Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40234672", "kind": "science-record", "revision": 4, "content_hash": "sha256:2d784d6fa32d611216bb1876048c8020f283c1843ecdb876334e0a3a37935638", "created_at": "2026-11-01T20:30:23Z", "updated_at": "2026-11-01T22:56:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.", "doi": "10.1038/s41598-025-97783-w", "pmid": "40234672", "authors": ["Svitlana Tretiak", "Teresa Mendes Maia", "Delphi Van Haver", "An Staes", "Simon Devos", "Tom Rijsselaere", "Evy Goossens", "Filip Van Immerseel", "Francis Impens", "Gunther Antonissen"], "journal": "Scientific reports", "year": 2025, "abstract": "Analysis of the blood proteome allows identification of proteins related to changes upon certain physiological conditions. The pathophysiology of necrotic enteritis (NE) has been extensively studied. While intestinal changes have been very well documented, data addressing NE-induced alterations in the blood proteome are scant, although these might have merit in diagnostics. In light of recent technological advancements in proteomics and pressing need for tools to access gut health, the current study employs mass-spectrometry (MS)-based proteomics to identify biomarkers for gastrointestinal health of chickens. Here, we report findings of an untargeted proteomics investigation conducted on blood plasma in chickens under NE challenge. Two MS-strategies were used for analysis: conventional data dependent acquisition coupled to standard nanoflow liquid chromatography (LC) (nano-DDA) and recently-developed data independent acquisition coupled to an Evosep One LC system (Evo-DIA). Despite superior completeness and quantification of the Evo-DIA-acquired data, high degree of agreement in identification and quantification was observed between both approaches. Additionally, we identified 15 differentially expressed proteins (shared by nano-DDA and Evo-DIA) that represent responses of animals to infection and may serve as potential biomarkers. Experimental validation through ELISA immunoassays and targeted MS for selected regulated proteins (CFD, HPS5, and MASP2) confirmed medium-to-high levels of inter-protein correlation. A GSEA analysis revealed enrichment in a number of processes related to adaptive and humoral immunity, immune activation and response in infected animals. Data are available via ProteomeXchange with identifiers PXD050461, PXD050473, and PXD061607.", "claims": [{"id": "claim-method", "statement": "To highlight significant changes in protein levels between control and NE animals, statistical testing was performed with limma39.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40234672", "locator": "sections[5] \"Necrotic enteritis leads to significant changes in the plasma proteome\" paragraph 5", "quote": "To highlight significant changes in protein levels between control and NE animals, statistical testing was performed with limma39."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40234672", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 15 differentially expressed proteins shared by nano-DDA and Evo-DIA that may serve as biomarkers of infection in chickens.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40234672", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Additionally, we identified 15 differentially expressed proteins (shared by nano-DDA and Evo-DIA) that represent responses of animals to infection and may serve as potential biomarkers."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 15 differentially expressed proteins shared by nano-DDA and Evo-DIA that may serve as biomarkers of infection in chickens.", "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:40234672"], "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:PXD050461"], "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:PXD050461"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40234672", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-97783-w", "sha256": "sha256:3c5595836ac13caf7896185cc2e086905285d47074262aa54e43bf5c95bce5b3", "bytes": 63073, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-97783-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12000508", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD050461", "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=PXD050461", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD050461", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Blood Proteome profiling for protein biomarker discovery in Broilers", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD050473", "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=PXD050473", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD050473", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Blood Proteome profiling for protein biomarker discovery in Broilers", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD061607", "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=PXD061607", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD061607", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Blood Proteome profiling for protein biomarker discovery in Broilers", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD050461 not downloaded", "asset:data:geo:PXD050461 licence not read", "asset:data:geo:PXD050473 not downloaded", "asset:data:geo:PXD050473 licence not read", "asset:data:geo:PXD061607 not downloaded", "asset:data:geo:PXD061607 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To highlight significant changes in protein levels between control and NE animals, statistical testing was performed with limma39."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["PXD050461", "PXD050473", "PXD061607"], "resolved_accessions": ["PXD050461", "PXD050473", "PXD061607"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Con-sortium via the PRIDE partner repository with the dataset identifiers PXD050461 (username: reviewer_pxd050461@ebi.ac.uk and password: 1JM2Jzxi; project DOI: 10.6019/PXD050461), PXD050473 (username: reviewer_pxd050473@ebi.ac.uk and pass-word: iAPj0rc5), and PXD061607 (username: reviewer_pxd061607@ebi.ac.uk and pass-word: IWdrZHtx9VAo)."], "basis": "The paper names PXD050461, PXD050473, PXD061607 in ProteomeXchange Con-sortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40234672", "data:geo:PXD050461"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD050461"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:50:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15867, "completion_tokens": 2506, "cached_tokens": 264}}, "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:40234672", "type": "paper", "label": "pmid:40234672"}, {"id": "source:pmid:40234672", "type": "manuscript", "label": "PMID 40234672 full text"}, {"id": "data:geo:PXD050461", "type": "dataset", "label": "GEO PXD050461"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40234672", "type": "paper", "label": "pmid:40234672"}, {"id": "source:pmid:40234672", "type": "manuscript", "label": "PMID 40234672 full text"}, {"id": "data:geo:PXD050461", "type": "dataset", "label": "GEO PXD050461"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40234672", "type": "extraction", "used": ["source:pmid:40234672"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD050461", "type": "accession_resolution", "used": ["data:geo:PXD050461"], "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:40234672", "parent_hash": "sha256:018a449043c4a8cbd241eeccf1a332c7e451ae2eddbd0a5f6c5ae397e7591c90", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD050461 licence not read", "asset:data:geo:PXD050461 not downloaded", "asset:data:geo:PXD050473 licence not read", "asset:data:geo:PXD050473 not downloaded", "asset:data:geo:PXD061607 licence not read", "asset:data:geo:PXD061607 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["biomarkers. Experimental validation through ELISA immunoassays and targeted MS for selected re"], "order_basis": "paper_text_order:1428", "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": 0.77, "evidence": [". Materials and methods Experimental design: in vivo necrotic enteritis model In the current stud"], "order_basis": "paper_text_order:8908", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ostridium perfringens type G strain CP56 was cultured in BHI broth (Sigma Aldrich, St. Louis, Missour"], "order_basis": "paper_text_order:10098", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To highlight significant changes in protein levels between control and NE animals, statistical testing was performed with limma39."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}