Proteomic analysis of protein purified derivative of Mycobacterium bovis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28372590", "kind": "science-record", "revision": 6, "content_hash": "sha256:51fe6b8f3ba7840ec72a3ae0361909906a44c089d5fcefb807a5e04297952d42", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of protein purified derivative of Mycobacterium bovis.", "doi": "10.1186/s12967-017-1172-1", "pmid": "28372590", "authors": ["Sante Roperto", "Mariaconcetta Varano", "Valeria Russo", "Roberta Lucà", "Monica Cagiola", "Marco Gaspari", "Dora Maria Ceccarelli", "Giovanni Cuda", "Franco Roperto"], "journal": "Journal of translational medicine", "year": 2017, "abstract": "BACKGROUND: Tuberculin skin test based on in vivo intradermal inoculation of purified protein derivative from Mycobacterium bovis (bPPD) is the diagnostic test for the control and surveillance of bovine tuberculosis (bTB).\nMETHODS: Proteomic analysis was performed on different bPPD preparations from M. bovis, strain AN5. Proteins were precipitated from bPPD solutions by TCA precipitation. The proteome of bPPD preparations was investigated by bottom-up proteomics, which consisted in protein digestion and nano-LC-MS/MS analysis. Mass spectrometry analysis was performed on a Q-exactive hybrid quadrupole-Orbitrap mass spectrometer coupled online to an Easy nano-LC1000 system.\nRESULTS: Three hundred and fifty-six proteins were identified and quantified by at least 2 peptides (99% confidence per peptide). One hundred and ninety-eight proteins, which had not been previously described, were detected; furthermore, the proteomic profile shared 80 proteins with previous proteomes from bPPDs from the United Kingdom and Brazil and 139 protein components from bPPD from Korea. Locus name of M. bovis (Mb) with orthologs from M. tuberculosis H37Rv, comparative gene and protein length, molecular mass, functional categories, gene name and function of each protein were reported. Ninety-two T cell mycobacterial antigens responsible for delayed-type hypersensitivity were detected, fifty-two of which were not previously reported in any bPPD proteome. Data are available via ProteomeXchange with identifier PXD005920.\nCONCLUSIONS: This study represents the highest proteome coverage of bPPD preparations to date. Since proteins perform cellular functions essential to health and/or disease, obtaining knowledge of their presence and variance is of great importance in understanding disease states and for advancing translational studies. Therefore, to better understand Mycobacterium tuberculosis complex biology during infection, survival, and persistence, the reproducible evaluation of the proteins that catalyze and control these processes is critically important. More active and more specific tuberculins would be desirable. Indeed, many antigens contained within bPPD are currently responsible for the cross-reactivity resulting in false-positive results as they are shared between non-tuberculous and tuberculous mycobacteria.", "claims": [{"id": "claim-data-access", "statement": "All data produced for the purpose of this project are available for consultation and for the public, upon request to the corresponding author (SR) at sante.roperto@unina.it.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28372590", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "All data produced for the purpose of this project are available for consultation and for the public, upon request to the corresponding author (SR) at sante.roperto@unina.it."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using bottom-up proteomics with nano-LC–MS/MS, the study identified 356 proteins by two or more peptides at 99% confidence per peptide in at least two of three LC–MS/MS datasets, with source data available through ProteomeXchange under identifier PXD005920.", "kind": "quantitative", "target": {"value": 99.0, "unit": "per cent", "tolerance": null, "source": "Altogether, we identified 356 proteins by 2 or more peptides (99% confidence per peptide) in at least 2 out 3 LC-MS/MS data sets (Fig. 1)."}, "evidence": [{"asset": "source:pmid:28372590", "locator": "sections[8] \"Identification of bPPD proteins by list-based nano-LC-MS/MS\" paragraph 2", "quote": "Altogether, we identified 356 proteins by 2 or more peptides (99% confidence per peptide) in at least 2 out 3 LC-MS/MS data sets (Fig. 1)."}, {"asset": "source:pmid:28372590", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Data are available via ProteomeXchange with identifier PXD005920."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using bottom-up proteomics with nano-LC–MS/MS, the study identified 356 proteins by two or more peptides at 99% confidence per peptide in at least two of three LC–MS/MS datasets, with source data available through ProteomeXchange under identifier PXD005920.", "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:28372590"], "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:PXD005920"], "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:PXD005920"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28372590", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-017-1172-1", "sha256": "sha256:9b5cabde9fcbaa65fd8d99131ea4384efc1bd30fed3f5cc1cf740948ba39b510", "bytes": 43474, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-017-1172-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5376687", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD005920", "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=PXD005920", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD005920", "version": null, "note": "All data produced for the purpose of this project are available for consultation and for the public, upon request to the corresponding author (SR) at sante.roperto@unina.it.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data produced for the purpose of this project are available for consultation and for the public, upon request to the corresponding author (SR) at sante.roperto@unina.it.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of protein purified derivative of Mycobacterium bovis", "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:28372590:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2d62e3c868b0a3a409b6d3de174dbcd880f0d4ec3a089a868284f6202262176b", "bytes": 1230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "The most abundant proteins in PPD preparations", "structure": {"pmcid": "PMC5376687", "section_index": 11, "section_title": "Semi-quantitative analysis of overall protein abundance and quantitative comparison of PPDs by dimethyl labelling", "row_count": 11, "column_count": 6}, "table": {"label": "Table 1", "caption": "The most abundant proteins in PPD preparations", "rows": [["Accession", "Description", "% Total weighted spectra", "It vs S", "NL vs S", "Ip vs S"], ["61223750", "ESAT-6-like protein EsxB", "35.0", "0.4 0.5; 0.4", "0.8 0.7; 0.9", "0.5 0.4; 0.6"], ["61223746", "6 kDa early secretory antigenic target", "15.2", "0.9 0.7; 1.0", "0.5 0.3; 0.7", "0.8 0.6; 1.1"], ["61228252", "Immunogenic protein MPB70", "5.0", "0.9 0.7; 1.1", "0.6 0.5; 0.7", "0.9 0.5; 1.6"], ["61223754", "ESAT-6-like protein EsxN", "3.3", "0.9 0.6; 1.3", "0.6 0.4; 0.9", "0.6 0.3; 1.0"], ["61217075", "14 kDa antigen", "2.2", "1.2 1.0; 1.3", "1.3 1.2; 1.4", "0.4 a 0.4; 0.4"], ["61217901", "Meromycolate extension acyl carrier protein", "1.9", "0.4 0.5; 0.4", "0.5 0.5; 0.6", "1.0 0.9; 1.0"], ["38605709", "10 kDa chaperonin; GroES protein", "1.9", "0.3 0.3; 0.3", "0.3 a 0.3; 0.3", "1.5 1.2; 1.9"], ["61228239", "Immunogenic protein MPB63", "1.5", "0.9 1.0; 0.8", "1.0 0.8; 1.4", "1.0 0.9; 1.2"], ["61233386", "50S ribosomal protein L7/L12", "1.2", "0.9 1.3; 0.6", "1.0 1.2; 0.9", "0.8 0.7; 0.8"], ["61221045", "60 kDa chaperonin 2", "1.2", "0.5 0.6; 0.4", "0.5 0.6; 0.5", "0.8 0.7; 0.8"]], "row_count": 11, "column_count": 6, "numeric_cells": 59, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:PXD005920 not downloaded", "asset:data:geo:PXD005920 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Permutation statistical analysis of peptide ratios using the quantitative proteomics p value calculator (qpPC)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Advanced quantification, such as data normalization and permutation statistical analysis of the peptide ratios was performed using quantitative proteomics p value calculator (qpPC) [24]."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 99.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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 (Permutation statistical analysis of peptide ratios using the quantitative proteomics p value calculator (qpPC)), 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": ["PXD005920"], "resolved_accessions": ["PXD005920"], "statements": ["All data produced for the purpose of this project are available for consultation and for the public, upon request to the corresponding author (SR) at sante.roperto@unina.it."], "basis": "The paper names PXD005920 in ProteomeXchange Consortium 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": [], "assets": ["source:pmid:28372590", "data:geo:PXD005920", "asset:table:pmid:28372590:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD005920"]}, "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": "2026-10-31T18:30:43Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 93905, "completion_tokens": 3516, "cached_tokens": 13295}}, "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:28372590", "type": "paper", "label": "pmid:28372590"}, {"id": "source:pmid:28372590", "type": "manuscript", "label": "PMID 28372590 full text"}, {"id": "data:geo:PXD005920", "type": "dataset", "label": "GEO PXD005920"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28372590", "type": "paper", "label": "pmid:28372590"}, {"id": "source:pmid:28372590", "type": "manuscript", "label": "PMID 28372590 full text"}, {"id": "data:geo:PXD005920", "type": "dataset", "label": "GEO PXD005920"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28372590", "type": "extraction", "used": ["source:pmid:28372590"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD005920", "type": "accession_resolution", "used": ["data:geo:PXD005920"], "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:28372590", "parent_hash": "sha256:47cd382bb4e62c4075d7b26e8ec423f12e274d0bc1ea40456901373968a1bea3", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD005920 licence not read", "asset:data:geo:PXD005920 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["Proteomic analysis of protein purified derivative of M", "lance of bovine tuberculosis (bTB). METHODS: Proteomic analysis was performed on different bPPD pre", "D preparations was investigated by bottom-up proteomics, which consisted in protein digestion and na", "y described, were detected; furthermore, the proteomic profile shared 80 proteins with previous pro"], "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": 0.77, "evidence": ["BACKGROUND: Tuberculin skin test based on in vivo intradermal inoculation of purified protein"], "order_basis": "paper_text_order:74", "id": "assay:2"}]}