Shotgun proteomics datasets acquired on Gammarus pulex animals sampled from the wild.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31687451", "kind": "science-record", "revision": 6, "content_hash": "sha256:bb31d43d20157f3e35ed6540aeccec048ae644c4e26678e6e063d05b961f26e1", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T21:22:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Shotgun proteomics datasets acquired on Gammarus pulex animals sampled from the wild.", "doi": "10.1016/j.dib.2019.104650", "pmid": "31687451", "authors": ["Duarte Gouveia", "Yannick Cogne", "Jean-Charles Gaillard", "Christine Almunia", "Olivier Pible", "Adeline François", "Davide Degli-Esposti", "Olivier Geffard", "Arnaud Chaumot", "Jean Armengaud"], "journal": "Data in brief", "year": 2019, "abstract": "This data article associated with the manuscript \"Comparative proteomics in the wild: accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium\" refers to the shotgun proteomics analysis performed on 40 Gammarus pulex animals sampled from the wild. Proteins were extracted, digested with trypsin, and the resulting peptides were identified by tandem mass spectrometry. Here, we present the list of proteins from males and the list of proteins from females that are differentially detected between the Brameloup and the Pollon populations. Data are available via ProteomeXchange with identifiers PXD013656 and PXD013712, respectively.", "claims": [{"id": "claim-method", "statement": "Fold changes for protein abundances were evaluated using the Tfold method [10] and statistically validated with a Student test considering sample with unequal variance and bilateral repartition of abundances of proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31687451", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Fold changes for protein abundances were evaluated using the Tfold method [10] and statistically validated with a Student test considering sample with unequal variance and bilateral repartition of abundances of proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31687451", "locator": "sections[8] \"Data availability\" paragraph 2", "quote": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females."}], "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:31687451"], "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:PXD013656"], "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:PXD013656"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31687451", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2019.104650", "sha256": "sha256:295c3f20f9e362ae5bd61f48527c32146797ad5fd307a854d86323affa074fc0", "bytes": 17859, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2019.104650", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6820120", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD013656", "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=PXD013656", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013656", "version": null, "note": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics of Gammarus pulex individual males sampled from the wild", "resolution_checked_at": "2026-10-31T18:28:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD013712", "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=PXD013712", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013712", "version": null, "note": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics of Gammarus pulex individual females sampled from the wild", "resolution_checked_at": "2026-10-31T18:28:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31687451:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dcdb687836bbec7b5faa43e26135f69cd99dca134fb209a4be89dbfc8eeda8b0", "bytes": 475, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl1", "version": null, "note": "Statistics of the shotgun proteomics data acquired on G. pulex individuals.", "structure": {"pmcid": "PMC6820120", "section_index": 3, "section_title": "Data", "row_count": 3, "column_count": 7}, "table": {"label": "Table 1", "caption": "Statistics of the shotgun proteomics data acquired on G. pulex individuals.", "rows": [["", "Individuals (n)", "Peptide-spectrum matches", "Peptide sequences", "Non-ambiguous peptide sequences", "Proteins", "Core proteome"], ["Male dataset", "20", "397465", "11435", "8134", "1385", "605"], ["Female dataset", "20", "448228", "12080", "8658", "1444", "607"]], "row_count": 3, "column_count": 7, "numeric_cells": 12, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:PXD013656 not downloaded", "asset:data:geo:PXD013656 licence not read", "asset:data:geo:PXD013712 not downloaded", "asset:data:geo:PXD013712 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Tfold method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Fold changes for protein abundances were evaluated using the Tfold method [10] and statistically validated with a Student test considering sample with unequal variance and bilateral repartition of abundances of proteins."}}], "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": "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 (Tfold method), 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": ["PXD013656", "PXD013712", "10.6019/PXD013656", "10.6019/PXD013712"], "resolved_accessions": ["PXD013656", "PXD013712"], "statements": ["The mass spectrometry and proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [11] partner repository with the dataset identifiers PXD013656 and 10.6019/PXD013656 for the proteomes from G. pulex males, and PXD013712 and 10.6019/PXD013712 for the proteoms from G. pulex females."], "basis": "The paper names PXD013656, PXD013712 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31687451", "data:geo:PXD013656", "asset:table:pmid:31687451:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD013656"]}, "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": "2026-10-31T18:16:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15698, "completion_tokens": 1779, "cached_tokens": 528}}, "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:31687451", "type": "paper", "label": "pmid:31687451"}, {"id": "source:pmid:31687451", "type": "manuscript", "label": "PMID 31687451 full text"}, {"id": "data:geo:PXD013656", "type": "dataset", "label": "GEO PXD013656"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31687451", "type": "paper", "label": "pmid:31687451"}, {"id": "source:pmid:31687451", "type": "manuscript", "label": "PMID 31687451 full text"}, {"id": "data:geo:PXD013656", "type": "dataset", "label": "GEO PXD013656"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31687451", "type": "extraction", "used": ["source:pmid:31687451"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD013656", "type": "accession_resolution", "used": ["data:geo:PXD013656"], "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:31687451", "parent_hash": "sha256:203b018d833210e51bcc42970a62339968c8ec6e0bd2a0aa82f1a4f29e5a5f33", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD013656 licence not read", "asset:data:geo:PXD013656 not downloaded", "asset:data:geo:PXD013712 licence not read", "asset:data:geo:PXD013712 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["Shotgun proteomics datasets acquired on Gammarus pulex animals", "associated with the manuscript \"Comparative proteomics in the wild: accounting for intrapopulation", "on exposed to cadmium\" refers to the shotgun proteomics analysis performed on 40 Gammarus pulex anim", "resulting peptides were identified by tandem mass spectrometry. Here, we present the list of proteins from"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hese were searched against a gender-specific RNAseq-derived database obtained previously by de n", "e thoroughly described in Ref. [6]. Briefly, RNA-seq was performed on a single genotyped animal,", "y by de novo assembly of G. pulex individual transcriptomes and identification of the most probable open", "reading frames [6]. The production of these transcriptomes and the construction of the protein database"], "order_basis": "paper_text_order:4790", "id": "assay:2"}]}