Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36763818", "kind": "science-record", "revision": 2, "content_hash": "sha256:71fef5c69700f024e467ec4c139a340a894d26a48128b3d880cac92679fe9a1e", "created_at": "2026-11-01T19:01:20Z", "updated_at": "2026-11-01T21:30:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction.", "doi": "10.1021/acs.jproteome.2c00758", "pmid": "36763818", "authors": ["Alienke van Pijkeren", "Anna-Sophia Egger", "Madlen Hotze", "Elisabeth Zimmermann", "Tobias Kipura", "Julia Grander", "André Gollowitzer", "Andreas Koeberle", "Rainer Bischoff", "Kathrin Thedieck", "Marcel Kwiatkowski"], "journal": "Journal of proteome research", "year": 2023, "abstract": "Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.", "claims": [{"id": "claim-method", "statement": "For volcano plots, two-tailed t-tests were performed for all protein groups and adjusted p-values were calculated using the Benjamini–Hochberg procedure using the rstatix package (https://cran.r-project.org/web/packages/rstatix/index.html).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36763818", "locator": "sections[13] \"Bioinformatics Data Processing of Proteome LC-MS/MS Data\" paragraph 2", "quote": "For volcano plots, two-tailed t-tests were performed for all protein groups and adjusted p-values were calculated using the Benjamini–Hochberg procedure using the rstatix package (https://cran.r-project.org/web/packages/rstatix/index.html)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The LC-MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD027338.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36763818", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The LC-MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD027338."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The number of extracted proteins was 3-fold higher for urea compared to SDC, and 55-fold higher compared to SDS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36763818", "locator": "sections[22] \"Quantitative Analysis of the Solubilized Proteome\" paragraph 5", "quote": "By comparing the number of differentially extracted proteins between extraction reagents, urea provides the highest extraction efficiency in isolating proteomes from the SPM-LLE interphase pellet. The number of extracted proteins was 3-fold higher for urea compared to SDC, and 55-fold higher compared to SDS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The number of extracted proteins was 3-fold higher for urea compared to SDC, and 55-fold higher compared to SDS.", "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:36763818"], "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. 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