Tips and tricks for LC–MS-based metabolomics and lipidomics analysis

Metabolomics and lipidomics are rapidly growing fields, leading to novel discoveries and advancing the understanding of biological processes at the molecular level. However, designing a proper workflow and choosing from countless options can be challenging, especially for beginners in the field. To address this challenge, we provide a comprehensive overview of metabolomics and lipidomics tools and a step-by-step guide that includes "tips and tricks" based on current metabolomics and lipidomics analysis approaches. We include power analysis, sample collection and preparation, separation and detection of metabolites using primarily liquid chromatography–mass spectrometry (LC–MS), processing of raw instrumental files, quality control, statistical analysis, and data sharing. This guide offers practical insights applicable to diverse research areas, covering all the essential steps in metabolomic and lipidomic profiling.