Comparing isogenic strains of Beijing genotype Mycobacterium tuberculosis after acquisition of Isoniazid resistance: A proteomics approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26929115", "kind": "science-record", "revision": 4, "content_hash": "sha256:bb532642f3594d78ed51fe9b0186b6a39d9a735b9be4d4bec7ac14a0cd40e935", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparing isogenic strains of Beijing genotype Mycobacterium tuberculosis after acquisition of Isoniazid resistance: A proteomics approach.", "doi": "10.1002/pmic.201500403", "pmid": "26929115", "authors": ["Luisa María Nieto R", "Carolina Mehaffy", "Karen M Dobos"], "journal": "Proteomics", "year": 2016, "abstract": "We determined differences in the protein abundance among two isogenic strains of Mycobacterium tuberculosis (Mtb) with different Isoniazid (INH) susceptibility profiles. The strains were isolated from a pulmonary tuberculosis patient before and after drug treatment. LC-MS/MS analysis identified 46 Mtb proteins with altered abundance after INH resistance acquisition. Protein abundance comparisons were done evaluating the different bacterial cellular fractions (membrane, cytosol, cell wall and secreted proteins). MS data have been deposited to the ProteomeXchange with identifier PXD002986.", "claims": [{"id": "claim-method", "statement": "Differences between protein abundances among the two different susceptibility profiles were tested by two tailed Student's t‐test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26929115", "locator": "sections[12] \"p\" paragraph 1", "quote": "Differences between protein abundances among the two different susceptibility profiles were tested by two tailed Student's t‐test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26929115", "locator": "sections[23] \"p\" paragraph 1", "quote": "The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper found 46 proteins with altered abundance after acquisition of INH resistance; protein-abundance differences were tested using a two-tailed Student's t-test, and the source MS proteomics data were deposited in ProteomeXchange via the PRIDE partner repository under identifier PXD002986.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We found 46 proteins either more or less abundant after acquisition of INHr (with p < 0.05) that were grouped in seven different categories (Fig. 1)."}, "evidence": [{"asset": "source:pmid:26929115", "locator": "sections[13] \"p\" paragraph 1", "quote": "We found 46 proteins either more or less abundant after acquisition of INHr (with p < 0.05) that were grouped in seven different categories (Fig. 1)."}, {"asset": "source:pmid:26929115", "locator": "sections[12] \"p\" paragraph 1", "quote": "Differences between protein abundances among the two different susceptibility profiles were tested by two tailed Student's t‐test."}, {"asset": "source:pmid:26929115", "locator": "sections[23] \"p\" paragraph 1", "quote": "The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper found 46 proteins with altered abundance after acquisition of INH resistance; protein-abundance differences were tested using a two-tailed Student's t-test, and the source MS proteomics data were deposited in ProteomeXchange via the PRIDE partner repository under identifier PXD002986.", "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:26929115"], "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:PXD002986"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD002986"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26929115", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/pmic.201500403", "sha256": "sha256:d49332b2e034efb2beea0d6386a16085d8e16fcc51ab501c09f369c5978417ef", "bytes": 18218, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/pmic.201500403", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5074239", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002986", "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=PXD002986", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002986", "version": null, "note": "The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics of Mycobacterium tuberculosis Beijing genotype after acquisition of Isoniazid resistance", "resolution_checked_at": "2026-10-31T18:28:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD002986 not downloaded", "asset:data:geo:PXD002986 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differences between protein abundances among the two different susceptibility profiles were tested by two tailed Student's t‐test."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD002986", "10.6019/PXD002986"], "resolved_accessions": ["PXD002986"], "statements": ["The proteomics MS data in this paper have been deposited in the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org ) via the PRIDE partner repository 18 : dataset identifier PXD002986."], "basis": "The paper names PXD002986 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:26929115", "data:geo:PXD002986"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002986"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:20Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 45820, "completion_tokens": 4027, "cached_tokens": 1840}}, "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:26929115", "type": "paper", "label": "pmid:26929115"}, {"id": "source:pmid:26929115", "type": "manuscript", "label": "PMID 26929115 full text"}, {"id": "data:geo:PXD002986", "type": "dataset", "label": "GEO PXD002986"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26929115", "type": "paper", "label": "pmid:26929115"}, {"id": "source:pmid:26929115", "type": "manuscript", "label": "PMID 26929115 full text"}, {"id": "data:geo:PXD002986", "type": "dataset", "label": "GEO PXD002986"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26929115", "type": "extraction", "used": ["source:pmid:26929115"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002986", "type": "accession_resolution", "used": ["data:geo:PXD002986"], "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:26929115", "parent_hash": "sha256:3760333473f58f6d0d21bf56e7460f8f2a4afd33f8f5e4c9581e694d2f03d50c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD002986 licence not read", "asset:data:geo:PXD002986 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"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": ["after acquisition of Isoniazid resistance: A proteomics approach.", "sis patient before and after drug treatment. LC-MS/MS analysis identified 46 Mtb proteins with alt"], "order_basis": "paper_text_order:74", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differences between protein abundances among the two different susceptibility profiles were tested by two tailed Student's t‐test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}