In-Depth Proteome Coverage of In Vitro-Cultured Treponema pallidum and Quantitative Comparison Analyses with In Vivo-Grown Treponemes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38636938", "kind": "science-record", "revision": 2, "content_hash": "sha256:caa60349da659fcdfa9aa76f64a981a5613ebafe20e7c37681e23eebb3e80542", "created_at": "2026-11-01T19:20:36Z", "updated_at": "2026-11-01T21:32:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In-Depth Proteome Coverage of In Vitro-Cultured Treponema pallidum and Quantitative Comparison Analyses with In Vivo-Grown Treponemes.", "doi": "10.1021/acs.jproteome.3c00891", "pmid": "38636938", "authors": ["Simon Houston", "Alloysius Gomez", "Andrew Geppert", "Mara C Goodyear", "Caroline E Cameron"], "journal": "Journal of proteome research", "year": 2024, "abstract": "Previous mass spectrometry (MS)-based global proteomics studies have detected a combined total of 86% of all Treponema pallidum proteins under infection conditions (in vivo-grown T. pallidum). Recently, a method was developed for the long-term culture of T. pallidum under in vitro conditions (in vitro-cultured T. pallidum). Herein, we used our previously reported optimized MS-based proteomics approach to characterize the T. pallidum global protein expression profile under in vitro culture conditions. These analyses provided a proteome coverage of 94%, which extends the combined T. pallidum proteome coverage from the previously reported 86% to a new combined total of 95%. This study provides a more complete understanding of the protein repertoire of T. pallidum. Further, comparison of the in vitro-expressed proteome with the previously determined in vivo-expressed proteome identifies only a few proteomic changes between the two growth conditions, reinforcing the suitability of in vitro-cultured T. pallidum as an alternative to rabbit-based treponemal growth. The MS proteomics data have been deposited in the MassIVE repository with the data set identifier MSV000093603 (ProteomeXchange identifier PXD047625).", "claims": [{"id": "claim-method", "statement": "Label-free quantification (LFQ) based on peptide ion peak intensities (MaxLFQ intensity values) was used to determine the relative abundance of proteins detected in each of the three in vitro-cultured T. pallidum samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38636938", "locator": "sections[19] \"Quantitation-Based Comparative Analyses of In Vivo-Grown and In Vitro-Cultured T. pallidum\" paragraph 2", "quote": "Label-free quantification (LFQ) based on peptide ion peak intensities (MaxLFQ intensity values) was used to determine the relative abundance of proteins detected in each of the three in vitro-cultured T. pallidum samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The MS proteomics data (raw data files and Scaffold search engine files) have been deposited to the MassIVE repository (https://massive.ucsd.edu/ProteoSAFe/private-dataset.jsp?task=fbf1937f5e784187b6cf655be16a592a) with the data set identifier MSV000093603.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38636938", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The MS proteomics data (raw data files and Scaffold search engine files) have been deposited to the MassIVE repository (https://massive.ucsd.edu/ProteoSAFe/private-dataset.jsp?task=fbf1937f5e784187b6cf655be16a592a) with the data set identifier MSV000093603."}], "state": "complete"}, {"id": "claim-target-result", "statement": "These analyses provided a proteome coverage of 94%, which extends the combined T. pallidum proteome coverage from the previously reported 86% to a new combined total of 95%.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38636938", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These analyses provided a proteome coverage of 94%, which extends the combined T. pallidum proteome coverage from the previously reported 86% to a new combined total of 95%."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "These analyses provided a proteome coverage of 94%, which extends the combined T. pallidum proteome coverage from the previously reported 86% to a new combined total of 95%.", "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:38636938"], "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:38636938", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.3c00891", "sha256": "sha256:0cb6b09c8dcd5e4eb699fbfc72388e738a387d832d55dc56b8814b40de4d5b7b", "bytes": 85537, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.3c00891", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11077495", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Label-free quantification (LFQ) based on peptide ion peak intensities using MaxLFQ intensity values", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Label-free quantification (LFQ) based on peptide ion peak intensities (MaxLFQ intensity values) was used to determine the relative abundance of proteins detected in each of the three in vitro-cultured T. pallidum samples."}}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Label-free quantification (LFQ) based on peptide ion peak intensities using MaxLFQ intensity values), 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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The MS proteomics data (raw data files and Scaffold search engine files) have been deposited to the MassIVE repository (https://massive.ucsd.edu/ProteoSAFe/private-dataset.jsp?task=fbf1937f5e784187b6cf655be16a592a) with the data set identifier MSV000093603."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38636938"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:16:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 24482, "completion_tokens": 1159, "cached_tokens": 0}}, "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:38636938", "type": "paper", "label": "pmid:38636938"}, {"id": "source:pmid:38636938", "type": "manuscript", "label": "PMID 38636938 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38636938", "type": "paper", "label": "pmid:38636938"}, {"id": "source:pmid:38636938", "type": "manuscript", "label": "PMID 38636938 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38636938", "type": "extraction", "used": ["source:pmid:38636938"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:38636938", "parent_hash": "sha256:5fea90a29aa9487e6788b4179232314b480508a12083a60b85ad62e8b9f9029c", "fork_of": null, "generation": 1}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["um and Quantitative Comparison Analyses with In Vivo-Grown Treponemes.", "allidum proteins under infection conditions (in vivo-grown T. pallidum). Recently, a method was d", "ssed proteome with the previously determined in vivo-expressed proteome identifies only a few pro", "usly optimized for the proteomic analyses of in vivo-grown T. pallidum.25 In the present in vitro"], "order_basis": "paper_text_order:64", "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": ["Previous mass spectrometry (MS)-based global proteomics studies have de", "ivo-expressed proteome identifies only a few proteomic changes between the two growth conditions, r", "Previous mass spectrometry (MS)-based global proteomics studies have detected a combined total of 86", "ve to rabbit-based treponemal growth. The MS proteomics data have been deposited in the MassIVE repo"], "order_basis": "paper_text_order:135", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_imaging", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ng high-speed centrifugation using darkfield microscopy, as described above. Supplementary Material"], "order_basis": "paper_text_order:3625", "id": "assay:3"}]}