| Summary: | Metabolomics has been used as a powerful tool for the analysis, and drug-lead identification in medicinal plants and herbal medicines. For the coverage of a broader range of plant-based metabolites using LC-MS, one of the important parameters is the selection of analysis mode and data processing for identification. This paper describes the utility of two distinctive acquisition modes in combination, a classic data-dependent acquisition (DDA) mode and a data-independent acquisition (DIA) mode for obtaining the mass spectrometry data of plant extracts using LC-ESI-QTOF/MS. Tribulus terrestris plant was used as a case study. We have applied three-step data analysis pipeline 1-annotation and putative identification of metabolites, 2-validation, and relative quantification, and 3-multivariate analysis using open-access MS-DIAL, Skyline, and Perseus software. A total of four samples of T. terrestris (aqueous extracts), two fruits, and two whole plant samples, from two different regions, were used. By combining data analysis results of plant fruit samples from two different regions, a total of 95 and 77 metabolites were identified in positive and negative ionization modes, respectively. Similarly, in the analysis of the whole plant from two different regions, 75 and 76 metabolites were identified in positive and negative ionization modes, respectively. We suggested the use of DDA mode for annotation, identification of metabolites, and generation of transition lists in MS-DIAL, furthermore, the use of DIA acquisition mode for enhancing metabolites sensitivity in complex samples, deconvolute MS1/MS2 spectra in Skyline for the quantitative performance and analytical reliability. The developed protocol can be used for the broader coverage of plant-based metabolites.
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