Metabolite profiling plays a crucial role in understanding drug metabolism and toxicity, but analytical accuracy can be compromised by errors introduced during sample preparation. This white paper details the establishment of a semi-preparative LC–MS/MS system for isolating and characterizing metabolites from in vitro and in vivo assays. Emphasis is placed on optimizing the evaporation stage to prevent compound degradation, false positives, and losses caused by temperature or solvent residues. Comparative evaluations demonstrate that centrifugal evaporation under controlled conditions enhances recovery, preserves metabolite integrity, and accelerates analytical workflows for preclinical research.
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