PNNL

Abstract

Integrative multi-omics analyses can empower more effective and complete understandings of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still very 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) proved to be robust and be applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the usefulness 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 the 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, clinical).