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      A Novel Approach of SWATH-Based Metabolomics Analysis Using the Human Metabolome Database Spectral Library

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          Abstract

          Metabolomics is a potential approach to paving new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development. The conventional metabolomics analysis pipeline depends on the data-independent acquisition (DIA) technique. Although powerful, it still suffers from stochastic, non-reproducible ion selection across samples. Despite the presence of different metabolomics workbenches, metabolite identification remains a tedious and time-consuming task. Consequently, sequential windowed acquisition of all theoretical MS (SWATH) acquisition has attracted much attention to overcome this limitation. This article aims to develop a novel SWATH platform for data analysis with a generation of an accurate mass spectral library for metabolite identification using SWATH acquisition. The workflow was validated using inclusion/exclusion compound lists. The false-positive identification was 3.4% from the non-endogenous drugs with 96.6% specificity. The workflow has proven to overcome background noise despite the complexity of the SWATH sample. From the Human Metabolome Database (HMDB), 1282 compounds were tested in various biological samples to demonstrate the feasibility of the workflow. The current study identified 377 compounds in positive and 303 in negative modes with 392 unique non-redundant metabolites. Finally, a free software tool, SASA, was developed to analyze SWATH-acquired samples using the proposed pipeline.

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          Journal
          IJMCFK
          International Journal of Molecular Sciences
          IJMS
          MDPI AG
          1422-0067
          September 2022
          September 18 2022
          : 23
          : 18
          : 10908
          Article
          10.3390/ijms231810908
          9500730
          36142821
          5ad11d36-554c-43f2-8571-9663199f5e7d
          © 2022

          https://creativecommons.org/licenses/by/4.0/

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