Metabolite annotation was performed using the MS-DIAL library search by comparing experimental MS/MS spectra against multiple reference spectral databases, including BioMSMS-PlaSMA, GNPS, MassBank, MassBankEU, Fiehn HILIC, PlaSMA, CASMI2016, Respect, KI-GIAR HILIC, Vaniya-Fiehn Natural Products Library, and BMDMS Natural Product Library (Tsugawa et al., 2015, 2020; Wang et al., 2016; Horai et al., 2010). Annotation was based on accurate precursor m/z, retention time, adduct assignment, and MS/MS spectral similarity. Unless confirmed using authentic standards, metabolite identifications should be regarded as MSI Level 2 (Sumner et al., 2007; Salek et al., 2013).
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["The lower organic phase extracts of samples were analyzed on a reverse-phase liquid chromatography platform. The separation was performed using UHPLC system (Bruker, Germany). Bruker intensity solo HPLC C18 2.1 x 100 mm, 2 μm column (Bruker, Germany) was used. The column temperature was set at 40°C at and the autosampler temperature was set at 4°C. Mobile phase A consisted of 100% water with 0.1% formic acid (FA). Mobile phase B consisted of 100% acetonitrile with 0.1% FA. The flow rate was set to 0.35 ml/min. The elution gradient was as follows: 99% A (0.0-2.0 min, 0.25 ml/min), 1% A (2.0-20.0 min, 0.25 ml/min), 99% A (20.1-28.3 min, 0.35 ml/min), 99% A (28.5- 30.0 min, 0.25 ml/min). The injection volume of the sample was 2 μL, applied for both positive and negative ionization polarity mode.
"],"publication":["Comparative metabolomic profiling and biological activities of Zygostelma benthamii Baill. (apocynaceae): unveiling organ-specific antioxidant, anti-inflammatory, and cytotoxic potentials."],"submitter_name":["Alfandy Hermansyah"],"submitter_affiliation":["Khonkaen University"],"organism_part":["root","leaf","stem"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Weight 150 mg of the sample into a 2 mL tube containing 50 mg of glass beads. Add 800 μL of methanol and 170 μL of HPLC water. Homogenize the sample using a PowerLyzer™ 24 homogenizer (Qiagen, Germany) at 3500 rpm for 2 cycles, with each cycle lasting 45 sec and a pause of 30 sec between cycles. Centrifuge (DLAB high speed micro centrifuge, China) at 15,000 rpm for 15 min and repeat this step twice. Transfer approximately 200 μL of the supernatant to a microtube and add 400 μL of chloroform and 200 μL of HPLC water. Vortex the mixture. Incubate the tube on ice at 4°C and vortex for 20 minutes. Centrifuge the mixture at 4000 xg and 4°C for 20 minutes to separate the phases. Collect 500 μL of the aqueous phase using a pipette and transfer it to a 1.5 mL microtube. Remove the solvent using a vacuum concentrator at 40°C overnight until the sample is dry. Add reconstitution buffer (200 μL methanol: 200 μL HPLC water) to the dried sample. Transfer 200 μL of the supernatant to an HPLC glass vial for LC-MS data acquisition.
"],"organism":["Plant"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15042"],"author":["Thitiwan Jumpa. Khon Kaen University. thitiju@kku.ac.th.","Supanath Kanjanawattanawong. Khon Kaen University. supanath@kku.ac.th.","Alfandy Hermansyah. Khon Kaen University. alfandyhermansyah@gmail.com."],"data_transformation_protocol":["The raw LC–MS data acquired using a Bruker mass spectrometer (.d format) were processed using MS-DIAL (Tsugawa et al., 2015). Native Bruker files were imported directly into MS-DIAL for peak detection, MS1 deisotoping, peak alignment, gap filling, and feature table generation (Tsugawa et al., 2015). Signal drift correction was performed using QC-based LOWESS normalization to minimize analytical variation while preserving biological variation (Kirwan et al., 2013; Dunn et al., 2011; Broadhurst et al., 2018). The aligned peak matrix together with MS/MS information was exported for downstream statistical analysis.
"],"study_factor":["Organ"],"submitter_email":["alfandyhermansyah@gmail.com"],"sample_collection_protocol":["Plant samples were collected from the conservation forest in Khon Kaen Province, Thailand (16°28'14.9'N 102°49'02.3' E), and verified by a taxonomist from our colleague's team. The plant was separated into roots, stems, and leaves, rinsed with tap water to remove soil, wiped with multipurpose paper, and stored at −20 °C.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","Observational study","Comparative Study","untargeted analysis","Bruker ESI-Q-TOF","leaf","Bruker Elute UHPLC system","Bruker compact ESI-Q-TOF mass spectrometer","untargeted metabolite profiling","experimental sample","Plant","root","Derived Spectral Data File","stem"],"curator_keywords":["Metabolomics","Observational study","Comparative Study","untargeted analysis","Bruker ESI-Q-TOF","leaf","Bruker Elute UHPLC system","Bruker compact ESI-Q-TOF mass spectrometer","untargeted metabolite profiling","experimental sample","Plant","root","Derived Spectral Data File","stem"],"mass_spectrometry_protocol":["The mass spectrometry was performed using the broadband collisioninduced dissociation (bbCID) method by compact ESI-Q-TOF system (Bruker, Germany). Sodium formate solution (2 mM sodium hydroxide, 0.1 % FA, 50% isopropanol) was directly injected as an external calibrant with the flow rate of 0.5 μL/min. The condition in positive ionization polarity mode: mass range 50-1300 m/z, cone voltage 35V, capillary voltage 4000V, source temperature 220°C, desolvation temperature 220°C, desolvation gas flow of 8 L/min. The conditions in negative ionization polarity mode: m/z range: 50-1300 m/z, cone voltage 31V, capillary voltage 4500V, source temperature 220°C, desolvation temperature 220°C, desolvation gas flow of 8 L/min.
"],"additional_accession":[]},"is_claimable":false,"name":"Comparative metabolomic profiling and biological activities of Zygostelma benthamii Baill. (apocynaceae): unveiling organ-specific antioxidant, anti-inflammatory, and cytotoxic potentials","description":"Zygostelma benthamii has been prized for its medicinal properties and is similar to ginseng. However, the specific chemicals in its various parts and their relationship to its therapeutic effects have not been thoroughly researched. Thus, we used a comprehensive metabolomics approach, LC-MS/MS and GC-MS, to identify all chemicals in its leaves, stems, and roots and to evaluate its medicinal attributes. Metabolic activity differed significantly among plant parts. The leaves contained the highest concentrations of phenolic and flavonoid compounds and were far superior at neutralizing damaging free radicals (IC50 = 60.344 +/- 1.409 ug/mL). Specifically, the leaf extract significantly suppressed human colorectal cancer cells (Caco-2) with an IC50 of 0.735 +/- 0.119 mg/mL, which was 4.2 times more effective than the root extract. Conversely, the root extract was most potent at reducing inflammation (IC50 = 1.22 +/- 0.12 mg/mL), even exceeding the efficacy of diclofenac, thereby validating the plant's historic use in restoring health. Chemical analysis identified Vitexin in the leaves and Syringic acid and Eleutheroside E in the roots. These findings suggest that the different chemical compositions of each plant part contribute to their distinct biological activities. The results indicate that Zygostelma benthamii leaves are a stronger and more consistent source of compounds with antioxidant and anticancer activities. This research supports the traditional medicinal use of the plant and provides a link between traditional knowledge and modern scientific evidence.
","dates":{"publication":"2026-07-29","submission":"2026-07-15"},"accession":"MTBLS15042","cross_references":{}}