Whole proteome analysis of mouse lymph nodes in cutaneous anthrax.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25329596", "kind": "science-record", "revision": 6, "content_hash": "sha256:ad5a9d7fee499c21a941f229aedd07171271249a57385efd20acaf0f728cedf8", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:19:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Whole proteome analysis of mouse lymph nodes in cutaneous anthrax.", "doi": "10.1371/journal.pone.0110873", "pmid": "25329596", "authors": ["Taissia G Popova", "Virginia Espina", "Weidong Zhou", "Claudius Mueller", "Lance Liotta", "Serguei G Popov"], "journal": "PloS one", "year": 2014, "abstract": "This study aimed to characterize a soluble proteome of popliteal lymph nodes during lymphadenitis induced by intradermal injection of Bacillus anthracis Sterne spores in mice using tandem LC-MS/MS and reverse-phase protein microarray with antibodies specific to epitopes of phosphorylated proteins. More than 380 proteins were detected in the normal intra-nodal lymph, while the infectious process resulted in the profound changes in the protein abundances and appearance of 297 unique proteins. These proteins belong to an array of processes reflecting response to wounding, inflammation and perturbations of hemostasis, innate immune response, coagulation and fibrinolysis, regulation of body fluid levels and vascular disturbance among others. Comparison of lymph and serum revealed 83 common proteins. Also, using 71 antibodies specific to total and phosphorylated forms of proteins we carried initial characterization of circulating lymph phosphoproteome which brought additional information regarding signaling pathways operating in the lymphatics. The results demonstrate that the proteome of intra-nodal lymph serves as a sensitive sentinel of the processes occurring within the lymph nodes during infection. The acute innate response of the lymph nodes to anthrax is accompanied by cellular damage and inflammation with a large number of up- and down-regulated proteins many of which are distinct from those detected in serum. MS data are available via ProteomeXchange with identifier PXD001342.", "claims": [{"id": "claim-method", "statement": "The 95% confidence intervals (CI) for a given protein were calculated using the t-test for 3 independent samples at each time point.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25329596", "locator": "sections[6] \"RPMA analysis\" paragraph 3", "quote": "The 95% confidence intervals (CI) for a given protein were calculated using the t-test for 3 independent samples at each time point."}], "state": "complete"}, {"id": "claim-data-access", "statement": "MS data are available via ProteomeXchange with identifier PXD001342.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25329596", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "MS data are available via ProteomeXchange with identifier PXD001342."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports that the intra-nodal lymph proteome serves as a sensitive sentinel of anthrax infection, with infection producing widespread up- and down-regulation of lymph-node proteins that was assessed using a label-free semi-quantitative mass-spectrometry approach based on normalized spectral-hit counts; the underlying MS data were deposited in ProteomeXchange through the PRIDE repository under accession PXD001342.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25329596", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results demonstrate that the proteome of intra-nodal lymph serves as a sensitive sentinel of the processes occurring within the lymph nodes during infection."}, {"asset": "source:pmid:25329596", "locator": "sections[1] \"Introduction\" paragraph 6", "quote": "we revealed aberrations caused by anthrax infection in the lymph proteome in murine model of cutaneous infection using a label-free semi-quantitative mass spectrometry-based approach"}, {"asset": "source:pmid:25329596", "locator": "sections[5] \"Mass spectrometry (MS) data acquisition and analysis\" paragraph 4", "quote": "For a particular protein, this rank served as a crude measure for comparing changes in protein abundance similar to the approach used by Faca et al. (2008) for analysis of plasma proteins [30]."}, {"asset": "source:pmid:25329596", "locator": "sections[5] \"Mass spectrometry (MS) data acquisition and analysis\" paragraph 3", "quote": "The results were then evaluated manually and submitted to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001342."}, {"asset": "source:pmid:25329596", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "MS data are available via ProteomeXchange with identifier PXD001342."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports that the intra-nodal lymph proteome serves as a sensitive sentinel of anthrax infection, with infection producing widespread up- and down-regulation of lymph-node proteins that was assessed using a label-free semi-quantitative mass-spectrometry approach based on normalized spectral-hit counts; the underlying MS data were deposited in ProteomeXchange through the PRIDE repository under accession PXD001342.", "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:25329596"], "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:PXD001342"], "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:PXD001342"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25329596", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0110873", "sha256": "sha256:9cae3bf14b7ceed4f8bad9893674b90e78488323da417ce260a0833c3a93345b", "bytes": 57245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0110873", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4203832", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001342", "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=PXD001342", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001342", "version": null, "note": "MS data are available via ProteomeXchange with identifier PXD001342.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "MS data are available via ProteomeXchange with identifier PXD001342.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Soluble lymph node proteome during anthrax infection in 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:25329596:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:75f637c72263986d4a4d7e3920763853537b87946bb4d7a6bff65fc8ec45376e", "bytes": 244, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#pone-0110873-t001", "version": null, "note": "DAVID-based analysis of enriched processes for proteins up-regulated in infection.", "structure": {"pmcid": "PMC4203832", "section_index": 9, "section_title": "DAVID Functional Annotation analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "DAVID-based analysis of enriched processes for proteins up-regulated in infection.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[1]#pone-0110873-t001"}}, {"id": "asset:table:pmid:25329596:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:affec0f9920b2fb1b936914a44270480af84e6072fa77629c6cdadd21dacb69e", "bytes": 307, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#pone-0110873-t002", "version": null, "note": "Proteins from naïve and B. anthracis-infected mice common between serum and lymph ranked according to their abundance in lymph during infection.", "structure": {"pmcid": "PMC4203832", "section_index": 9, "section_title": "DAVID Functional Annotation analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Proteins from naïve and B. anthracis-infected mice common between serum and lymph ranked according to their abundance in lymph during infection.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[2]#pone-0110873-t002"}}, {"id": "asset:table:pmid:25329596:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eb299c47594e3986460536635e07ada9c826a7ec96e86cf05e36361f5a930ee1", "bytes": 289, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#pone-0110873-t003", "version": null, "note": "Relative abundance of phosphoproteins and related signaling proteins in lymph of infected mice in comparison with naïve mice.", "structure": {"pmcid": "PMC4203832", "section_index": 10, "section_title": "Phosphoprotein content of lymph proteome", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Relative abundance of phosphoproteins and related signaling proteins in lymph of infected mice in comparison with naïve mice.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#pone-0110873-t003"}}], "gaps": ["asset:data:geo:PXD001342 not downloaded", "asset:data:geo:PXD001342 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The 95% confidence intervals (CI) for a given protein were calculated using the t-test for 3 independent samples at each time point."}}], "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), 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": ["PXD001342"], "resolved_accessions": ["PXD001342"], "statements": ["MS data are available via ProteomeXchange with identifier PXD001342."], "basis": "The paper names PXD001342 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:25329596", "data:geo:PXD001342", "asset:table:pmid:25329596:1", "asset:table:pmid:25329596:2", "asset:table:pmid:25329596:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001342"]}, "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": "2026-10-31T18:23:02Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 99423, "completion_tokens": 4186, "cached_tokens": 75126}}, "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:25329596", "type": "paper", "label": "pmid:25329596"}, {"id": "source:pmid:25329596", "type": "manuscript", "label": "PMID 25329596 full text"}, {"id": "data:geo:PXD001342", "type": "dataset", "label": "GEO PXD001342"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25329596", "type": "paper", "label": "pmid:25329596"}, {"id": "source:pmid:25329596", "type": "manuscript", "label": "PMID 25329596 full text"}, {"id": "data:geo:PXD001342", "type": "dataset", "label": "GEO PXD001342"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25329596", "type": "extraction", "used": ["source:pmid:25329596"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001342", "type": "accession_resolution", "used": ["data:geo:PXD001342"], "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:25329596", "parent_hash": "sha256:ec85899565b84b70a70d820b6d68bb182dfe8e49ef580dfaf2642bc89b8fe96d", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD001342 licence not read", "asset:data:geo:PXD001342 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Whole proteome analysis of mouse lymph nodes in cutaneous anthrax.", "njection of Bacillus anthracis Sterne spores in mice using tandem LC-MS/MS and reverse-phase prot", "f 1% tracer dye Evans Blue in PBS. Groups of mice were euthanized at daily intervals on days 1 to 3", "iteal and inguinal LNs of four control naïve mice were visualized by injection of 1% Evans Blue dye"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["anthracis Sterne spores in mice using tandem LC-MS/MS and reverse-phase protein microarray with an", "s as described in Materials and Methods. The LC-MS/MS experiments using four independent samples f", "proteins are expected to be present in every LC-MS/MS run with 99% confidence. The most variable s", "same time point were pooled and analyzed by LC-MS/MS. Overall the MS identifications in control a"], "order_basis": "paper_text_order:210", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ng tandem LC-MS/MS and reverse-phase protein microarray with antibodies specific to epitopes of phos"], "order_basis": "paper_text_order:245", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["rrows) are visible. Infiltrating neutrophils immunostained brown for myeloperoxidase (red arrows) are p"], "order_basis": "paper_text_order:6981", "id": "assay:4"}]}