Development of an integrative proteomics, metabolomics and lipidomics methodology - a case study of plant defense molecular networks.

Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physico-chemical properties. Therefore, several sets/aliquots of the samples need to be collected for extraction of different biomolecules. To overcome this challenge, we adapted a bi-phasic fractionation method to extract proteins, metabolites, and lipids from the same sample for liquid chromatography-tandem mass spectrometry-based multi-omics. To document utility of the new method, we used uninfected leaves of bacterial pathogen-treated Arabidopsis plants to generate multi-omics datasets from the same sample. In total, we were able to identify and quantify 1849 proteins, 1967 metabolites and 425 lipid species by extracting the three components from single samples. The molecules were integrated into molecular networks. Our work demonstrates the clear advantages of the new multi-omics method, including sample conservation, high reproducibility, and tight correlation between different types of biomolecules.