MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.
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).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.Author Video: An author video summary of this article is available.
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Ernesto S
ES
Nakayasu
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Carrie D
CD
Nicora
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Amy C
AC
Sims
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Kristin E
KE
Burnum-Johnson
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Young-Mo
YM
Kim
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Jennifer E
JE
Kyle
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Melissa M
MM
Matzke
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Anil K
AK
Shukla
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Rosalie K
RK
Chu
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Athena A
AA
Schepmoes
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Jon M
JM
Jacobs
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.
Ralph S
RS
Baric
National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Bobbie-Jo
BJ
Webb-Robertson
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Richard D
RD
Smith
Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Thomas O
TO
Metz
MERS-CoV; lipidomics; metabolomics; multi-omics analysis; proteomics; sample preparation