MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well e...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2016-06-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00043-16 |
| _version_ | 1818461076578107392 |
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| author | Ernesto S. Nakayasu Carrie D. Nicora Amy C. Sims Kristin E. Burnum-Johnson Young-Mo Kim Jennifer E. Kyle Melissa M. Matzke Anil K. Shukla Rosalie K. Chu Athena A. Schepmoes Jon M. Jacobs Ralph S. Baric Bobbie-Jo Webb-Robertson Richard D. Smith Thomas O. Metz |
| author_facet | Ernesto S. Nakayasu Carrie D. Nicora Amy C. Sims Kristin E. Burnum-Johnson Young-Mo Kim Jennifer E. Kyle Melissa M. Matzke Anil K. Shukla Rosalie K. Chu Athena A. Schepmoes Jon M. Jacobs Ralph S. Baric Bobbie-Jo Webb-Robertson Richard D. Smith Thomas O. Metz |
| author_sort | Ernesto S. Nakayasu |
| collection | DOAJ |
| description | ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available. |
| first_indexed | 2024-12-14T23:40:24Z |
| format | Article |
| id | doaj.art-6bfbb8695fd0439ea537209e08d93cb9 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-14T23:40:24Z |
| publishDate | 2016-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-6bfbb8695fd0439ea537209e08d93cb92022-12-21T22:43:31ZengAmerican Society for MicrobiologymSystems2379-50772016-06-011310.1128/mSystems.00043-16MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic AnalysesErnesto S. Nakayasu0Carrie D. Nicora1Amy C. Sims2Kristin E. Burnum-Johnson3Young-Mo Kim4Jennifer E. Kyle5Melissa M. Matzke6Anil K. Shukla7Rosalie K. Chu8Athena A. Schepmoes9Jon M. Jacobs10Ralph S. Baric11Bobbie-Jo Webb-Robertson12Richard D. Smith13Thomas O. Metz14Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USADepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USADepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USANational Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAEarth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USAABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available.https://journals.asm.org/doi/10.1128/mSystems.00043-16metabolomicsmulti-omics analysislipidomicsproteomicssample preparationMERS-CoV |
| spellingShingle | Ernesto S. Nakayasu Carrie D. Nicora Amy C. Sims Kristin E. Burnum-Johnson Young-Mo Kim Jennifer E. Kyle Melissa M. Matzke Anil K. Shukla Rosalie K. Chu Athena A. Schepmoes Jon M. Jacobs Ralph S. Baric Bobbie-Jo Webb-Robertson Richard D. Smith Thomas O. Metz MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses mSystems metabolomics multi-omics analysis lipidomics proteomics sample preparation MERS-CoV |
| title | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses |
| title_full | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses |
| title_fullStr | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses |
| title_full_unstemmed | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses |
| title_short | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses |
| title_sort | mplex a robust and universal protocol for single sample integrative proteomic metabolomic and lipidomic analyses |
| topic | metabolomics multi-omics analysis lipidomics proteomics sample preparation MERS-CoV |
| url | https://journals.asm.org/doi/10.1128/mSystems.00043-16 |
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