title: Integrating MS1 and MS2 Scans in High-Resolution Parallel Reaction Monitoring Assays for Targeted Metabolite Quantification and Dynamic13C-Labeling Metabolism Analysis.
abstract: Quantification of targeted metabolites, especially trace metabolites and structural isomers, in complex biological materials 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 intensity data acquired independently as part of each PRM scan cycle are often underutilized in the PRM assay. In this study, we developed an 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 our workflow to process the MS1/MS2 ion intensity data, and eliminate noisy signals and transitions with interferences. This integrated MS1/MS2 PRM approach was applied to targeted metabolite quantification in engineered E. coli strains for understanding of metabolic pathway modulation. In addition, this new approach, when first implemented in a dynamic13C-labeling experiment, showed its unique advantage in capturing and correcting isotopomer labeling curves to facilitate nonstationary13C-labeling metabolism analysis.
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.|iHuman Institute, ShanghaiTech University , Shanghai 201210, China.
authors.forename: Zhucui
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Life Sciences, Nankai University , Tianjin 300071, China.
authors.forename: Yujing
authors.initials: Y
authors.lastname: Li
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Wujiu
authors.initials: W
authors.lastname: Chen
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Qichen
authors.initials: Q
authors.lastname: Cao
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis , St. Louis, Missouri 63130, United States.
authors.forename: Ni
authors.initials: N
authors.lastname: Wan
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis , St. Louis, Missouri 63130, United States.
authors.forename: Yinjie J
authors.initials: YJ
authors.lastname: Tang
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, China.
authors.forename: Qinhong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: iHuman Institute, ShanghaiTech University , Shanghai 201210, China.
authors.forename: Wenqing
authors.identifier: 0000-0002-5245-2477
authors.initials: W
authors.lastname: Shui
mesh_terms: D002247:Carbon Isotopes; D004926:Escherichia coli / Q000166:cytology / Q000378:metabolism*; D013058:Mass Spectrometry; D055432:Metabolomics
chemical_list: D002247:Carbon Isotopes