Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis

Abstract

Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. To gain a better understanding of the multifaceted networks of myriad regulatory layers in complex organisms, integration of different multiomic layers is increasingly performed, including joint extraction methods of diverse biomolecular classes and comprehensive data analyses of different omics. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. Although liquid chromatography–mass spectrometry (LC-MS) analysis is similar for different biomolecular classes, the integration on the instrument level is lagging behind. The recent advancements in high flow proteomics enable us to take a first step towards integration of protein and lipid analysis. Here, we describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow. MOST achieved great robustness and reproducibility. Its application to a Saccharomyces cerevisiae study consisting of 20 conditions revealed 2842 protein groups and 325 lipids and potential molecular relationships.

Multi-Omic Analysis to Characterize Metabolic Adaptation of the E. coli Lipidome in Response to Environmental Stress

“…Unfortunately, lipidome analysis strategies involving characterisation of the changes in bacterial lipid composition and structure are not necessarily sufficient to fully describe the adaptations that occur in lipid metabolism in response to a particular environmental stress, as changes in the lipidome may result from alterations in the expression or activity of a specific enzyme, or a collection of enzymes, involved in a particular metabolic pathway. Thus, 'multi-omics' analysis approaches (e.g., lipidomics and proteomics), which enable the identification, characterisation and quantification of both lipids and proteins extracted from a single sample [35][36][37][38][39], may provide a more holistic understanding of bacterial lipid membrane adaptation mechanisms, including elucidation of the relationship between a specific stress and alterations in individual lipids and specific lipid metabolism enzymes [40,41].…”

Non-volatile organic compounds in exhaled breath particles correspond to active tuberculosis

“…The SPE-based sample preparation was rapid, with the separation process taking ~ 3 min per sample, and the use of a C18 resin column makes it adaptable to automation. Notably, dual mobile phases for polar and nonpolar molecule separation have been used by others, reinforcing the reliability and reproducibility of this approach 15 .

Figure 2 Method development for the separation of small molecules and lipids from one sample using duel mobile phase solvents.

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Integrated proteomic and metabolomic analyses of the mitochondrial neurodegenerative disease MELAS

“…Recent advancements in multi-omics analysis have enabled systematic insights into disease processes and correlations of different classes of biomolecules in disease pathogenesis. [11][12][13][14][15][16] In this study, we designed a global and integrated mass spectrometry (MS)-based strategy for parallel proteomics and metabolomics to provide novel insights into the pathogenic pathways of MELAS. Integrated omics experiments were conducted on dermal fibroblasts derived from a female exhibiting the cardinal symptoms of MELAS.…”