From Sample to Insight: The Metabolomics Workflow at the Kanbar Core Facility

Metabolomics provides a direct window into biochemical activity by linking small-molecule dynamics with genetics, physiology and phenotype. At the Kanbar Core Facility Metabolomics Unit, we have established an end-to-end workflow that supports both targeted and untargeted LC-MS based studies across diverse biological systems. Our pipeline includes optimized procedures for sample collection, quenching, extraction and cleanup, followed by high-resolution mass spectrometry on Orbitrap and triple quadrupole platforms. Emphasis is placed on maintaining metabolite stability, selecting extraction chemistries according to the analytical goal and minimizing matrix related variability. We routinely apply complementary analytical strategies. Untargeted profiling provides broad metabolic fingerprinting and enables biomarker discovery, while targeted quantification supports pathway focused and hypothesis driven studies. Representative results demonstrate how extraction conditions, ionization modes and chromatographic selection affect sensitivity and metabolite coverage. The resulting multidimensional datasets support clustering, differential analysis and pathway interpretation, enabling biologically meaningful conclusions.

This poster will present the complete workflow of our unit from sample preparation to metabolite identification, together with examples of successful analyses that highlight the procedures for informative metabolomics results.