Integrating MS1 and MS2 Scans in High-Resolution Parallel Reaction Monitoring Assays for Targeted Metabolite Quantification and Dynamic 13C-Labeling Metabolism Analysis

Quantification of 'targeted metabolites, especially trace- metabolites and structural isomers, in complex biological anaterials is an ongoing challenge for metabolomics. Initially developed for proteomic analysis, the parallel reaction monitoring (PRM) technique exploiting high-resolution MS2 fragment ion data..has shown high. promise for targeted metabolite quantification. Notably, MS1 ion interisity data acquired independently as part of each PRM scan cycle are often-underutilized in the PRM assay. In this study, we developed ari MS1/MS2-combined PRM workflow, for, quantification of central carbon- metabolism intermediates,, amino acids and shikimate pathway-related metabolites on an orthogonal QqTOF system. Concentration curve assessment revealed that exploiting both MS1 and MS2 scans in PRM analysis afforded higher sensitivity, :wider dynamic range and better reproducibility than relying on either scan mode for quantification. Furthermore, Skyline was incorporated into out workflow to process the MSS/MS2 ion intensity data, and eliminate noisy signals and transitions with interferences. This iritegrated MS1/MS2 PRM approach was applied to targeted metabolite quantification in engineered E. coil strains for understanding of metabolic pathway modulation. In addition, this new approach, when first implemented in a dynamic C-13-labeling experiment, showed its unique advantage in capturing arid correcting isotopomer labeling curves to facilitate nonstationary C-13-labeling metabolism analysis.