Proteomic data set of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27437436", "kind": "science-record", "revision": 5, "content_hash": "sha256:4c447213b958f5b8014f6781fd03f9779bf52df6f212a680da53b121c2c3458b", "created_at": "2026-11-01T15:40:19Z", "updated_at": "2026-11-01T18:48:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic data set of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates.", "doi": "10.1016/j.dib.2016.06.022", "pmid": "27437436", "authors": ["Tobias Goris", "Christian L Schiffmann", "Jennifer Gadkari", "Lorenz Adrian", "Martin von Bergen", "Gabriele Diekert", "Nico Jehmlich"], "journal": "Data in brief", "year": 2016, "abstract": "Sulfurospirillum multivorans is a free-living, physiologically versatile Epsilonproteobacterium able to couple the reductive dehalogenation of chlorinated and brominated ethenes to growth (organohalide respiration). We present proteomic data of S. multivorans grown with different electron donors (formate or pyruvate) and electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE]). To obtain information on the cellular localization of proteins, membrane extracts and soluble fractions were separated before data collection from both fractions. The proteome analysis of S. multivorans was performed by mass spectrometry (nanoLC-MS/MS). Raw data have been deposited at ProteomeXchange, \"ProteomeXchange provides globally coordinated proteomics data submission and dissemination\" [1], via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011. The data might support further research in organohalide respiration and in the general metabolism of free-living Epsilonproteobacteria. The dataset is associated with a previously published study \"Proteomics of the organohalide-respiring Epsilonproteobacterium S. multivorans adapted to tetrachloroethene and other energy substrates\" [2].", "claims": [{"id": "claim-data-access", "statement": "Data are within this article. The mass spectrometry proteomics data have been deposited at ProteomeXchange via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27437436", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data are within this article. The mass spectrometry proteomics data have been deposited at ProteomeXchange via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports no statistical method; the source data were deposited at ProteomeXchange via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27437436", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present proteomic data of S. multivorans grown with different electron donors (formate or pyruvate) and electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE])."}, {"asset": "source:pmid:27437436", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw data have been deposited at ProteomeXchange, “ProteomeXchange provides globally coordinated proteomics data submission and dissemination” [1], via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper reports no statistical method; the source data were deposited at ProteomeXchange via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011.", "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:27437436"], "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:27437436", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.06.022", "sha256": "sha256:af4119b7819411805152c03223d32e450892ce5a6e85216d1f1df8f93e6c2ff0", "bytes": 13391, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.06.022", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4939420", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:27437436:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d0168fabb78e240c07e315e4a7c3527b2485d5feb70785ad4853e104d15a6815", "bytes": 1855, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0005", "version": null, "note": "Sulfurospirillum multivorans proteome data that are provided at PRIDE. For each condition three biological samples were processed.", "structure": {"pmcid": "PMC4939420", "section_index": 4, "section_title": "1. Data", "row_count": 44, "column_count": 4}, "table": {"label": "Table 1", "caption": "Sulfurospirillum multivorans proteome data that are provided at PRIDE. For each condition three biological samples were processed.", "rows": [["Cultivation condition", "", "Sample name for LC-MS/MS and database search file (numbers indicates the replicates)"], ["Electron donor", "Electron acceptor", "Extract/Fraction"], ["Pyruvate (Py)", "tetrachloroethene (PCE)", "Soluble", "*_Smult_PyPCELE1"], ["", "", "", "*_Smult_PyPCELE2"], ["", "", "", "*_Smult_PyPCELE3"], ["", "", "Membrane", "*_Smult_PyPCEME1"], ["", "", "", "*_Smult_PyPCEME2"], ["", "", "", "*_Smult_PyPCEME3"], ["", "", "", ""], ["Pyruvate (Py)", "nitrate (Ni)", "Soluble", "*_Smult_PyNOLE1"], ["", "", "", "*_Smult_PyNOLE2"], ["", "", "", "*_Smult_PyNOLE3"], ["", "", "Membrane", "*_Smult_PyNOME1"], ["", "", "", "*_Smult_PyNOME2"], ["", "", "", "*_Smult_PyNOME3"], ["", "", "", ""], ["Pyruvate (Py)", "fumarate (Fu)", "Soluble", "*_Smult_PyFuLE1"], ["", "", "", "*_Smult_PyFuLE2"], ["", "", "", "*_Smult_PyFuLE3"], ["", "", "Membrane", "*_Smult_PyFuME1"], ["", "", "", "*_Smult_PyFuME2"], ["", "", "", "*_Smult_PyFuME3"], ["", "", "", ""], ["", "", "", ""], ["Formate (Fo)", "tetrachloroethene (PCE)", "Soluble", "*_Smult_FoPCELE1"], ["", "", "", "*_Smult_FoPCELE2"], ["", "", "", "*_Smult_FoPCELE3"], ["", "", "Membrane", "*_Smult_FoPCEME1"], ["", "", "", "*_Smult_FoPCEME2"], ["", "", "", "*_Smult_FoPCEME3"], ["", "", "", ""], ["Formate (Fo)", "nitrate (Ni)", "Soluble", "*_Smult_FoNOLE1"], ["", "", "", "*_Smult_FoNOLE2"], ["", "", "", "*_Smult_FoNOLE3"], ["", "", "Membrane", "*_Smult_FoNOME1"], ["", "", "", "*_Smult_FoNOME2"], ["", "", "", "*_Smult_FoNOME3"], ["", "", "", ""], ["Formate (Fo)", "fumarate (Fu)", "Soluble", "*_Smult_FoFuLE1"], ["", "", "", "*_Smult_FoFuLE2"], ["", "", "", "*_Smult_FoFuLE3"], ["", "", "Membrane", "*_Smult_FoFuME1"], ["", "", "", "*_Smult_FoFuME2"], ["", "", "", "*_Smult_FoFuME3"]], "row_count": 44, "column_count": 4, "numeric_cells": 0, "header_rows": 2, "locator": "section[4]/table-wrap[1]#t0005"}}], "gaps": []}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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. 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