Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry

TLDR

Although transcriptome, proteome, and interactome maps exist for many eukaryotes, lipidomes remain relatively uncharacterized. The study aims to demonstrate that automated shotgun lipidomics can enable absolute quantification of individual lipid species from a single sample of 2 million yeast cells. The authors applied this approach to Saccharomyces cerevisiae, streamlining processing of a single 2 million‑cell sample. The method quantified 250 lipid species across 21 classes, achieving ~95 % coverage of the yeast lipidome with 125‑fold sensitivity improvement, and revealed that growth temperature and lipid‑biosynthesis defects ripple through the lipid composition, establishing the platform as a resource for eukaryotic lipidome characterization.

Abstract

Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sample of only 2 million yeast cells. By comparative lipidomics, we achieved the absolute quantification of 250 molecular lipid species covering 21 major lipid classes. This analysis provided approximately 95% coverage of the yeast lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast lipidome. This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches.