MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/m_MTBLS13506_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/m_MTBLS13506_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/a_MTBLS13506_LC-MS_positive_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/a_MTBLS13506_LC-MS_negative_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/s_MTBLS13506.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506/i_Investigation.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13506Identification of metabolites was based on the accurate precursor ions, product ions, retention times and fragmentation patterns of primary and secondary mass spectra. Three levels of metabolite annotation were set based on previous studies. MultiQuant v3.0.2 (AB Sciex) was used for MRM-based quantification of metabolites. The signal intensities of characteristic ions were obtained for each metabolite in the samples, and their chromatographic peak areas were integrated to indicate the metabolite’s relative abundance. The peak areas were corrected with retention time and peak type to facilitate quantitative comparisons of metabolites between samples. PCA was performed to analyse the differences in metabolite composition using R v4.3.2. DAMs were identified based on fold-change 1.5 and P < 0.05 (two-sided Student’s t-test). Functional pathway enrichment analysis of DAMs was performed using the KEGG database (https://www.genome.jp/kegg/).MetaboLightsPublicLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - negative - hilicChromatographic separation was performed on a Nexera X2 UPLC system (Shimadzu, Kyoto, Japan) equipped with a Zorbax SB-C18 column (1.8 μm, 2.1 mm × 100 mm; Agilent, Foster City, CA, USA). The mobile phase consisted of pure water with 0.1 % formic acid (solvent A) and acetonitrile with 0.1% formic acid (solvent B). Gradient elution started at 95% A, linearly changed to 5% A at 9 min and held for 1 min, then ramped to 95% A in 1.1 min and held for 2.9 min. The column oven temperature was 40°C, the flow rate was set to 0.35 mL min-1 and the injection volume was 4 μL.widely targeted metabolomic analysis.Northwest A&F UnversityWenjiang FuBacterialFruitmass spectrometryMetabolite extraction from bacterial cultures and tomato fruits was performed with a solvent containing methanol, acetonitrile and water (2:2:1, v/v/v). Briefly, a 100-mL culture or 100-mg fruit sample was mixed with 800 µL of the extraction solvent by vortexing for 30 s and then homogenized in a grinding mill at 60 Hz for 4 min. The mixture was ultrasonically shaken in an ice-water bath for 10 min and incubated at -20°C for 2 h, followed by centrifugation at 12 000 ×g for 15 min. The supernatant (600 µL) was vacuum concentrated and then re-dissolved in 50 µL of acetonitrile-water mixture (1:1, v/v).Solanum lycopersicumLysobacter sp.https://www.ebi.ac.uk/metabolights/MTBLS13506Hangxian Lai. Northwest A&F unversity. laihangxian@163.com.Wenjiang Fu. Northwest A&F unversity. fuwenjiang@nwafu.edu.cn.Triple quadrupole scans were acquired by MRM assays with collision gas (nitrogen) set to medium. Declustering potential and collision energy for individual MRM transitions were further optimized. A specific set of MRM transitions were monitored for each period according to the metabolites eluted within this period. Mass spectra were collected and processed using Analyst v1.6.3 (AB Sciex, Foster City, CA, USA). The obtained mass spectra were matched against the public database HMDB9 if the standards were unavailable, or against the self-built database MWDB (Metware Biotechnology Co., Ltd.) if the standards were available.Groupfuwenjiang@nwafu.edu.cnSingle colonies of bacteria were cultured in BEP medium with and without treatment for 16 h. Samples from three fresh BEP mediums were collected as one biological replicate, with three biological replicates per treatment. Fruit samples from three pots (one plant per pot) were collected as one biological replicate, with three biological replicates per treatment.MetabolomicsBacterialFruitTomatoBacterialFruitTomatoThe effluent was alternatively introduced into an UPLC-QQQ LIT-MS/MS system (AB4500 Q-TRAP; Applied Biosystems, Framingham, MA, USA) equipped with an ESI turbo ion-spray interface. The ESI ion source was operated at a temperature of 550°C. The ESI ion source was operated with the following parameters: ion source, turbo spray; temperature, 550 C; spray voltage, 5500 V (positive ion mode) / –4500 V (negative ion mode); gas I, 50 psi; gas II, 60 psi; curtain gas, 25.0 psi; and collision-activated dissociation, high. Instrument tuning and mass calibration were performed with 10 and 100 μmol/L polypropylene glycol solutions in triple quadrupole and linear ion trap modes, respectively. Triple quadrupole scans were acquired by MRM assays with collision gas (nitrogen) set to medium.falsewidely targeted metabolomic analysisBased on widely targeted metabolomic analysis, we explored the differences in metabolite composition and content of tomato fruits with different genotypes or exogenous metabolites were added. In addition, we also investigated the effects of different treatments on the composition and content of bacterial metabolites.2025-12-142025-12-14MTBLS13506