This thesis investigates new lipidomics concepts using liquid chromatography and high resolution mass spectrometry, focusing on SWATH technology. The goal was to implement solutions that provide a more complete picture of the lipidome while maintaining data quality and throughput. Critical aspects of SWATH are discussed in the context of metabolomic and lipidomic data quantification and processing. A platform combining automated sample preparation and a dual HILIC-SWATH system for parallel lipidomics and metabolomics is presented. Chapters 4 and 5 present hybrid approaches for accurate quantitative and qualitative analysis of lipid sum and species composition in biology. In the final chapter, SWATH is used for lipid analysis in Toxoplasma gondii genetic knockouts in the sphingolipid pathway.