Published June 30, 2022
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MS/MS-based molecular networking accelerated discovery of germacrane-type sesquiterpene lactones from Elephantopus scaber L
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- 1. * & Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural
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Xu, Wei, Bai, Ming, Liu, De-Feng, Qin, Shu-Yan, Lv, Tian-Ming, Li, Qian, Lin, Bin, Song, Shao-Jiang, Huang, Xiao-Xiao (2022): MS/MS-based molecular networking accelerated discovery of germacrane-type sesquiterpene lactones from Elephantopus scaber L. Phytochemistry (113136) 198: 1-11, DOI: 10.1016/j.phytochem.2022.113136, URL: http://dx.doi.org/10.1016/j.phytochem.2022.113136
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- urn:lsid:plazi.org:pub:6657FFA0FFC3FFE6FFA7B92E51025B6E
References
- Colorless crystals of 1, 2, 4 and 5 were obtained by recrystallization from MeOH. All X-ray crystallographic data were acquired by a Bruker D8 VENTURE PHOTON II diffractometer with Cu K α (radiation λ = 1.54178 A) at T = 153 K. Their structures were solved by SHELXS method and then refined anisotropically with SHELXL-2018/3 using a full-matrix least-squares procedure based on F2 (Uson et al., 2018). The crystallographic data of 1, 2, 4 and 5 have been deposied with the Cambridge Crystallographic Data Centre (CCDC number 2104415, 2, 106,219, 2,104,416, 2,104,417). The data can be obtained, free of charge, from the Cambridge Crystallographic Data Centre (www.ccdc. cam.ac.uk/data_request/cif).
- The fractions of the n -BuOH fraction from E. scaber were analyzed by HPLC-ESI-MS/MS. The HPLC system was coupled with an AB SCIEX 4000 Q-Trap MS instrument (Applied Biosystems, Foster City, CA). The ESI dual source, EMS-IDA-EPI mode, and positive ion mode were employed. The mobile phase consisted of acetonitrile (A) and water (B). The gradient elution was applied using 20%-95% A for 0-30 min. MS scans were operated from m/z 100-1000. MSConvert software was applied to the.wiff of MS/MS data to the.mzXML format. Then, these. mzXML files were imported into MZmine 2. Mass detection was realized by keeping the noise level at 1500 (for MS) and 300 (for MS2) and the mass detector as the centroid. The chromatograms were prepared for peak detection at a minimum time span of 0.01 min, a minimum height of 0, and a m/z tolerance of 10.0 ppm. Chromatographic deconvolution was achieved by a baseline cut-off algorithm with a minimum peak height of 2000. The peak duration ranged from 0.01 to 3.00 min, and the baseline level was 1000. The MS2 scan pairing was 0.2 Da and the retention time range was 0.1 min. The isotopic peak group was deisotoped with a m/z tolerance of 0.0 m/z and 10.0 ppm, retention time tolerance of 0.1 min and maximum charge of 3. Alignments were established by a join aligner with a m/z tolerance of 0.0 m/z and 10.0 ppm and a retention time tolerance of 0.1 min. After peak filtering, gap filling was prepared for 10% intensity tolerance. Then, the MZmine project was exported as.mzXML files. These data were submitted to the online platform at the Global Natural Product Social Molecular Networking website (gnps.ucsd.edu) to generate the molecular network with edges that were filtered to have a cosine score above 0.65 and more than 6 matched peaks. The parameters include the parent ion mass tolerance (0.02 Da), fragment ion mass tolerance (0.5 Da), and a minimum cluster size of 1. The MS/MS spectra of the compounds were compared pairwise to find similarities in fragmentation pathways, i.e., the same fragment ions or similar neutral losses. The molecules presenting similar fragmentation patterns were grouped in the same cluster, while the molecules with different MS/MS spectra were not associated. Once the clusters had been built, the molecular family of the associated compounds could be determined. The resulting molecular network was constructed using the Cytoscape 3.7.1 program to allow more approachable visual exploration of the detectable metabolite profile in a crude extract and the correlation of standard compounds with their analogues. The results of GNPS could be accessed at http://gnps.ucsd. edu/ProteoSAFe/status.jsp?task=6c07217182fa4f14951955c85dc6e b30.