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      Two-dimensional liquid chromatography and ion mobility-mass spectrometry for the multicomponent characterization of different parts of the medicinal plant Gynostemma longipes

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          Abstract

          Herba Gynostemma (Jiaogulan) is an herbaceous plant of the genus Gynostemma in the family Cucurbitaceae. Gynostemma longipes has lipid-lowering activity, thus, it is used as a medicinal material. However, its medicinal using parts have been recorded as whole plants or aerial parts in different provincial quality standards; therefore, it is necessary to conduct a comprehensive compositional analysis of the different parts of G. longipes (rhizomes, stems, and leaves) used in traditional medicine. In this study, offline two-dimensional liquid chromatography-ion mobility-quadrupole time-of-flight mass spectrometry (2D-LC/IM-QTOF-MS) was used to analyze the different parts of G. longipes obtained from Shaanxi province, China. By combining the retention times, mass fragments, collision cross-section values, reference standards, and information concerning literature compounds, 396 components were identified from the three parts of the plant, including 94 groups of isomers, and 217 components were identified or tentatively identified as new compounds. In the rhizomes, leaves, and stems, 240, 220, and 168 compounds, respectively, were identified. Differential analysis of the compounds in the rhizomes and aerial parts was also carried out, and 36 differential components were identified, of which 32 had higher contents in the rhizomes. Therefore, these findings indicate that the number of chemical components and the content of major differential components are higher in the rhizomes than the leaves and stems of G. longipes from the Maobaling Planting Base in Pingli county, Shaanxi province. Thus, the rhizomes of G. longipes are also an important part for medicinal use. These results will contribute to the establishment of quality control methods for G. longipes.

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          TBtools - an integrative toolkit developed for interactive analyses of big biological data

          The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
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            Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics

            The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curate an ion mobility CCS atlas, namely AllCCS, and develop an integrated strategy for metabolite annotation using known or unknown chemical structures. The AllCCS atlas covers vast chemical structures with >5000 experimental CCS records and ~12 million calculated CCS values for >1.6 million small molecules. We demonstrate the high accuracy and wide applicability of AllCCS with medium relative errors of 0.5–2% for a broad spectrum of small molecules. AllCCS combined with in silico MS/MS spectra facilitates multi-dimensional match and substantially improves the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AllCCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.
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              Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts

              A comprehensive characterization of the lipidome from limited starting material remains very challenging. Here we report a high-sensitivity lipidomics workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry (TIMS). Taking advantage of parallel accumulation–serial fragmentation (PASEF), we fragment on average 15 precursors in each of 100 ms TIMS scans, while maintaining the full mobility resolution of co-eluting isomers. The acquisition speed of over 100 Hz allows us to obtain MS/MS spectra of the vast majority of isotope patterns. Analyzing 1 µL of human plasma, PASEF increases the number of identified lipids more than three times over standard TIMS-MS/MS, achieving attomole sensitivity. Building on high intra- and inter-laboratory precision and accuracy of TIMS collisional cross sections (CCS), we compile 1856 lipid CCS values from plasma, liver and cancer cells. Our study establishes PASEF in lipid analysis and paves the way for sensitive, ion mobility-enhanced lipidomics in four dimensions.
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                Author and article information

                Contributors
                Journal
                Front Chem
                Front Chem
                Front. Chem.
                Frontiers in Chemistry
                Frontiers Media S.A.
                2296-2646
                01 September 2023
                2023
                : 11
                : 1203418
                Affiliations
                [1] 1 Beijing Institute of Radiation Medicine , Beijing, China
                [2] 2 Waters Technologies Limited , Shanghai, China
                [3] 3 Shaanxi Cuiyuankang Health Industry Group Co., Ltd. , Shaanxi, China
                [4] 4 Peking Union Medical College , Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences , Beijing, China
                Author notes

                Edited by: Janardhan Reddy Koduru, Kwangwoon University, Republic of Korea

                Reviewed by: Subba Reddy Alla, Sri Venkateswara University, India

                Wen Xu, Fujian University of Traditional Chinese Medicine, China

                *Correspondence: Baiping Ma, mabaiping@ 123456sina.com
                Article
                1203418
                10.3389/fchem.2023.1203418
                10502315
                37720716
                ffa5c55b-5700-4466-88ea-34b323d5d1d2
                Copyright © 2023 Zheng, Li, Yang, Lu, Li, Zhang, Yuan, Chen, Wang, Guo and Ma.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 10 April 2023
                : 21 August 2023
                Funding
                This study was financially supported by the National Natural Science Foundation of China (Grant No. 82074008).
                Categories
                Chemistry
                Original Research
                Custom metadata
                Analytical Chemistry

                gynostemma longipes,different parts,two-dimensional liquid chromatography,characteristic mass fragments,collision cross-section values

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