Spleen proteomics data from high fat diet fed mice.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32904176", "kind": "science-record", "revision": 6, "content_hash": "sha256:1b24ef73c89add69d96bedecd02b96e9d7ba1912d82ae4bb6d07427b6477242c", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T21:23:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Spleen proteomics data from high fat diet fed mice.", "doi": "10.1016/j.dib.2020.106110", "pmid": "32904176", "authors": ["Sara L Svahn", "Bagmi Pattanaik", "Louise Grahnemo", "Saray Gutierrez", "Intawat Nookaew", "John-Olov Jansson", "Maria E Johansson"], "journal": "Data in brief", "year": 2020, "abstract": "The composition of the diet affects many processes in the body, including body weight and endocrine system. We have previously shown that dietary fat also affects the immune system. Mice fed high fat diet rich in polyunsaturated fatty acids survive S. aureus infection to a much greater extent than mice fed high fat diet rich in saturated fatty acids. Here we present data regarding the dietary effects on protein expression in spleen from mice fed three different diets, I) low fat/chow diet (LFD, n = 4), II) high fat diet rich in saturated fatty acids (HFD-S, n = 4) and III) high fat diet rich in polyunsaturated fatty acids (HFD-P, n = 4). We performed mass spectrophotometry based quantitative proteomics analysis of isolated spleen by implementing the isobaric tags for relative and absolute quantification (iTRAQ) approach. Mass spectrometry data were analyzed using Proteome Discoverer 2.4 software using the search engine mascot against Mus musculus in SwissProt. 924 proteins are identified in all sets (n = 4) for different dietary effects taken for statistical analysis using Qlucore Omics Explorer software. Only 20 proteins were found to be differentially expressed with a cut-off value of false discovery rate < 0.1 (q-value) when comparing HFD-S and HFD-P but no differentially expressed proteins were found when LFD was compared with HFD-P or HFD-S. The identified proteins and statistical analysis comparing HFD-S and HFD-P diets are available as a supplementary file S1. We identified a subset of proteins that showed an inverse expression pattern between two high fat diets. These differentially expressed proteins were further classified by gene ontology for their role in biological processes and molecular functions. Mass spectrometry raw data are also available via ProteomeXchange with identifier PXD020365.", "claims": [{"id": "claim-method", "statement": "Qlucore Omics Explorer 3.6 (Lund, Sweden https://qlucore.com) was used for statistical analysis using t-test two-groups comparison (HFD-S vs LFD; HFD-P vs LFD; HFD-P vs HFD-S).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32904176", "locator": "sections[8] \"Data analysis\" paragraph 3", "quote": "Qlucore Omics Explorer 3.6 (Lund, Sweden https://qlucore.com) was used for statistical analysis using t-test two-groups comparison (HFD-S vs LFD; HFD-P vs LFD; HFD-P vs HFD-S)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Analyzed data are available within the article and raw mass spectrometric proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020365.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32904176", "locator": "sections[1] \"p\" paragraph 1", "quote": "Analyzed data are available within the article and raw mass spectrometric proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020365."}], "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:32904176"], "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:PXD020365"], "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:PXD020365"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32904176", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2020.106110", "sha256": "sha256:f39e1c62ce1de7ce7a88c1d460feec9e7f39e3930212ad8121c1661f476b2723", "bytes": 17326, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2020.106110", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7451803", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD020365", "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=PXD020365", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD020365", "version": null, "note": "Analyzed data are available within the article and raw mass spectrometric proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020365.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Analyzed data are available within the article and raw mass spectrometric proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020365.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Spleen proteomics data from high fat diet fed mice", "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:32904176:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:636975971786fa00e01d6732d1b254991a9fbab0180f6512011ef624ab23be03", "bytes": 2237, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#utbl0001", "version": null, "note": null, "structure": {"pmcid": "PMC7451803", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject", "Endocrinology, Diabetes, and Metabolism"], ["Specific subject area", "dietary proteomics"], ["Type of data", "Raw data, Excel files, Tables, Figures"], ["How data were acquired", "Samples were analyzed on an LTQ-Orbitrap Velos mass spectrometer interfaced with an Easy-nLC (Thermo Fisher Scientific).For relative quantification, the MS raw data files for each iTRAQ set were merged in the search using Proteome Discoverer version 2.4 (Thermo Fisher Scientific).The database search was performed with the Mascot search engine (Matrix Science) against Mus musculus in SwissProt version July 2019 (Swiss Institute of Bioinformatics, Switzerland)."], ["Data format", "AnalyzedRaw"], ["Parameters for data collection", "C57BL/6 mice were fed one of three different diets for 8 weeks, I) low fat/chow diet (LFD), II) high fat diet rich in saturated fatty acids (HFD-S), or III) high fat diet rich in polyunsaturated fatty acids (HFD-P). Proteins from spleen were extracted and analyzed using quantitative proteomics. n = 4 per group."], ["Description of data collection", "The experimental layout is presented in Fig. 1. Data presented in this manuscript are spleen proteins affected by three different diets, I) low fat/chow diet (LFD), II) high fat diet rich in saturated fatty acids (HFD-S), or III) high fat diet rich in polyunsaturated fatty acids (HFD-P) (Table 1). We identified 924 proteins present in all datasets of different dietary conditions (Supplementary file S1). With a cut-off value of false discovery rate < 0.1 (q-value), the number of differentially expressed proteins data is presented in a Venn diagram (Fig. 2), and Table 2 and the two high fat diets are visualized in a heat map (Fig. 3). 20 differentially expressed proteins were further classified by gene ontology (Fig 4)."], ["Data source location", "Gothenburg, Sweden"], ["Data accessibility", "Analyzed data are available within the article and raw mass spectrometric proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020365."]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:32904176:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b6d4db433cdfd77a2097ca8c948a53c2415a236ad756883282ed12fe5128b9b1", "bytes": 975, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Energy density and composition of experimental diets: low fat/chow diet (LFD), high fat diet rich in saturated fatty acids (HFD-S), or high fat diet rich in polyunsaturated fatty acids (HFD-P). From Svahn SL et al [2,3].", "structure": {"pmcid": "PMC7451803", "section_index": 3, "section_title": "Data description", "row_count": 17, "column_count": 4}, "table": {"label": "Table 1", "caption": "Energy density and composition of experimental diets: low fat/chow diet (LFD), high fat diet rich in saturated fatty acids (HFD-S), or high fat diet rich in polyunsaturated fatty acids (HFD-P). From Svahn SL et al [2,3].", "rows": [["", "LFD", "HFD-S", "HFD-P"], ["Energy density (kcal/g)", "3.9", "5.2", "5.2"], ["Macronutrients (% kcal)", "", "", ""], ["Protein", "20", "20", "20"], ["Carbohydrate", "70", "20", "20"], ["Fat", "10", "60", "60"], ["Fat source (% of total fat)", "", "", ""], ["Soybean oil", "55.6", "9.3", "9.3"], ["Lard", "44.4", "90.7", "27.8"], ["Menhaden oil", "-", "-", "63.0"], ["Fatty acids (% by wt of total fatty acids)", "", "", ""], ["∑ SFA", "22.7", "32.0", "28.7"], ["∑ MUFA", "29.8", "36.0", "27.5"], ["∑ PUFA", "47.5", "32.0", "43.9"], ["∑ n-3 total fat", "5.2", "2.1", "25.6"], ["∑ n-6 total fat", "42.4", "29.9", "16.2"], ["n-6/n-3", "8.2", "14.1", "0.6"]], "row_count": 17, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl0001"}}, {"id": "asset:table:pmid:32904176:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b8734feb30be2767042d87f417267bcbfc92d99513737fc3e8115c84f2798e25", "bytes": 1084, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#tbl0002", "version": null, "note": "Protein ID and respective protein names presented in the heat map.", "structure": {"pmcid": "PMC7451803", "section_index": 3, "section_title": "Data description", "row_count": 21, "column_count": 2}, "table": {"label": "Table 2", "caption": "Protein ID and respective protein names presented in the heat map.", "rows": [["Protein ID", "Protein name"], ["Q9CY02", "Alpha-hemoglobin-stabilizing protein"], ["P84228", "Histone H3,2"], ["P43276", "Histone H1,5"], ["P09405", "Nucleolin"], ["P42932", "T-complex protein 1 subunit theta"], ["P54071", "Isocitrate dehydrogenase [NADP], mitochondrial"], ["Q8VIJ6", "Splicing factor, proline- and glutamine-rich"], ["Q3TEA8", "Heterochromatin protein 1-binding protein 3"], ["O89100", "GRB2-related adaptor protein 2"], ["Q3UTJ2", "Sorbin and SH3 domain-containing protein 2"], ["Q8R409", "Protein HEXIM1"], ["P42209", "Septin-1"], ["Q8BYZ1", "ABI gene family member 3"], ["Q6PIU9", "Uncharacterized protein FLJ45252 homolog"], ["Q8CI51", "PDZ and LIM domain protein 5"], ["Q62507", "Cochlin"], ["Q3TJD7", "PDZ and LIM domain protein 7"], ["Q9D154", "Leukocyte elastase inhibitor A"], ["Q8C3W1", "Uncharacterized protein C1orf198 homolog"], ["O54724", "Caveolae-associated protein 1"]], "row_count": 21, "column_count": 2, "numeric_cells": 26, "header_rows": 1, "locator": "section[3]/table-wrap[2]#tbl0002"}}], "gaps": ["asset:data:geo:PXD020365 not downloaded", "asset:data:geo:PXD020365 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test two-groups comparison", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Qlucore Omics Explorer 3.6 (Lund, Sweden https://qlucore.com) was used for statistical analysis using t-test two-groups comparison (HFD-S vs LFD; HFD-P vs LFD; HFD-P vs HFD-S)."}}], "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 (t-test two-groups comparison), 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. 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Mass spectrometry data were analyzed using Proteome Discoverer", "iological processes and molecular functions. Mass spectrometry raw data are also available via ProteomeXcha", "ed mass spectrophotometry based quantitative proteomics analysis of isolated spleen by implementing"], "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": ["erials and methods Six-week-old male C57BL/6 mice were obtained from Harlan Netherlands B.V. (Horst", "therlands B.V. (Horst, The Netherlands). The mice were housed under standard conditions of light an"], "order_basis": "paper_text_order:1911", "id": "assay:2"}]}