Data for comparative proteomics of ovaries from five non-model, crustacean amphipods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26380837", "kind": "science-record", "revision": 7, "content_hash": "sha256:a98ee932e53733fbd295d1ae2514f57472919eae356b3a3bb14896aff3ea1a39", "created_at": "2026-11-01T15:40:10Z", "updated_at": "2026-11-01T21:58:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data for comparative proteomics of ovaries from five non-model, crustacean amphipods.", "doi": "10.1016/j.dib.2015.07.037", "pmid": "26380837", "authors": ["Judith Trapp", "Christine Almunia", "Jean-Charles Gaillard", "Olivier Pible", "Arnaud Chaumot", "Olivier Geffard", "Jean Armengaud"], "journal": "Data in brief", "year": 2015, "abstract": "Ovaries were taken from five sexually mature amphipods: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, Hyallela azteca and Parhyale hawaiensis. The soluble proteome extracted from individual pair of ovaries from five biological replicates was trypsin digested and the resulting peptides were analyzed by high resolution tandem mass spectrometry. The spectra were assigned with four protein sequence databases with different specificities: a RNAseq-derived G. fossarum database; a RNAseq-derived P. hawaiensis database; both originating from ovaries transcriptome; the Daphnia pulex database derived from whole-genome sequencing and the NCBInr database. The best interpretation was obtained for most animals with the specific RNA-seq protein database previously established by means of RNAseq carried out on G. fossarum. Proteins identified in the five amphipod species allow defining the core-proteome of female reproductive tissues of the Senticaudata suborder. The data accompanying the manuscript describing the database searches and comparative analysis Trapp et al., 2015 [1] have been deposited to the ProteomeXchange with identifiers PXD002253 (G. fossarum), PXD002254 (G. pulex), PXD002255 (G. roeseli), PXD002256 (H. Azteca), and PXD002257 (P. hawaiensis).", "claims": [{"id": "claim-data-access", "statement": "Deposited to the ProteomeXchange with identifiers PXD002253 forG. fossarum, PXD002309 forG. pulex, PXD002311 forG. roeseli, PXD002308 forH. Azteca, and PXD002310 forP. hawaiensis(http://proteomecentral.proteomexchange.org).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26380837", "locator": "sections[1] \"p\" paragraph 1", "quote": "Deposited to the ProteomeXchange with identifiers PXD002253 forG. fossarum, PXD002309 forG. pulex, PXD002311 forG. roeseli, PXD002308 forH. Azteca, and PXD002310 forP. hawaiensis(http://proteomecentral.proteomexchange.org)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified the core ovary proteome of five amphipod species; no inferential statistical method or statistical test is reported, and protein quantification was based on the normalized spectral abundance factor, while the underlying data were deposited in ProteomeXchange.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26380837", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteins identified in the five amphipod species allow defining the core-proteome of female reproductive tissues of the Senticaudata suborder."}, {"asset": "source:pmid:26380837", "locator": "sections[7] \"Protein sequence databases and MS/MS assignments\" paragraph 2", "quote": "The normalized spectral abundance factor (NSAF) for each protein was calculated as the total spectral count divided by the molecular mass expressed in kDa [13]."}, {"asset": "source:pmid:26380837", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data accompanying the manuscript describing the database searches and comparative analysis Trapp et al., 2015 [1] have been deposited to the ProteomeXchange with identifiers PXD002253 (G. fossarum), PXD002254 (G. pulex), PXD002255 (G. roeseli), PXD002256 (H. Azteca), and PXD002257 (P. hawaiensis)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified the core ovary proteome of five amphipod species; no inferential statistical method or statistical test is reported, and protein quantification was based on the normalized spectral abundance factor, while the underlying data were deposited in ProteomeXchange.", "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:26380837"], "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:PXD002253"], "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:PXD002253"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26380837", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.07.037", "sha256": "sha256:26b4b49e484ab099715b7b5eb2a5aaa8331fd6225530fa4f02a563d8f7b1af83", "bytes": 13892, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.07.037", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4556749", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002253", "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=PXD002253", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002253", "version": null, "note": "Deposited to the ProteomeXchange with identifiers PXD002253 forG. fossarum, PXD002309 forG. pulex, PXD002311 forG. roeseli, PXD002308 forH. 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