Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection
Identifieur interne : 002461 ( Ncbi/Merge ); précédent : 002460; suivant : 002462Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection
Auteurs :Source :
- MERS Coronavirus ; 2019.
Abstract
Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snapshot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of biosafety level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins, and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes, and their subsequent informatics pipelines.
Url:
DOI: 10.1007/978-1-0716-0211-9_14
PubMed: 31883096
PubMed Central: 7121680
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection.</title>
<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>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</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, NC, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC</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="Bloodsworth, Kent J" sort="Bloodsworth, Kent J" uniqKey="Bloodsworth K" first="Kent J" last="Bloodsworth">Kent J. Bloodsworth</name>
<affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
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<author><name sortKey="Kim, Young Mo" sort="Kim, Young Mo" uniqKey="Kim Y" first="Young-Mo" last="Kim">Young-Mo Kim</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Moore, Ronald J" sort="Moore, Ronald J" uniqKey="Moore R" first="Ronald J" last="Moore">Ronald J. Moore</name>
<affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</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>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
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</author>
<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>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</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>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. Thomas.metz@pnnl.gov.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Methods in molecular biology (Clifton, N.J.)</title>
<idno type="eISSN">1940-6029</idno>
<imprint><date when="2020" type="published">2020</date>
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<front><div type="abstract" xml:lang="en">Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snapshot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of biosafety level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins, and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes, and their subsequent informatics pipelines.</div>
</front>
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