Proteomic datasets of uninfected and Staphylococcus aureus-infected goat milk.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32426435", "kind": "science-record", "revision": 3, "content_hash": "sha256:b2f96d66077b6ac95a09c24e9c7111956350b8e18d1feb2748b92efd434afd39", "created_at": "2026-11-01T15:41:01Z", "updated_at": "2026-11-01T18:52:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic datasets of uninfected and Staphylococcus aureus-infected goat milk.", "doi": "10.1016/j.dib.2020.105665", "pmid": "32426435", "authors": ["Salvatore Pisanu", "Carla Cacciotto", "Daniela Pagnozzi", "Sergio Uzzau", "Claudia Pollera", "Martina Penati", "Valerio Bronzo", "Maria Filippa Addis"], "journal": "Data in brief", "year": 2020, "abstract": "We present a proteomic dataset generated from half-udder Alpine goat milk. The milk samples belonged to 3 groups: i) mid-lactation, low somatic cell count, uninfected milk (MLU, n=3); ii) late lactation, high somatic cell count, uninfected milk (LHU, n=3); and late lactation, high somatic cell count, Staphylococcus aureus subclinically infected milk (LHS, n=3). The detailed description of results is reported in the research article entitled \"Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: new perspectives for monitoring and understanding mastitis in dairy goats\". After milk defatting, high speed centrifugation and trypsin digestion of milk with the FASP protocol, peptide mixtures were analyzed by LC-MS/MS on a Q-Exactive. Peptide identification was carried out using Sequest-HT in Proteome Discoverer. Then, the Normalized Abundance Spectrum Factor (NSAF) value was calculated by label free quantitation using the spectral counting approach, and Gene Ontology (GO) annotation by Uniprot was carried out by reporting biological process, molecular function and cellular component. The MS data have been deposited to the ProteomeXchange via the PRIDE with the dataset identifier PXD017243.", "claims": [{"id": "claim-data-access", "statement": "Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32426435", "locator": "sections[1] \"p\" paragraph 1", "quote": "Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243"}], "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:32426435"], "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:PXD017243"], "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:PXD017243"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32426435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2020.105665", "sha256": "sha256:6ebcfecfee4f1e5992c67c03ac41ed560a81974e3d0627bd9467ba5f730a2aa4", "bytes": 7571, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2020.105665", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7225386", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD017243", "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=PXD017243", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD017243", "version": null, "note": "Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: new perspectives for monitoring and understanding mastitis in dairy goats", "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:32426435:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:80d319f53d267d747dc3c5aded26fb9e9799e4ff728bfdb368e2ab832e86138f", "bytes": 2140, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#utbl0001", "version": null, "note": null, "structure": {"pmcid": "PMC7225386", "section_index": 1, "section_title": "p", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject", "Biology"], ["Specific subject area", "Proteomics"], ["Type of data", "TablesFilesrawFiles .msf"], ["How data was acquired", "Sample preparation: filter-aided sample preparation (FASP).Instrument: Q Exactive mass spectrometer interfaced with an UltiMate 3000 RSLCnanoLC system (Thermo Fisher Scientific).Peptide identification: Proteome Discoverer (version 1.4; Thermo Scientific) SEQUEST-HT. Gene ontology annotation: UniProt Knowledgebase (UniProtKB)."], ["Data format", "RAW data (Thermo proprietary), msf files (Proteome Discoverer) and supplementary Excel files (1-3) with data analysis output."], ["Parameters for data collection", "Half-udder goat milk collected along the course of an entire lactation (middle and late lactation) from Alpine goat half-udders."], ["Description of data collection", "Half-udder goat milk was defatted, submitted to high-speed centrifugation, and proteins were digested by Filter-aided sample preparation (FASP). Peptide mixtures were analyzed by mass spectrometry with a Q-Exactive interfaced with an UltiMate 3000 RSLCnanoLC system (Thermo Scientific, San Jose, CA, USA).Identifications and Peptide spectrum matches (PSMs) data were obtained with Proteome Discoverer and used to calculate protein relative abundance and to perform Gene Ontology annotation with the UniprotKB database."], ["Data source location", "Tramariglio, Alghero (Sassari), Italy"], ["Data accessibility", "Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243"], ["Related research article", "S. Pisanu, C. Cacciotto, P. Pagnozzi, S. Uzzau, C. Pollera, M. Penati, V. Bronzo, M.F. Addis. Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: new perspectives for monitoring and understanding mastitis in dairy goats. Journal of Proteomics, submitted [2]."]], "row_count": 10, "column_count": 2, "numeric_cells": 5, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:32426435:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:07fcc3f2273fbb9d0c49a2d818a46c1ec1a8b0e592a38500d61d7653b866838f", "bytes": 741, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Somatic cell count and bacteriological culture results of the half-udder goat milk samples used for generating the dataset.", "structure": {"pmcid": "PMC7225386", "section_index": 3, "section_title": "Data Description", "row_count": 10, "column_count": 5}, "table": {"label": "Table 1", "caption": "Somatic cell count and bacteriological culture results of the half-udder goat milk samples used for generating the dataset.", "rows": [["Sample number", "Stage of lactationb", "SCCa (cells/mL x 103)", "Bacteriology result", "Acronym"], ["1", "Middle", "13", "Sterile", "MLUc"], ["2", "Middle", "16", "Sterile", "MLU"], ["3", "Middle", "27", "Sterile", "MLU"], ["4", "Late", "2488", "Sterile", "LHUd"], ["5", "Late", "2942", "Sterile", "LHU"], ["6", "Late", "3365", "Sterile", "LHU"], ["7", "Late", "3936", "Staphylococcus aureus", "LHSe"], ["8", "Late", "3938", "Staphylococcus aureus", "LHS"], ["9", "Late", "4066", "Staphylococcus aureus", "LHS"]], "row_count": 10, "column_count": 5, "numeric_cells": 19, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl0001"}}], "gaps": ["asset:data:geo:PXD017243 not downloaded", "asset:data:geo:PXD017243 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": ["PXD017243"], "resolved_accessions": ["PXD017243"], "statements": ["Analyzed data is provided in supplementary files 1-3 within this article.Raw data repository name: PRIDE [1].Dataset identifier: PXD017243. direct URL to data (raw and msf files): http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017243"], "basis": "The paper names PXD017243 in ProteomeXchange via PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32426435", "data:geo:PXD017243", "asset:table:pmid:32426435:1", "asset:table:pmid:32426435:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017243"]}, "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": "2026-10-31T18:19:52Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 7201, "completion_tokens": 1086, "cached_tokens": 776}}, "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:32426435", "type": "paper", "label": "pmid:32426435"}, {"id": "source:pmid:32426435", "type": "manuscript", "label": "PMID 32426435 full text"}, {"id": "data:geo:PXD017243", "type": "dataset", "label": "GEO PXD017243"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32426435", "type": "paper", "label": "pmid:32426435"}, {"id": "source:pmid:32426435", "type": "manuscript", "label": "PMID 32426435 full text"}, {"id": "data:geo:PXD017243", "type": "dataset", "label": "GEO PXD017243"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32426435", "type": "extraction", "used": ["source:pmid:32426435"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017243", "type": "accession_resolution", "used": ["data:geo:PXD017243"], "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:32426435", "parent_hash": "sha256:fd8a651b72a83326759b94e5d64e4063d87fbeed0e12792987b28d26bb5da4f9", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD017243 licence not read", "asset:data:geo:PXD017243 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": ["Proteomic datasets of uninfected and Staphylococcus au", "We present a proteomic dataset generated from half-udder Alpine goa", "protocol, peptide mixtures were analyzed by LC-MS/MS on a Q-Exactive. Peptide identification was"], "order_basis": "paper_text_order:0", "id": "assay:1"}]}