Raw N-glycan mass spectrometry imaging data on formalin-fixed mouse kidney.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30364692", "kind": "science-record", "revision": 5, "content_hash": "sha256:3b1921734ccce9cc92bf891be12449e650c882364ba7fb79f4cf8e053c72aaea", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T18:49:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Raw N-glycan mass spectrometry imaging data on formalin-fixed mouse kidney.", "doi": "10.1016/j.dib.2018.08.186", "pmid": "30364692", "authors": ["Ove J R Gustafsson", "Matthew T Briggs", "Mark R Condina", "Lyron J Winderbaum", "Matthias Pelzing", "Shaun R McColl", "Arun V Everest-Dass", "Nicolle H Packer", "Peter Hoffmann"], "journal": "Data in brief", "year": 2018, "abstract": "Provided is the annotated raw data for N-glycan mass spectrometry imaging (MSI) annotations in thin cross-sections of formalin-fixed and paraffin-embedded murine kidney. Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808. This brief is the first in a set of submissions from our group which will make raw data publicly accessible for existing and future MSI studies.", "claims": [{"id": "claim-data-access", "statement": "Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30364692", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30364692"], "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:PXD009808"], "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:PXD009808"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30364692", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2018.08.186", "sha256": "sha256:8c7bdf418f3a0f81fbeb9ec9a7983dce3b16c7757067deb40c9dc63726bb2ead", "bytes": 5748, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2018.08.186", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6197570", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD009808", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD009808", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD009808", "version": null, "note": "Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Raw N-glycan MALDI mass spectrometry imaging data on formalin-fixed mouse kidney", "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:30364692:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7a1bc76cfa5f0dc2c3ed4fe7849a30d2406fa80e2e3de65bff6d5ca759a2b502", "bytes": 301, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t0025", "version": null, "note": null, "structure": {"pmcid": "PMC6197570", "section_index": 6, "section_title": "Experimental design, materials and methods", "row_count": 3, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Number of sections", "4"], ["PNGase F replicate spots (total)", "2/tissue region (N = 4)"], ["Control replicate spots", "4 replicate spots in kidney cortex"]], "row_count": 3, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[6]/table-wrap[1]#t0025"}}, {"id": "asset:table:pmid:30364692:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8dc061fe2c91375f392837ae863758edf38b2a4c349438057047d862e82e5894", "bytes": 289, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[2]#t0030", "version": null, "note": null, "structure": {"pmcid": "PMC6197570", "section_index": 6, "section_title": "Experimental design, materials and methods", "row_count": 3, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Number of sections", "3"], ["PNGase F regions (total)", "1 per kidney, complete section (N = 2)"], ["Control regions", "1 (half kidney section)"]], "row_count": 3, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[6]/table-wrap[2]#t0030"}}, {"id": "asset:table:pmid:30364692:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:62862193144deb1f6354454eeaf32106eee1926c1902216e27e7aa7715e622e7", "bytes": 636, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[3]#t0005", "version": null, "note": "List of chemicals and suppliers.", "structure": {"pmcid": "PMC6197570", "section_index": 6, "section_title": "Experimental design, materials and methods", "row_count": 8, "column_count": 2}, "table": {"label": "Table 1", "caption": "List of chemicals and suppliers.", "rows": [["Item", "Details (supplier)"], ["Glycerol-free PNGase F", "P0705L, 75000 NEB units (New England BioLabs, Ipswich, MA, USA)"], ["Formalin", "Sigma-Aldrich"], ["Trifluoroacetic acid (TFA)", "Merck (Darmstadt, Germany)"], ["Ethanol (EtOH)", "Merck (Darmstadt, Germany)"], ["Sodium chloride (NaCl)", "Merck (Darmstadt, Germany)"], ["2,5-dihydroxybenzoic acid (DHB)", "Sigma-Aldrich/Bruker Daltonics (Bremen, Germany)"], ["Xylene", "Chem-Supply (Gillman, South Australia)"]], "row_count": 8, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[6]/table-wrap[3]#t0005"}}, {"id": "asset:table:pmid:30364692:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9a597dc54e94c5c42cb7282b7406be42091dcd4b9eeec8b9e96498f9c11d76c1", "bytes": 417, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[4]#t0010", "version": null, "note": "Mass standards used to externally calibrate mass spectrometry data.", "structure": {"pmcid": "PMC6197570", "section_index": 6, "section_title": "Experimental design, materials and methods", "row_count": 4, "column_count": 3}, "table": {"label": "Table 2", "caption": "Mass standards used to externally calibrate mass spectrometry data.", "rows": [["Item", "Supplier", "m/z"], ["Man5GlcNAc2", "Prozyme (CA, USA)", "[M+Na]+: 1257.4225"], ["Man3GlcNAc5", "Prozyme (CA, USA)", "[M+Na]+: 1542.5551"], ["Man3Gal4GlcNAc6", "Prozyme (CA, USA)", "[M+Na]+: 2393.8457"]], "row_count": 4, "column_count": 3, "numeric_cells": 3, "header_rows": 1, "locator": "section[6]/table-wrap[4]#t0010"}}, {"id": "asset:table:pmid:30364692:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4a73dfdd8fd1f0a217c84be3f6e664d4e425c59735e130b872ff11c28bd93c2f", "bytes": 755, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[5]#t0015", "version": null, "note": "Consumables and equipment, including suppliers.", "structure": {"pmcid": "PMC6197570", "section_index": 6, "section_title": "Experimental design, materials and methods", "row_count": 10, "column_count": 2}, "table": {"label": "Table 3", "caption": "Consumables and equipment, including suppliers.", "rows": [["Item", "Supplier"], ["Indium tin oxide (ITO) slides", "Bruker Daltonics (Bremen, Germany)"], ["Poly Ethylene Naphthalate (PEN) slides", "MicroDissect (Herborn, Germany)"], ["0.025 µm VWSP nitrocellulose membranes", "Millipore (Cork, Ireland)"], ["TP 1020 processors", "Leica Biosystems (North Ryde, Australia)"], ["EG 114OH embedder", "Leica Biosystems"], ["Microm HM 325 microtome", "Zeiss (Gottingen, Germany)"], ["TM-sprayer", "HTX Instruments (NC, USA)"], ["UltrafleXtreme MALDI-ToF/ToF", "Bruker Daltonics"], ["Chemical Inkjet Printer (ChIP)-1000", "Shimadzu (Japan)"]], "row_count": 10, "column_count": 2, "numeric_cells": 5, "header_rows": 1, "locator": "section[6]/table-wrap[5]#t0015"}}], "gaps": ["asset:data:geo:PXD009808 not downloaded", "asset:data:geo:PXD009808 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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": ["PXD009808"], "resolved_accessions": ["PXD009808"], "statements": ["Relevant meta-data have been provided in this brief and the raw MSI data can be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808."], "basis": "The paper names PXD009808 in PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30364692", "data:geo:PXD009808", "asset:table:pmid:30364692:1", "asset:table:pmid:30364692:2", "asset:table:pmid:30364692:3", "asset:table:pmid:30364692:4", "asset:table:pmid:30364692:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD009808"]}, "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": "2026-10-31T18:12:39Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 6261, "completion_tokens": 1159, "cached_tokens": 792}}, "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:30364692", "type": "paper", "label": "pmid:30364692"}, {"id": "source:pmid:30364692", "type": "manuscript", "label": "PMID 30364692 full text"}, {"id": "data:geo:PXD009808", "type": "dataset", "label": "GEO PXD009808"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30364692", "type": "paper", "label": "pmid:30364692"}, {"id": "source:pmid:30364692", "type": "manuscript", "label": "PMID 30364692 full text"}, {"id": "data:geo:PXD009808", "type": "dataset", "label": "GEO PXD009808"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30364692", "type": "extraction", "used": ["source:pmid:30364692"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD009808", "type": "accession_resolution", "used": ["data:geo:PXD009808"], "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:30364692", "parent_hash": "sha256:9b1701654e7b584e26d6fce78bc8266a3f87debd338955a0f01b161e4b987e90", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PXD009808 licence not read", "asset:data:geo:PXD009808 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Raw N-glycan mass spectrometry imaging data on formalin-fixed mouse kidney.", "vided is the annotated raw data for N-glycan mass spectrometry imaging (MSI) annotations in thin cross-sect", "Mass standards used to externally calibrate mass spectrometry data. Consumables and equipment, including s", "n be accessed using ProteomeXchange with the PRoteomics IDEntifications (PRIDE) identifier PXD009808"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["spectrometry imaging data on formalin-fixed mouse kidney.", "ions of formalin-fixed and paraffin-embedded murine kidney. Relevant meta-data have been provide"], "order_basis": "paper_text_order:18", "id": "assay:2"}]}