Development and thorough evaluation of a multi-omics sample preparation workflow for comprehensive LC-MS/MS-based metabolomics, lipidomics and proteomics datasets

The importance of sample preparation selection if often overlooked particularly for untargeted multi-omics approaches that gained popularity in recent years. To minimize issues with sample heterogeneity and additional freeze-thaw cycles during sample splitting, multiple -omics datasets (e.g. metabolomics, lipidomics and proteomics) should ideally be generated from the same set of samples. For sample extraction, commonly biphasic organic solvent systems are used that require extensive multi-step protocols. Individual studies have recently also started to investigate monophasic (all-in-one) extraction procedures. The aim of the current study was to develop and systematically compare ten different mono- and biphasic extraction solvent mixtures for their potential to aid in the most comprehensive metabolomics, lipidomics and proteomics datasets. As the focus was on human postmortem tissue samples (muscle and liver tissue), four tissue homogenization parameters were also evaluated. Untargeted liquid chromatography mass spectrometry-based metabolomics, lipidomic and proteomics methods were utilized along with 1D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and bicinchoninic acid (BCA) assay results. Optimal homogenization was found to be achieved by bead-homogenizing 20 mg of muscle or liver tissue with 200 μL (1:10 ratio) Water:Methanol (1:2) using 3 × 30 s pulses. The supernatant of the homogenate was further extracted. Comprehensive ranking, taking nine different processing parameters into account, showed that the monophasic extraction solvents, overall, showed better scores compared to the biphasic solvent systems, despite their recommendation for one or all of the -omics extractions. The optimal extraction solvent was found to be Methanol:Acetone (9:1), resulting in the most comprehensive metabolomics, lipidomics and proteomics datasets, showing the potential to be automated, hence, allowing for high-throughput analysis of samples and opening the door for comprehensive multi-omics results from routine clinical cases in the future.