PXD000717", "PXD000720", "PXD000721", "PXD000731", "PXD000733", "PXD000734"], "statements": ["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 [1]) with the dataset identifiers PXD000717, PXD000720, PXD000721, PXD000731, PXD000733 and PXD000734. Data related to the peptides (trypsin digests only) were also uploaded to Peptide Atlas (Farrah et al., 2013 [2]) and are available with the dataset identifiers PASS00407, PASS00409, PASS00411, PASS00412, PASS00413 and PASS00414."], "basis": "The paper names PXD000717, PXD000720, PXD000721, PXD000731, PXD000733, PXD000734 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26217725", "data:geo:PXD000717", "asset:table:pmid:26217725:1", "asset:table:pmid:26217725:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000717"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:17Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 27244, "completion_tokens": 7715, "cached_tokens": 1544}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26217725", "type": "paper", "label": "pmid:26217725"}, {"id": "source:pmid:26217725", "type": "manuscript", "label": "PMID 26217725 full text"}, {"id": "data:geo:PXD000717", "type": "dataset", "label": "GEO PXD000717"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26217725", "type": "paper", "label": "pmid:26217725"}, {"id": "source:pmid:26217725", "type": "manuscript", "label": "PMID 26217725 full text"}, {"id": "data:geo:PXD000717", "type": "dataset", "label": "GEO PXD000717"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26217725", "type": "extraction", "used": ["source:pmid:26217725"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000717", "type": "accession_resolution", "used": ["data:geo:PXD000717"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26217725", "parent_hash": "sha256:7c32de8b023c3f2b0db804c226488b547ae167ebb7ad5a221b09e59f9ac30a4e", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD000717 licence not read", "asset:data:geo:PXD000717 not downloaded", "asset:data:geo:PXD000720 licence not read", "asset:data:geo:PXD000720 not downloaded", "asset:data:geo:PXD000721 licence not read", "asset:data:geo:PXD000721 not downloaded", "asset:data:geo:PXD000731 licence not read", "asset:data:geo:PXD000731 not downloaded", "asset:data:geo:PXD000733 licence not read", "asset:data:geo:PXD000733 not downloaded", "asset:data:geo:PXD000734 licence not read", "asset:data:geo:PXD000734 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Dataset from proteomic analysis of rat, mouse, and human liver microsomes and S9 fractions", "Dataset from proteomic analysis of rat, mouse, and human liver microsomes and S9 fr", "Rat, mouse and human liver microsomes and S9 fractions", "Rat, mouse and human liver microsomes and S9 fra"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Dataset from proteomic analysis of rat, mouse, and human liver micr", "ectrometry (HR-MS/MS). The mass spectrometry proteomics data have been deposited to the ProteomeXcha", "th a research article published in EuPA Open Proteomics [3].", "es 1 and 2 for details). Processed data from proteomic analysis of rat, mouse, and human liver micr"], "order_basis": "paper_text_order:0", "id": "assay:2"}]}