MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.
Identifieur interne : 002A37 ( PubMed/Checkpoint ); précédent : 002A36; suivant : 002A38MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.
Auteurs : Ernesto S. Nakayasu [États-Unis] ; Carrie D. Nicora [États-Unis] ; Amy C. Sims [États-Unis] ; Kristin E. Burnum-Johnson [États-Unis] ; Young-Mo Kim [États-Unis] ; Jennifer E. Kyle [États-Unis] ; Melissa M. Matzke [États-Unis] ; Anil K. Shukla [États-Unis] ; Rosalie K. Chu [États-Unis] ; Athena A. Schepmoes [États-Unis] ; Jon M. Jacobs [États-Unis] ; Ralph S. Baric [États-Unis] ; Bobbie-Jo Webb-Robertson [États-Unis] ; Richard D. Smith [États-Unis] ; Thomas O. Metz [États-Unis]Source :
- mSystems [ 2379-5077 ]
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.
DOI: 10.1128/mSystems.00043-16
PubMed: 27822525
Affiliations:
- États-Unis
- Caroline du Nord, Washington (État)
- Chapel Hill (Caroline du Nord)
- Université de Caroline du Nord à Chapel Hill
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:27822525Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.</title><author><name sortKey="Nakayasu, Ernesto S" sort="Nakayasu, Ernesto S" uniqKey="Nakayasu E" first="Ernesto S" last="Nakayasu">Ernesto S. Nakayasu</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nicora, Carrie D" sort="Nicora, Carrie D" uniqKey="Nicora C" first="Carrie D" last="Nicora">Carrie D. Nicora</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C" last="Sims">Amy C. Sims</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Burnum Johnson, Kristin E" sort="Burnum Johnson, Kristin E" uniqKey="Burnum Johnson K" first="Kristin E" last="Burnum-Johnson">Kristin E. Burnum-Johnson</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Kim, Young Mo" sort="Kim, Young Mo" uniqKey="Kim Y" first="Young-Mo" last="Kim">Young-Mo Kim</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Kyle, Jennifer E" sort="Kyle, Jennifer E" uniqKey="Kyle J" first="Jennifer E" last="Kyle">Jennifer E. Kyle</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Matzke, Melissa M" sort="Matzke, Melissa M" uniqKey="Matzke M" first="Melissa M" last="Matzke">Melissa M. Matzke</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Shukla, Anil K" sort="Shukla, Anil K" uniqKey="Shukla A" first="Anil K" last="Shukla">Anil K. Shukla</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Chu, Rosalie K" sort="Chu, Rosalie K" uniqKey="Chu R" first="Rosalie K" last="Chu">Rosalie K. Chu</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Schepmoes, Athena A" sort="Schepmoes, Athena A" uniqKey="Schepmoes A" first="Athena A" last="Schepmoes">Athena A. Schepmoes</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Jacobs, Jon M" sort="Jacobs, Jon M" uniqKey="Jacobs J" first="Jon M" last="Jacobs">Jon M. Jacobs</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Webb Robertson, Bobbie Jo" sort="Webb Robertson, Bobbie Jo" uniqKey="Webb Robertson B" first="Bobbie-Jo" last="Webb-Robertson">Bobbie-Jo Webb-Robertson</name><affiliation wicri:level="2"><nlm:affiliation>National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D" last="Smith">Richard D. Smith</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Metz, Thomas O" sort="Metz, Thomas O" uniqKey="Metz T" first="Thomas O" last="Metz">Thomas O. Metz</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="????"><PubDate><MedlineDate>2016 May-Jun</MedlineDate></PubDate></date><idno type="RBID">pubmed:27822525</idno><idno type="pmid">27822525</idno><idno type="doi">10.1128/mSystems.00043-16</idno><idno type="wicri:Area/PubMed/Corpus">000F02</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000F02</idno><idno type="wicri:Area/PubMed/Curation">000F02</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000F02</idno><idno type="wicri:Area/PubMed/Checkpoint">002A37</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002A37</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.</title><author><name sortKey="Nakayasu, Ernesto S" sort="Nakayasu, Ernesto S" uniqKey="Nakayasu E" first="Ernesto S" last="Nakayasu">Ernesto S. Nakayasu</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nicora, Carrie D" sort="Nicora, Carrie D" uniqKey="Nicora C" first="Carrie D" last="Nicora">Carrie D. Nicora</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C" last="Sims">Amy C. Sims</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Burnum Johnson, Kristin E" sort="Burnum Johnson, Kristin E" uniqKey="Burnum Johnson K" first="Kristin E" last="Burnum-Johnson">Kristin E. Burnum-Johnson</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Kim, Young Mo" sort="Kim, Young Mo" uniqKey="Kim Y" first="Young-Mo" last="Kim">Young-Mo Kim</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Kyle, Jennifer E" sort="Kyle, Jennifer E" uniqKey="Kyle J" first="Jennifer E" last="Kyle">Jennifer E. Kyle</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Matzke, Melissa M" sort="Matzke, Melissa M" uniqKey="Matzke M" first="Melissa M" last="Matzke">Melissa M. Matzke</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Shukla, Anil K" sort="Shukla, Anil K" uniqKey="Shukla A" first="Anil K" last="Shukla">Anil K. Shukla</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Chu, Rosalie K" sort="Chu, Rosalie K" uniqKey="Chu R" first="Rosalie K" last="Chu">Rosalie K. Chu</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Schepmoes, Athena A" sort="Schepmoes, Athena A" uniqKey="Schepmoes A" first="Athena A" last="Schepmoes">Athena A. Schepmoes</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Jacobs, Jon M" sort="Jacobs, Jon M" uniqKey="Jacobs J" first="Jon M" last="Jacobs">Jon M. Jacobs</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Webb Robertson, Bobbie Jo" sort="Webb Robertson, Bobbie Jo" uniqKey="Webb Robertson B" first="Bobbie-Jo" last="Webb-Robertson">Bobbie-Jo Webb-Robertson</name><affiliation wicri:level="2"><nlm:affiliation>National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D" last="Smith">Richard D. Smith</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Metz, Thomas O" sort="Metz, Thomas O" uniqKey="Metz T" first="Thomas O" last="Metz">Thomas O. Metz</name><affiliation wicri:level="2"><nlm:affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></analytic><series><title level="j">mSystems</title><idno type="ISSN">2379-5077</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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, <i>in vitro</i>, and clinical). <b>IMPORTANCE</b> 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. <b>Author Video</b>: An author video summary of this article is available.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27822525</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2379-5077</ISSN><JournalIssue CitedMedium="Print"><Volume>1</Volume><Issue>3</Issue><PubDate><MedlineDate>2016 May-Jun</MedlineDate></PubDate></JournalIssue><Title>mSystems</Title><ISOAbbreviation>mSystems</ISOAbbreviation></Journal><ArticleTitle>MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e00043-16</ELocationID><Abstract><AbstractText>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, <i>in vitro</i>, and clinical). <b>IMPORTANCE</b> 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. <b>Author Video</b>: An author video summary of this article is available.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nakayasu</LastName><ForeName>Ernesto S</ForeName><Initials>ES</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nicora</LastName><ForeName>Carrie D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sims</LastName><ForeName>Amy C</ForeName><Initials>AC</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burnum-Johnson</LastName><ForeName>Kristin E</ForeName><Initials>KE</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Young-Mo</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kyle</LastName><ForeName>Jennifer E</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Matzke</LastName><ForeName>Melissa M</ForeName><Initials>MM</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shukla</LastName><ForeName>Anil K</ForeName><Initials>AK</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Rosalie K</ForeName><Initials>RK</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schepmoes</LastName><ForeName>Athena A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jacobs</LastName><ForeName>Jon M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baric</LastName><ForeName>Ralph S</ForeName><Initials>RS</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Webb-Robertson</LastName><ForeName>Bobbie-Jo</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Richard D</ForeName><Initials>RD</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Metz</LastName><ForeName>Thomas O</ForeName><Initials>TO</Initials><AffiliationInfo><Affiliation>Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>DP3 DK094343</GrantID><Acronym>DK</Acronym><Agency>NIDDK NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U19 AI106772</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>05</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>mSystems</MedlineTA><NlmUniqueID>101680636</NlmUniqueID><ISSNLinking>2379-5077</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">MERS-CoV</Keyword><Keyword MajorTopicYN="N">lipidomics</Keyword><Keyword MajorTopicYN="N">metabolomics</Keyword><Keyword MajorTopicYN="N">multi-omics analysis</Keyword><Keyword MajorTopicYN="N">proteomics</Keyword><Keyword MajorTopicYN="N">sample preparation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>03</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>03</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>11</Month><Day>9</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27822525</ArticleId><ArticleId IdType="doi">10.1128/mSystems.00043-16</ArticleId><ArticleId IdType="pii">mSystems00043-16</ArticleId><ArticleId IdType="pmc">PMC5069757</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Front Microbiol. 2014 Apr 07;5:109</Citation><ArticleIdList><ArticleId IdType="pubmed">24778628</ArticleId></ArticleIdList></Reference><Reference><Citation>Analyst. 2013 Nov 7;138(21):6243-5</Citation><ArticleIdList><ArticleId IdType="pubmed">23803965</ArticleId></ArticleIdList></Reference><Reference><Citation>J Chromatogr A. 2004 Jan 16;1023(2):317-20</Citation><ArticleIdList><ArticleId IdType="pubmed">14753699</ArticleId></ArticleIdList></Reference><Reference><Citation>Biol Chem. 2015 Jun;396(6-7):585-95</Citation><ArticleIdList><ArticleId IdType="pubmed">25525752</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biosyst. 2013 Jun;9(6):1522-34</Citation><ArticleIdList><ArticleId IdType="pubmed">23559334</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Oct 15;27(20):2866-72</Citation><ArticleIdList><ArticleId IdType="pubmed">21852304</ArticleId></ArticleIdList></Reference><Reference><Citation>J Integr Bioinform. 2010 Feb 02;7(2):112</Citation><ArticleIdList><ArticleId IdType="pubmed">20134079</ArticleId></ArticleIdList></Reference><Reference><Citation>MethodsX. 2014 Jul 18;1:74-80</Citation><ArticleIdList><ArticleId IdType="pubmed">26150938</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2014 Jul;79(1):173-80</Citation><ArticleIdList><ArticleId IdType="pubmed">24804825</ArticleId></ArticleIdList></Reference><Reference><Citation>J Immunol. 2013 Aug 15;191(4):1744-52</Citation><ArticleIdList><ArticleId IdType="pubmed">23851680</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Nov;13(11):2498-504</Citation><ArticleIdList><ArticleId IdType="pubmed">14597658</ArticleId></ArticleIdList></Reference><Reference><Citation>MBio. 2011 Mar 01;2(1):e00325-10</Citation><ArticleIdList><ArticleId IdType="pubmed">21285433</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2015 Apr 23;10(4):e0123188</Citation><ArticleIdList><ArticleId IdType="pubmed">25905710</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Feb 1;28(3):373-80</Citation><ArticleIdList><ArticleId IdType="pubmed">22135418</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Proteomics. 2005 Sep;4(9):1265-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15958392</ArticleId></ArticleIdList></Reference><Reference><Citation>Mass Spectrom Rev. 2006 May-Jun;25(3):450-82</Citation><ArticleIdList><ArticleId IdType="pubmed">16429408</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Microbiol Rep. 2014 Aug;6(4):389-95</Citation><ArticleIdList><ArticleId IdType="pubmed">24992538</ArticleId></ArticleIdList></Reference><Reference><Citation>Anal Bioanal Chem. 2012 Mar;402(9):2923-33</Citation><ArticleIdList><ArticleId IdType="pubmed">22354571</ArticleId></ArticleIdList></Reference><Reference><Citation>Anal Chem. 2009 May 1;81(9):3429-39</Citation><ArticleIdList><ArticleId IdType="pubmed">19358599</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 2000 Jul;74(14):6425-32</Citation><ArticleIdList><ArticleId IdType="pubmed">10864654</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 1951 Aug;191(2):833-41</Citation><ArticleIdList><ArticleId IdType="pubmed">14861228</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2011 May 19;473(7347):337-42</Citation><ArticleIdList><ArticleId IdType="pubmed">21593866</ArticleId></ArticleIdList></Reference><Reference><Citation>J Proteome Res. 2010 Nov 5;9(11):5748-56</Citation><ArticleIdList><ArticleId IdType="pubmed">20831241</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteomics. 2004 Apr;4(4):1195-203</Citation><ArticleIdList><ArticleId IdType="pubmed">15048999</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 2013 Sep;87(17):9953-8</Citation><ArticleIdList><ArticleId IdType="pubmed">23824802</ArticleId></ArticleIdList></Reference><Reference><Citation>ISME J. 2013 Jan;7(1):110-21</Citation><ArticleIdList><ArticleId IdType="pubmed">22763648</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2012 Mar 16;148(6):1293-307</Citation><ArticleIdList><ArticleId IdType="pubmed">22424236</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Syst Biol. 2012 Jun 26;8:558</Citation><ArticleIdList><ArticleId IdType="pubmed">22735334</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteomics. 2004 Jan;4(1):78-83</Citation><ArticleIdList><ArticleId IdType="pubmed">14730673</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Jan 15;25(2):211-7</Citation><ArticleIdList><ArticleId IdType="pubmed">19038984</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Proteomics. 2014 Dec;13(12):3639-46</Citation><ArticleIdList><ArticleId IdType="pubmed">25433089</ArticleId></ArticleIdList></Reference><Reference><Citation>Can J Biochem Physiol. 1959 Aug;37(8):911-7</Citation><ArticleIdList><ArticleId IdType="pubmed">13671378</ArticleId></ArticleIdList></Reference><Reference><Citation>Anal Chem. 2011 Aug 15;83(16):6135-40</Citation><ArticleIdList><ArticleId IdType="pubmed">21692516</ArticleId></ArticleIdList></Reference><Reference><Citation>Lancet. 2015 Sep 5;386(9997):995-1007</Citation><ArticleIdList><ArticleId IdType="pubmed">26049252</ArticleId></ArticleIdList></Reference><Reference><Citation>Anal Biochem. 2013 Feb 1;433(1):10-8</Citation><ArticleIdList><ArticleId IdType="pubmed">23068038</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Microbiol. 2015 Apr 17;6:209</Citation><ArticleIdList><ArticleId IdType="pubmed">25941514</ArticleId></ArticleIdList></Reference><Reference><Citation>J Natl Cancer Inst Monogr. 2011;2011(42):8-15</Citation><ArticleIdList><ArticleId IdType="pubmed">21672890</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 1957 May;226(1):497-509</Citation><ArticleIdList><ArticleId IdType="pubmed">13428781</ArticleId></ArticleIdList></Reference><Reference><Citation>NMR Biomed. 2002 Feb;15(1):37-44</Citation><ArticleIdList><ArticleId IdType="pubmed">11840551</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2014 May 6;111(18):6846-51</Citation><ArticleIdList><ArticleId IdType="pubmed">24753604</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Proteomics. 2013 Oct;12(10):2992-3005</Citation><ArticleIdList><ArticleId IdType="pubmed">23792921</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteomics. 2011 Dec;11(24):4736-41</Citation><ArticleIdList><ArticleId IdType="pubmed">22038874</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteomics. 2012 Apr;12(8):1074-92</Citation><ArticleIdList><ArticleId IdType="pubmed">22577010</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2008 Jul 1;24(13):1556-8</Citation><ArticleIdList><ArticleId IdType="pubmed">18453552</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2015 May 14;521(7551):208-12</Citation><ArticleIdList><ArticleId IdType="pubmed">25739499</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2006;1(2):769-74</Citation><ArticleIdList><ArticleId IdType="pubmed">17406306</ArticleId></ArticleIdList></Reference><Reference><Citation>J Proteome Res. 2010 Oct 1;9(10):5422-37</Citation><ArticleIdList><ArticleId IdType="pubmed">20722421</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2007 Aug 1;23(15):2021-3</Citation><ArticleIdList><ArticleId IdType="pubmed">17545182</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Nord</li><li>Washington (État)</li></region><settlement><li>Chapel Hill (Caroline du Nord)</li></settlement><orgName><li>Université de Caroline du Nord à Chapel Hill</li></orgName></list><tree><country name="États-Unis"><region name="Washington (État)"><name sortKey="Nakayasu, Ernesto S" sort="Nakayasu, Ernesto S" uniqKey="Nakayasu E" first="Ernesto S" last="Nakayasu">Ernesto S. Nakayasu</name></region><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><name sortKey="Burnum Johnson, Kristin E" sort="Burnum Johnson, Kristin E" uniqKey="Burnum Johnson K" first="Kristin E" last="Burnum-Johnson">Kristin E. Burnum-Johnson</name><name sortKey="Chu, Rosalie K" sort="Chu, Rosalie K" uniqKey="Chu R" first="Rosalie K" last="Chu">Rosalie K. Chu</name><name sortKey="Jacobs, Jon M" sort="Jacobs, Jon M" uniqKey="Jacobs J" first="Jon M" last="Jacobs">Jon M. Jacobs</name><name sortKey="Kim, Young Mo" sort="Kim, Young Mo" uniqKey="Kim Y" first="Young-Mo" last="Kim">Young-Mo Kim</name><name sortKey="Kyle, Jennifer E" sort="Kyle, Jennifer E" uniqKey="Kyle J" first="Jennifer E" last="Kyle">Jennifer E. Kyle</name><name sortKey="Matzke, Melissa M" sort="Matzke, Melissa M" uniqKey="Matzke M" first="Melissa M" last="Matzke">Melissa M. Matzke</name><name sortKey="Metz, Thomas O" sort="Metz, Thomas O" uniqKey="Metz T" first="Thomas O" last="Metz">Thomas O. Metz</name><name sortKey="Nicora, Carrie D" sort="Nicora, Carrie D" uniqKey="Nicora C" first="Carrie D" last="Nicora">Carrie D. Nicora</name><name sortKey="Schepmoes, Athena A" sort="Schepmoes, Athena A" uniqKey="Schepmoes A" first="Athena A" last="Schepmoes">Athena A. Schepmoes</name><name sortKey="Shukla, Anil K" sort="Shukla, Anil K" uniqKey="Shukla A" first="Anil K" last="Shukla">Anil K. Shukla</name><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C" last="Sims">Amy C. Sims</name><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D" last="Smith">Richard D. Smith</name><name sortKey="Webb Robertson, Bobbie Jo" sort="Webb Robertson, Bobbie Jo" uniqKey="Webb Robertson B" first="Bobbie-Jo" last="Webb-Robertson">Bobbie-Jo Webb-Robertson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002A37 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 002A37 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:27822525
|texte= MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:27822525" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |