Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23870090", "kind": "science-record", "revision": 7, "content_hash": "sha256:def5715c04e3d0a8610694280867aa0ed6b19c677f5d2cbca697ada927352701", "created_at": "2026-11-01T15:40:03Z", "updated_at": "2026-11-01T21:58:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis.", "doi": "10.1186/1559-0275-10-8", "pmid": "23870090", "authors": ["Thottethodi Subrahmanya Keshava Prasad", "Renu Verma", "Satish Kumar", "Raja Sekhar Nirujogi", "Gajanan J Sathe", "Anil K Madugundu", "Jyoti Sharma", "Vinuth N Puttamallesh", "Anjali Ganjiwale", "Vithal P Myneedu", "Aditi Chatterjee", "Akhilesh Pandey", "Hc Harsha", "Jayasuryan Narayana"], "journal": "Clinical proteomics", "year": 2013, "abstract": "BACKGROUND: Purified protein derivative (PPD) has been used for more than half a century as an antigen for the diagnosis of tuberculosis infection based on delayed type hypersensitivity. Although designated as \"purified,\" in reality, the composition of PPD is highly complex and remains ill-defined. In this report, high resolution mass spectrometry was applied to understand the complexity of its constituent components. A comparative proteomic analysis of various PPD preparations and their functional characterization is likely to help in short-listing the relevant antigens required to prepare a less complex and more potent reagent for diagnostic purposes.\nRESULTS: Proteomic analysis of Connaught Tuberculin 68 (PPD-CT68), a tuberculin preparation generated from M. tuberculosis, was carried out in this study. PPD-CT68 is the protein component of a commercially available tuberculin preparation, Tubersol, which is used for tuberculin skin testing. Using a high resolution LTQ-Orbitrap Velos mass spectrometer, we identified 265 different proteins. The identified proteins were compared with those identified from PPD M. bovis, PPD M. avium and PPD-S2 from previous mass spectrometry-based studies. In all, 142 proteins were found to be shared between PPD-CT68 and PPD-S2 preparations. Out of the 354 proteins from M. tuberculosis-derived PPDs (i.e. proteins in either PPD-CT68 or PPD-S2), 37 proteins were found to be shared with M. avium PPD and 80 were shared with M. bovis PPD. Alignment of PPD-CT68 proteins with proteins encoded by 24 lung infecting bacteria revealed a number of similar proteins (206 bacterial proteins shared epitopes with 47 PPD-CT68 proteins), which could potentially be involved in causing cross-reactivity. The data have been deposited to the ProteomeXchange with identifier PXD000377.\nCONCLUSIONS: Proteomic and bioinformatics analysis of different PPD preparations revealed commonly and differentially represented proteins. This information could help in delineating the relevant antigens represented in various PPDs, which could further lead to development of a lesser complex and better defined skin test antigen with a higher specificity and sensitivity.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [73] with the dataset identifier PXD000377.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23870090", "locator": "sections[9] \"Data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [73] with the dataset identifier PXD000377."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High-resolution LC-MS/MS proteomic analysis identified 265 different proteins in PPD-CT68; the source mass-spectrometry data were deposited in ProteomeXchange under identifier PXD000377.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23870090", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using a high resolution LTQ-Orbitrap Velos mass spectrometer, we identified 265 different proteins."}, {"asset": "source:pmid:23870090", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data have been deposited to the ProteomeXchange with identifier PXD000377."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High-resolution LC-MS/MS proteomic analysis identified 265 different proteins in PPD-CT68; the source mass-spectrometry data were deposited in ProteomeXchange under identifier PXD000377.", "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:23870090"], "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:PXD000377"], "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:PXD000377"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:23870090", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1559-0275-10-8", "sha256": "sha256:d2ac75e36a2b0b388ed8525ca81f3216b5a51cd5acca8e2562e08b913bfaf958", "bytes": 42780, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1559-0275-10-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3729367", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000377", "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=PXD000377", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000377", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [73] with the dataset identifier PXD000377.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [73] with the dataset identifier PXD000377.", "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 purified protein derivative of mycobacterium tuberculosis", "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:23870090:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53a906622e0344fff5bfa2549fc326aa22792f147f78fae51b0296acd626a093", "bytes": 3005, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "Functional classification of proteins common in all PPDs", "structure": {"pmcid": "PMC3729367", "section_index": 4, "section_title": "Functional analysis of proteins common among all PPDs", "row_count": 19, "column_count": 5}, "table": {"label": "Table 1", "caption": "Functional classification of proteins common in all PPDs", "rows": [["", "Gene symbol", "Description", "Function", "Reference"], ["1", "AcpP", "Acyl carrier protein", "It shuttles the intermediates between the enzymes of type II fatty acid synthase system", "[31]"], ["2", "FbpA", "Secreted antigen 85-A", "It participates in cell wall biosynthesis, and interacts with the host macrophage as fibronectin-binding protein. It is also involved in establishment and maintenance of a persistent tuberculosis infection", "[32,33]"], ["3", "GroES", "Co-chaperonin", "It is a dominant immunogenic protein", "[34]"], ["4", "DnaK", "Molecular chaperone", "It is highly antigenic and act as co-repressors for heat shock protein transcriptional repressor (hspR)", "[35]"], ["5", "Tpx", "Thiol peroxidase", "It protects M. tuberculosis against oxidative and nitrosative stress", "[36]"], ["6", "RpiL", "50S ribosomal protein L7/L12", "It is involved in interaction with translation factors", "[37]"], ["7", "BfrA", "Bacterioferritin", "It is an intracellular iron storage protein, which protects Mycobacterium from oxidative stress mediated by excess iron", "[38]"], ["8", "SahH", "S-adenosyl-L-homocysteine hydrolase", "It is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine", "[39]"], ["9", "TrxC", "Thioredoxin", "It is involved in redox homeostasis and uses it to protect the pathoen against the oxidative intermediates generated by the macrophages", "[40]"], ["10", "FixB", "Electron transfer flavoprotein subunit alpha", "It is electron transfer flavoprotein subunit alpha, in some bacteria it functions as nitrogen fixing agent but its function in M .tuberculosis is not clear", "[41]"], ["11", "PepA", "Serine protease", "It is a serine protease associated with cell membrane, which stimulates peripheral blood mononuclear cells from healthy PPD donors to proliferate and secrete gamma interferon", "[42]"], ["12", "Wag31", "Hypothetical protein", "It is a cell division initiation protein involved in regulation of genes including virulence factors and antigens", "[43]"], ["13", "Mpt64", "Hypothetical protein", "It is an immunogenic protein which elicits delayed type hypersensitivity skin response", "[44]"], ["14", "Apa", "Alanine and proline rich secreted protein", "It is a cell surface glycoprotein which binds to host lectins and cheat the innate immune system", "[45]"], ["15", "LprG", "Lipoprotein LprG", "It plays a role in M. tuberculosis infection by inducing increased suppression of the immune response due to elevated nitric oxide production", "[46]"], ["16", "Rv1893", "Hypothetical protein", "Function unknown", "[47]"], ["17", "Rv1855c", "Oxidoreductase", "Probable monooxygenase", "[48]"], ["18", "Gap", "Glyceraldehyde-3-phosphate dehydrogenase", "It has glyceraldehyde-3-phosphate dehydrogenase activity", "[49]"]], "row_count": 19, "column_count": 5, "numeric_cells": 44, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:PXD000377 not downloaded", "asset:data:geo:PXD000377 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}], "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": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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A comparative proteomic analysis of various PPD preparations and the", "nt reagent for diagnostic purposes. RESULTS: Proteomic analysis of Connaught Tuberculin 68 (PPD-CT6", "ange with identifier PXD000377. CONCLUSIONS: Proteomic and bioinformatics analysis of different PPD"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}