Data on European seabass fed with methionine-enriched diets obtained through label free shotgun proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33392368", "kind": "science-record", "revision": 8, "content_hash": "sha256:bef80ec3d26e9817ea19ccf9c1424ad86e297b413c5e1c626139822e2844f4be", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T22:45:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data on European seabass fed with methionine-enriched diets obtained through label free shotgun proteomics.", "doi": "10.1016/j.dib.2020.106675", "pmid": "33392368", "authors": ["Ana Paula Farinha", "Denise Schrama", "Tomé Silva", "Luís E C Conceição", "Rita Colen", "Sofia Engrola", "Pedro Rodrigues", "Marco Cerqueira"], "journal": "Data in brief", "year": 2021, "abstract": "This data article is associated with the research article \"Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics\". Here it is described the data obtained from proteomic analysis of 36 European seabass juveniles (3 fish x 3 replicate tanks) after 18 days of feeding with experimental diets containing four inclusion levels of methionine (Met): 0.77%, 1%, 1.36% and 1.66% Met (w/w). We analysed this dataset and compared it with that obtained during the long-term feeding period i.e., 85 days. Fish liver proteins were digested with trypsin and purified peptides were analysed by LC-MS/MS. Proteins were identified with at least two peptides at 0.1% Decoy false discovery rate (FDR). In this dataset, we present the analysis of the differential abundant proteins (DAP) with significant differences across treatments after 18 days of feeding (One-Way ANOVA, p < 0.05). Treatment's comparisons were also performed between the 18- and 85-days feeding trials through Two-Way ANOVA (p < 0.05). MS/MS raw data are available via ProteomeXChange with identifiers PXD019610 and 10.6019/PXD019610 (18-days dataset); and PXD019622 and 10.6019/PXD019622 (85-days dataset). This dataset corresponds to fish sampled after 18-days of experimental trial and is made available to support the study conducted in the afore-mentioned article, by performing the analysis during a short-term period of feeding. The data presented may be further used in other nutritional studies e.g., addressing hepatic changes mediated by Met.", "claims": [{"id": "claim-method", "statement": "In this dataset, we present the analysis of the differential abundant proteins (DAP) with significant differences across treatments after 18 days of feeding (One-Way ANOVA, p < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392368", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this dataset, we present the analysis of the differential abundant proteins (DAP) with significant differences across treatments after 18 days of feeding (One-Way ANOVA, p < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are with this article and the MS/MS raw and msf files have been deposited to the ProteomeXChange Consortium via the PRIDE repository and are publicly available on http://www.ebi.ac.uk/pride/archive/projects/PXD019610Data identifiers: PXD019610 and 10.6019/PXD019610", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392368", "locator": "sections[1] \"Specifications Table\" paragraph 2", "quote": "Data are with this article and the MS/MS raw and msf files have been deposited to the ProteomeXChange Consortium via the PRIDE repository and are publicly available on http://www.ebi.ac.uk/pride/archive/projects/PXD019610Data identifiers: PXD019610 and 10.6019/PXD019610"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33392368"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33392368", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2020.106675", "sha256": "sha256:6108b04c5ba44a852184d73f56f1f41f94e0e58818a1b88d94f9ac2963f945aa", "bytes": 23362, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2020.106675", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7773569", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33392368:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5ef087147bb9ffc657db0078e16358b3954551c1c036d81387a71bd2e3b4a2ea", "bytes": 2270, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#utbl0001", "version": null, "note": null, "structure": {"pmcid": "PMC7773569", "section_index": 1, "section_title": "Specifications Table", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject", "Biology"], ["Specific subject area", "Fish proteomics, Label-free quantitative mass spectrometry"], ["Type of data", "FigureTable"], ["How data were acquired", "Mass spectrometry, by using reverse phase nano liquid chromatography (Ultimate 3000 system) coupled online to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Scientific, Bremen, Germany) in data-dependent acquisition mode. Scaffold software (version Scaffold_4.8.9, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications, and perform quantitative analysis based on extracted ion chromatograms and for the TOP3 resulting most intense ion peak areas."], ["Data format", "Raw dataAnalysed data through uni- and multi-variate statistical analyses."], ["Parameters for data collection", "Liver protein samples were obtained from fish fed with the following dietary methionine (Met) inclusion levels: 0.77% Met (w/w), 1% Met (w/w), 1.36% Met (w/w) and 1.66% Met (w/w); diets M0.65, M0.85, M1.25 and M1.5, correspondingly."], ["Description of data collection", "The four experimental diets were tested in triplicate and 3 fish/tank were randomly sampled for proteomic analysis, in a total of 9 fish/treatment. Protein samples were analyzed by label free shotgun proteomics (LC-MS/MS)."], ["Data source location", "European seabass juveniles were reared at Ramalhete Field Station (CCMAR, Universidade do Algarve, Faro) - Portugal, between May and August of 2018."], ["Data accessibility", "Data are with this article and the MS/MS raw and msf files have been deposited to the ProteomeXChange Consortium via the PRIDE repository and are publicly available on http://www.ebi.ac.uk/pride/archive/projects/PXD019610Data identifiers: PXD019610 and 10.6019/PXD019610"], ["Related research article", "A.P. Farinha, D. Schrama, T. Silva, L.E.C. Conceição, R. Colen, S. Engrola, P. Rodrigues, M. Cerqueira. Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics. Journal of Proteomics. In Press. https://doi.org/10.1016/j.jprot.2020.104047"]], "row_count": 10, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this dataset, we present the analysis of the differential abundant proteins (DAP) with significant differences across treatments after 18 days of feeding (One-Way ANOVA, p < 0.05)."}}], "targets": [], "gaps": []}, "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": "R4", "reachable": false, "accessions": ["PXD019610 and 10.6019/PXD019610", "PXD019622 and 10.6019/PXD019622"], "resolved_accessions": [], "statements": ["Data are with this article and the MS/MS raw and msf files have been deposited to the ProteomeXChange Consortium via the PRIDE repository and are publicly available on http://www.ebi.ac.uk/pride/archive/projects/PXD019610Data identifiers: PXD019610 and 10.6019/PXD019610"], "basis": "The paper names PXD019610 and 10.6019/PXD019610, PXD019622 and 10.6019/PXD019622, but the accession does not resolve in the repository (no reason recorded, no reason recorded), so the data cannot be reached from here. 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