Dataset generated using hyperplexing and click chemistry to monitor temporal dynamics of newly synthesized macrophage secretome post infection by mycobacterial strains.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27672675", "kind": "science-record", "revision": 7, "content_hash": "sha256:a9828b1a7f04b9c26a70c300b68b983d3825afa31319d53fedd73e62ed5ed5aa", "created_at": "2026-11-01T15:40:20Z", "updated_at": "2026-11-01T21:59:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset generated using hyperplexing and click chemistry to monitor temporal dynamics of newly synthesized macrophage secretome post infection by mycobacterial strains.", "doi": "10.1016/j.dib.2016.08.055", "pmid": "27672675", "authors": ["Ajay Kumar", "Shilpa Jamwal", "Mukul Kumar Midha", "Baseerat Hamza", "Suruchi Aggarwal", "Amit Kumar Yadav", "Kanury V S Rao"], "journal": "Data in brief", "year": 2016, "abstract": "Here we provide data for SILAC and iTRAQ based hyperplexing combined with BONCAT based click chemistry for selective enrichment of newly synthesized proteins secreted by THP1 macrophages at various time points after infection with four different strains of Mycobacterium tuberculosis. The macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 strains of M. tuberculosis. Newly-synthesized secreted host proteins were observed, starting from six hours post-infection till 26 h, at 4 h intervals. We have combined BONCAT with hyperplexing (18-plex), which blends SILAC and iTRAQ, for the first time. Two sets of triplex SILAC were used to encode the strains of M. tuberculosis - H37Ra & H37Rv in one and BND433 & JAL2287 in another with a control in each. BONCAT was used to enrich the secretome for newly synthesized proteins while 6-plex iTRAQ labeling was employed to quantify the temporal changes in the captured proteome. Each set of 18-plex was run in 4 MS replicates with two linear and two non-linear separation modes. This new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ, achieves 18-plex quantitation in a single MS run. Hyperplexing enables large scale spatio-temporal systems biology studies where large number of samples can be processed simultaneously and in quantitative manner. Data are available via ProteomeXchange with identifier ProteomeXchange: PXD004281.", "claims": [{"id": "claim-method", "statement": "The results were filtered at 1% false discovery rate (FDR) [13] using MaxQuant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672675", "locator": "sections[13] \"Database search and relative quantification\" paragraph 2", "quote": "The results were filtered at 1% false discovery rate (FDR) [13] using MaxQuant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is publicly available via ProteomeXchange with identifier ProteomeXchange: PXD004281 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD004281).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672675", "locator": "sections[5] \"Data\" paragraph 2", "quote": "Data is publicly available via ProteomeXchange with identifier ProteomeXchange: PXD004281 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD004281)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study achieved 18-plex quantitative proteomics in a single mass-spectrometry run by combining BONCAT, triplex SILAC, and 6-plex iTRAQ; the source data are available through ProteomeXchange under identifier PXD004281.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27672675", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ, achieves 18-plex quantitation in a single MS run."}, {"asset": "source:pmid:27672675", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier ProteomeXchange: PXD004281."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study achieved 18-plex quantitative proteomics in a single mass-spectrometry run by combining BONCAT, triplex SILAC, and 6-plex iTRAQ; the source data are available through ProteomeXchange under identifier PXD004281.", "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:27672675"], "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:27672675", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.08.055", "sha256": "sha256:f7f41bf2ad8095b1defade10407809ce66f710c564d560ab3bdf145d0b844aa6", "bytes": 16153, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.08.055", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5030312", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "image_quantification", "specific": "densitometry", "label": "Image analysis / quantification", "dsl_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["image_stack"], "evidence": {"score": 0.8, "band": "high", "quote": "optical density"}}, {"id": "method-2", "family": null, "specific": null, "label": "1% false discovery rate (FDR) filtering using MaxQuant", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The results were filtered at 1% false discovery rate (FDR) [13] using MaxQuant."}}], "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": "R1", "expressible": true, "required_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: densitometry."}, "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": ["ProteomeXchange: PXD004281"], "resolved_accessions": [], "statements": ["Data is publicly available via ProteomeXchange with identifier ProteomeXchange: PXD004281 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD004281)."], "basis": "The paper names ProteomeXchange: PXD004281, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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