Drug Metabolism and Drug–Drug Interactions Studied Using High-Throughput Ambient Mass Spectrometry

Abstract

Rapid characterization of drug metabolism and drug–drug interactions (DDIs) with quantitative rigor remains challenging due to complex samples and labor-intensive workflows. We present a high-throughput (HT) ambient mass spectrometry (MS) approach using desorption electrospray ionization (DESI) that unites three complementary capabilities available using two different mass spectrometers: (A) untargeted screening to survey the metabolic space, (B) product ion scan tandem MS to characterize novel metabolites, and (C) multiple reaction monitoring (MRM) to deliver precise quantitation of substrates and metabolites. Applying the methodology to diverse in vitro systems, we track substrate depletion, metabolite formation, and DDIs with quantitative accuracy (error <9% for MRM quantitation) validated against liquid chromatography (LC) MS. The method operates two to three orders of magnitude faster (1 s/sample) than traditional LC–MS methods. This allows hundreds of substrate–enzyme–DDI combinations to be followed in time-resolved fashion using ∼4 × 10⁴ individual DESI-MS measurements, acquired at a rate of >3,000 measurements/hour. By combining HT screening and targeted monitoring, the DESI-MS approach delivers metabolic discovery with robust quantitation, overcoming a central bottleneck in large-scale drug metabolism studies. This investigation aims to provide a high-throughput analytical approach with broad utility in drug discovery, toxicology, and precision medicine workflows.