SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery

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Brief introduction: The complexity of metabolome presents a great analytical challenge for quantitative metabolite profiling, and restricts the application of metabolomics for biomarker discovery. Targeted metabolomics using multiple-reaction monitoring (MRM) technique has excellent capability for quantitative analysis, but is severely restricted by metabolite coverage in one analysis. To address this challenge, we developed a new strategy, namely, SWATHtoMRM, which utilizes the broad coverage of SWATH-MS technology to develop high-coverage targeted metabolomics method. Specifically, SWATH-MS technique was first utilized to untargeted profile the one pooled sample, and to acquire the MS2 spectra for all metabolites. Then, SWATHtoMRM was used to extract large-scale MRM transitions for targeted analysis with a coverage as high as 1000-2000 metabolites in one experiment. The qualification performances of SWATHtoMRM method including good reproducibility, high sensitivity, and broad dynamic range were systematically evaluated and demonstrated. SWATHtoMRM offers a new approach to develop high-throughput targeted metabolomics method and further facilitates discovering potential reliable biomarkers for diseases benefitting from comprehensive metabolites profiling and accurate quantification.



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Binary package: SWATHtoMRM_1.0.0.zip

Source package: SWATHtoMRM_1.0.0.tar.gz

SWATHtoMRM instruction and demo report

SWATHtoMRM demo data


Reference: H. Zha, Y. Cai, Y. Yin, Z. Wang, K. Li, and Z.-J. Zhu* (Corresponding Author), SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery, Analytical Chemistry, 2018, 90, 4062-4070. Web Link (†, Co-first authors)