title: Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology.
abstract: Interconnected molecular networks are at the heart of signaling pathways that mediate adaptive plasticity of eukaryotic cells. To gain deeper insights into the underlying molecular mechanisms, a comprehensive and representative analysis demands a deep and parallel coverage of a broad spectrum of molecular species. Therefore, we introduce a simultaneous metabolite, protein, lipid extraction (SIMPLEX) procedure, a novel strategy for the quantitative investigation of lipids, metabolites, and proteins. Compared with unimolecular workflows, SIMPLEX offers a fundamental turn in study design since multiple molecular classes can be accessed in parallel from one sample with equal efficiency and reproducibility. Application of this method in mass-spectrometry-based workflows allowed the simultaneous quantification of 360 lipids, 75 metabolites, and 3327 proteins from 10(6)cells. The versatility of this method is shown in a model system for adipogenesis- peroxisomal proliferator-activated receptor gamma (PPARG) signaling in mesenchymal stem cells-where we utilized SIMPLEX to explore cross-talk within and between all three molecular classes and identified novel potential molecular entry points for interventions, indicating that SIMPLEX provides a superior strategy compared with conventional workflows.
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK.
authors.forename: Cristina
authors.identifier: http://orcid.org/0000-0002-3771-2410
authors.initials: C
authors.lastname: Coman
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK.
authors.forename: Fiorella Andrea
authors.initials: FA
authors.lastname: Solari
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK.
authors.forename: Andreas
authors.identifier: http://orcid.org/0000-0002-0272-9220
authors.initials: A
authors.lastname: Hentschel
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK.
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK.
authors.forename: René Peiman
authors.identifier: http://orcid.org/0000-0002-4960-5460
authors.initials: RP
authors.lastname: Zahedi
authors.affiliation: ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK robert.ahrends@isas.de.
authors.forename: Robert
authors.identifier: http://orcid.org/0000-0003-0232-3375
authors.initials: R
authors.lastname: Ahrends
mesh_terms: D000818:Animals; D002460:Cell Line; D053263:Gene Regulatory Networks; D008055:Lipids / Q000302:isolation & purification*; D055432:Metabolomics / Q000379:methods*; D051379:Mice; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods*; D057188:Workflow
chemical_list: D008055:Lipids
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