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Title: MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

Abstract

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. Themetabolite,protein, andlipidextraction (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). IMPORTANCEIn 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,more » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1327119
Report Number(s):
PNNL-SA-114737
Journal ID: ISSN 2379-5077; 48199; 48680; 47664; WN9030198
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: mSystems; Journal Volume: 1; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Nakayasu, Ernesto S., Nicora, Carrie D., Sims, Amy C., Burnum-Johnson, Kristin E., Kim, Young-Mo, Kyle, Jennifer E., Matzke, Melissa M., Shukla, Anil K., Chu, Rosalie K., Schepmoes, Athena A., Jacobs, Jon M., Baric, Ralph S., Webb-Robertson, Bobbie-Jo, Smith, Richard D., Metz, Thomas O., and Chia, Nicholas. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. United States: N. p., 2016. Web. doi:10.1128/mSystems.00043-16.
Nakayasu, Ernesto S., Nicora, Carrie D., Sims, Amy C., Burnum-Johnson, Kristin E., Kim, Young-Mo, Kyle, Jennifer E., Matzke, Melissa M., Shukla, Anil K., Chu, Rosalie K., Schepmoes, Athena A., Jacobs, Jon M., Baric, Ralph S., Webb-Robertson, Bobbie-Jo, Smith, Richard D., Metz, Thomas O., & Chia, Nicholas. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. United States. doi:10.1128/mSystems.00043-16.
Nakayasu, Ernesto S., Nicora, Carrie D., Sims, Amy C., Burnum-Johnson, Kristin E., Kim, Young-Mo, Kyle, Jennifer E., Matzke, Melissa M., Shukla, Anil K., Chu, Rosalie K., Schepmoes, Athena A., Jacobs, Jon M., Baric, Ralph S., Webb-Robertson, Bobbie-Jo, Smith, Richard D., Metz, Thomas O., and Chia, Nicholas. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses". United States. doi:10.1128/mSystems.00043-16.
@article{osti_1327119,
title = {MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses},
author = {Nakayasu, Ernesto S. and Nicora, Carrie D. and Sims, Amy C. and Burnum-Johnson, Kristin E. and Kim, Young-Mo and Kyle, Jennifer E. and Matzke, Melissa M. and Shukla, Anil K. and Chu, Rosalie K. and Schepmoes, Athena A. and Jacobs, Jon M. and Baric, Ralph S. and Webb-Robertson, Bobbie-Jo and Smith, Richard D. and Metz, Thomas O. and Chia, Nicholas},
abstractNote = {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. Themetabolite,protein, andlipidextraction (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). IMPORTANCEIn 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.},
doi = {10.1128/mSystems.00043-16},
journal = {mSystems},
number = 3,
volume = 1,
place = {United States},
year = 2016,
month = 5
}
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