GNPS MS Self Service Metabolomics Spring 2024
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 6545 Q-TOF LC/MS
ORGANISM(S): Camellia Sinensis (ncbitaxon:4442)
SUBMITTER: 
Claudia Boot
PROVIDER: MSV000094716 | GNPS | Wed May 08 08:59:00 BST 2024
REPOSITORIES: GNPS
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Project description: Not available
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Project description:Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
| S-EPMC8219731 | biostudies-literature
Project description:Keemun black tea is a fully fermented tea. These LC-MS data help us know the chemical diversity during processing of Keemun black tea.
| MSV000090278 | GNPS
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant. In the study presented here, two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were kept at 4°C for 4,12, 24 h, respectively, and 28°C for as control. These samples were used to acquire expression profiles of a total of 3,511 unique genes, leading to the successful construction of supervised
2015-05-14 | E-GEOD-53632 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal myometrial and fibroid samples. Uterine fibroids (leiomyomas) affect Black women disproportionately in terms of prevalence, incidence, and severity of symptoms. The causes of this racial disparity are essentially unknown. We hypothesized that myometria of Black women are more susceptible to developing fibroids and examined the transcriptomic and DNA methylation profiles of myometria and fibroids from Black and White women for comparison. Myometrial samples cluster by race in both their transcriptome and DNA methylation profiles, whereas fibroid samples only cluster by race in the latter. More differentially expressed genes (DEGs) were detected in the Black and White myometrial comparison than in the fibroid comparison. Leiomyoma gene set expression analysis showed four different clusters of DEGs, including a cluster with highest expression in Black myometrial samples and elevated in all fibroids. One of the DEGs in this group, VWF, was significantly hypomethylated at two CpG probes near a putative enhancer site in Black myometrial and in all fibroid samples compared with White myometrial samples, suggesting that VWF expression is responsive to DNA hypomethylation, a known stress response. These results suggest that the molecular basis for the disparity in fibroid disease between Black and White women could be found in the myometria before fibroid development and not in the fibroids themselves.
2022-09-21 | GSE207349 | GEO
Project description:Uterine fibroids (leiomyomas) affect Black women disproportionately in terms of prevalence, incidence, and severity of symptoms. The causes of this racial disparity are essentially unknown. We hypothesized that myometria of Black women are more susceptible to developing fibroids and examined the transcriptomic and DNA methylation profiles of myometria and fibroids from Black and White women for comparison. Myometrial samples cluster by race in both their transcriptome and DNA methylation profiles, whereas fibroid samples only cluster by race in the latter. More differentially expressed genes (DEGs) were detected in the Black and White myometrial comparison than in the fibroid comparison. Leiomyoma gene set expression analysis showed four different clusters of DEGs, including a cluster with highest expression in Black myometrial samples and elevated in all fibroids. One of the DEGs in this group, VWF, was significantly hypomethylated at two CpG probes near a putative enhancer site in Black myometrial and in all fibroid samples compared with White myometrial samples, suggesting that VWF expression is responsive to DNA hypomethylation, a known stress response. These results suggest that the molecular basis for the disparity in fibroid disease between Black and White women could be found in the myometria before fibroid development and not in the fibroids themselves.
2022-09-21 | GSE207209 | GEO
Project description:This study aims at assessing the capability of comparing and combining different instrumental platforms in an untargeted approach with a view of detecting chemical contaminants in food matrices at low levels. A strategy based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) and chemometrics has been applied on two different complex food contamination scenarios, with tea as study product. The first scenario aimed at mimic the presence of a dozen of contaminants at levels just above regulatory limits (i.e. 10 and 30 μg/kg); the second scenario, more complex, aimed at simulate the presence of several different contaminations at levels close to regulatory limits (10 μg/kg) in different samples. This work was carried on two LC-HRMS platforms (with respectively ToF and Orbitrap mass analyzer technologies), and a highly automated data treatment workflow was implemented to deal with data acquired on both platforms. The untargeted approach performed well on all scenarios (even the most complex) and analytical platforms. Performance comparison between LC-HRMS technologies was made possible thanks to a vendor-neutral data treatment process. </br><br/> Sub-samples of black tea (Keemun type, gross, China) were spiked at 10 µg/kg levels with two different spiking mixes: Three sub-samples were spiked with a pool of 11 contaminants (spiking mix n°1); and Three sub-samples were spiked with 3 others contaminants (malathion, OTA, BPS, spiking mix n°2). Samples were then extracted with a generic method and analyzed by LC-HRMS (in both positive and negative ionization modes) on two platforms (respectively Orbitrap and ToF to generate a total of four data sets. </br></br> Black tea spiked with contaminants is reported in the current study MTBLS772. </br> Green tea spiked with contaminants is reported in MTBLS771. </br><br/> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS771' target='_blank'><span class='label label-success'>MTBLS771</span></a>
2019-02-12 | MTBLS772 | MetaboLights
Project description:White tea is considered the least processed form of tea and is reported to have a series of potent bioactivities, such as antioxidant, anti-inflammatory, anti-mutagenic, and anti-cancer activities. However, the chemical composition of white tea and the dynamic changes of the metabolites during the manufacturing process are far from clear. In this study, we applied a nontargeted metabolomics approach based on ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to comprehensively profile the characteristic metabolites of white tea. There were significant differences in the content of amino acids, catechins, dimeric catechins, flavonol and flavone glycosides, and aroma precursors in white tea compared with green and black teas that were manufactured from the same fresh tea leaves. Furthermore, the dynamic changes of the metabolites in the tea samples with various withering durations of 0, 4, 8, 12, 16, 20, 24, 28, and 36 h were also profiled. To the best of our knowledge, this study offers the most comprehensive characterization of the metabolites and their changes in white tea.
2017-03-23 | MTBLS403 | MetaboLights
Project description:Dryopteris ramosa (family; Dryopteridaceae) has been reported for its medicinal importance in cancer, gastrointestinal disorders, and infections. The present study aimed to investigate the detailed phytochemical profile of D. ramosa and its cytotoxic potential using various cancer cell lines. The phytochemical profile of D. ramosa methanolic extract and its fractions were established by employing UHPLC-MS/MS and Global Natural Product Social (GNPS) molecular networking. Moreover, the cytotoxic activity of extract and fractions was evaluated against human liver (HepG-2) and prostate cancer (PC-3) cells using MTT assay. Overall, 18 compounds including flavonoids, flavonoid O-glycosides, isoflavone di-C-glycoside, flavanol, flavanone, rotenoid, phloroglucinol derivative, coumarin derivative, benzofuranone, abietic acid, and phenolic acid were observed as the major phytochemical bioactive constituents in the extract and fractions of D. ramosa. In MTT assay, chloroform fraction showed highest anti-proliferative activity against liver cancer cells (IC50 = 53.49 μg/mL) followed by n-hexane fraction (IC50 = 55.36 μg/mL), D. ramosa extract (IC50 = 85.67 μg/mL) and ethyl acetate (IC50 = 125.00 μg/mL) fraction. However, n-hexane and chloroform fractions presented maximum cytotoxic effect against prostate cancer cells with respective IC50 values of 214.53 and 281.47 μg/mL. Moreover, all the tested samples showed negligible toxicity against non-cancer (BHK-21) cells. The results indicated that D. ramosa is rich in flavonoids, phloroglucinol derivative, and phenolic acids and showed positive results in cytotoxic studies, especially against liver cancer. Therefore, it can be considered safe for the development of anticancer drugs, especially against liver cancer. Dryopteris ramosa; Dryopteridaceae; GNPS molecular networking; HepG-2 cells; PC-3 cells; UHPLC-MS/MS.
| S-EPMC9647349 | biostudies-literature
