MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/m_MTBLS13602_GC-MS_positive__metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/a_MTBLS13602_LC-MS_GC-MS_positive__metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/s_MTBLS13602.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260981b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/H21260978b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A22000733b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260971b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260972b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260979b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260982b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260969b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260973b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A22000730b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260977b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260980b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260970b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/H21260968b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/H21260967b.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602/FILES/DERIVED_FILES/A21260966b.mzMLprimary200OKftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13602<p>Identification was based on reference standard methods. All target analytes (13 sugars and sugar alcohols) were known compounds, and high-purity reference standards were provided prior to the start of the project. Standard solutions of each target compound were individually injected and analyzed under identical instrument conditions. For each reference standard, its chromatographic retention time (RT) on the specific column and its characteristic ions detected in Selected Ion Monitoring (SIM) mode were recorded to establish a reference library. During actual sample analysis, detected chromatographic peaks were compared with the established reference library. A peak was identified as the corresponding target metabolite only when both of the following conditions were met simultaneously: the retention time of the peak in the sample matched the RT of the reference standard within an acceptable tolerance window; and in SIM mode, the sample peak exhibited responses across all predefined characteristic ion channels, with ion abundance ratios consistent with those of the reference standard. Following successful qualitative identification, absolute quantification was performed using an external standard method.</p>MetaboLightsPublicGas Chromatography MS - positive<p>Dried and derivatized plant tissue extracts were analyzed using an Agilent 8890 gas chromatograph equipped with a DB-5MS capillary column (30 m × 0.25 mm × 0.25 μm). Separation was achieved under a programmed temperature gradient from 170°C to 310°C, with helium as the carrier gas at a constant flow rate of 1.0 mL/min. Samples were injected in split mode (5:1 ratio). This chromatographic method effectively resolved 13 trimethylsilylated sugar derivatives prior to selective ion monitoring (SIM) detection by mass spectrometry.</p>Recreating viable YYh genotype uncovers the role of CpYYL underlying YY lethality in papaya.Yiting ZhuangFujian Agriculture and Forestry UniversityOvulemass spectrometry<p _msttexthash='57622084' _msthash='1674'>Sample Preparation and Derivatization Protocol for GC-MS Analysis</p><p _msttexthash='57622084' _msthash='1674'>Lyophilization: Biological samples were freeze-dried under vacuum to remove moisture.</p><p _msttexthash='57622084' _msthash='1674'>Grinding: The dried samples were ground into a homogeneous powder using a grinding mill (30 Hz, 1.5 min).</p><p _msttexthash='57622084' _msthash='1674'>Extraction: Exactly 20 mg of the powder was weighed and extracted with 500 μL of a methanol: isopropanol: water (3:3:2, v/v/v) mixture. The mixture was vortexed for 3 minutes, followed by ultrasonication in an ice-water bath for 30 minutes.</p><p _msttexthash='57622084' _msthash='1674'>Clean-up and Internal Standard Addition: The extract was centrifuged at 14,000 rpm for 3 minutes at 4°C. A 50 μL aliquot of the supernatant was transferred, and 20 μL of a ribitol internal standard solution (1,000 μg/mL) was added. The mixture was dried under a stream of nitrogen and then further dried in a freeze dryer.</p><p _msttexthash='57622084' _msthash='1674'>Derivatization:</p><p _msttexthash='57622084' _msthash='1674'>Methoximation: 100 μL of methoxyamine hydrochloride in pyridine (15 mg/mL) was added to the dried residue. The mixture was incubated at 37°C for 2 hours to protect carbonyl groups (aldehydes/ketones).</p><p _msttexthash='57622084' _msthash='1674'>Silylation: Subsequently, 100 μL of BSTFA was added, and the mixture was incubated at 37°C for 30 minutes to derivative active hydrogen groups (e.g., -OH, -NH) into more volatile trimethylsilyl (TMS) ethers, yielding the final derivatization solution.</p><p _msttexthash='57622084' _msthash='1674'>Dilution and Vial Preparation for Injection: A 50 μL aliquot of the derivatization solution was diluted to 1 mL with n-hexane. After mixing, the solution was transferred into an amber glass autosampler vial for GC-MS analysis.</p>Papayahttps://www.ebi.ac.uk/metabolights/MTBLS13602Ray Ming. Fujian Agriculture and Forestry University. Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China. rayming@illinois.edu.Jingjing Yue. Fujian Agriculture and Forestry University. Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China. jingjingyue11@126.com.<p>1. Overview of the Data Transformation Workflow</p><p>The data transformation pipeline for this project was designed for targeted quantitative analysis of gas chromatography-mass spectrometry (GC-MS) data. The primary objective was to process the raw instrument signals through a series of standardized steps to generate a final data table containing the absolute concentrations of 13 target sugars in each sample.</p><p>2. Main Processing Steps and Methods</p><p>Data Acquisition and Generation: Raw data were acquired in Selected Ion Monitoring (SIM) mode using an Agilent 8890-5977B GC-MS system and stored in the Agilent proprietary data format (.D files).</p><p>Peak Detection and Integration: Raw data files were imported into data processing software for automated peak detection, identification, and integration. This step determined the retention time window, peak area, and peak height for each target compound and its corresponding internal standard (ribitol), based on known retention times and characteristic ions listed in ion_component.xlsx.</p><p>Internal Standard Calibration: To correct for variations in sample preparation and instrument performance, the peak area of each target analyte was normalized against the peak area of the internal standard (ribitol), yielding a peak area ratio.</p><p>Quantitative Calculation: The normalized peak area ratios were applied to pre-established external standard calibration curves for quantification. Calibration curves were constructed using standard solutions at known concentrations, with linear equations, correlation coefficients (R²), and quantitative ranges documented in equation.xlsx. This step converted the instrument response into absolute concentrations (µg/mL) for each compound.</p><p>Unit Conversion and Final Output: The calculated concentrations were converted to biologically relevant units (e.g., mg/g dry weight) based on sample weight, extraction volume, and dilution factors used during sample preparation. The final results were compiled into a comprehensive data matrix, delivered as the *.levels.xlsx file series.</p><p>3. Software Used</p><p>Data Acquisition Software: Agilent MassHunter or ChemStation (specific version not stated in the report) was used for instrument control and raw data generation.</p><p>Data Processing and Quantification Software: Data processing was performed using a combination of:</p><p>Vendor Software: The Agilent MassHunter Quantitative Analysis module was likely used for raw data peak integration, calibration curve fitting, and concentration calculation.</p><p>Internal Platform: MetWare employed its proprietary analysis platform or custom scripts for batch processing, calibration curve integration, internal standard normalization, unit conversion, and generation of standardized report files.</p>Ovule growth timeGenderzhuang-yt@qq.com<p>Fresh papaya ovules were collected from the Fujian Agriculture and Forestry University Yongchun Base, immediately frozen with liquid nitrogen, and then freeze-dried. The dried material was ground into fine powder using a grinder (MM 400, Retsch) with zirconium beads at a frequency of 30 Hz for 1.5 minutes. Approximately 20 mg of the powder was extracted with 500 μL of methanol:isopropanol:water (3:3:2, v/v/v). The mixture was vortexed for 3 minutes, sonicated for 30 minutes, and then centrifuged at 14,000 rpm at 4°C for 3 minutes. A 50 μL aliquot of the supernatant was transferred and mixed with 20 μL of an internal standard solution (ribitol, 1000 μg/mL). The mixture was dried under a gentle stream of nitrogen and then freeze-dried to complete dryness. The dried residue was subjected to a two-step derivatization procedure. First, it was mixed with 100 μL of methoxyamine hydrochloride (15 mg/mL) in pyridine and incubated at 37°C for 2 hours for oximation. Subsequently, 100 μL of BSTFA containing 1% TMCS was added. After vortexing, the mixture was further incubated at 37°C for 30 minutes for trimethylsilylation. Finally, the derivatized samples were diluted with an appropriate volume of solvent prior to GC-MS analysis.</p>Metabolomicsgas chromatography-mass spectrometrysugartargeted metabolitesgas chromatography-mass spectrometrysugartargeted metabolites<p>Instrument Model and Manufacturer:</p><p>Instrument: Agilent 8890 Gas Chromatograph coupled with a 5977B Mass Spectrometer (GC-MS)</p><p>Manufacturer: Agilent Technologies</p><p>Ion Source: Electron Ionization (EI)</p><p>Ionization Mode: Positive ion mode</p><p>Scan Mode: Selected Ion Monitoring (SIM). In SIM mode, the system monitors only specific characteristic ions for the 13 target sugar compound derivatives and the internal standard (ribitol).</p><p>Oven Temperature Program:</p><p>The initial temperature was held at 170°C for 2 minutes, then increased at 10°C/min to 240°C, followed by a further increase at 5°C/min to 280°C, and finally ramped at 25°C/min to 310°C, where it was held for 4 minutes. The total duration was approximately 19.5 minutes.</p><p>Transfer Line Temperature: 240°C</p><p>Ion Source Temperature: 230°C</p><p>Quadrupole Temperature: 150°C</p><p>Ionization Voltage (Electron Energy): 70 eV</p><p>Carrier Gas: Helium</p><p>Column Flow Rate: 1.0 mL/min</p><p>Scan Rate: Not applicable in SIM mode.</p>D-SorbitolD-ArabinoseL-RhamnoseInositolD-FructoseSucroseTrehaloseL-FucoseGlucoseMaltoseXylitolLactoseD-GalactosefalseTargeted Profiling of 16 Sugars in Papaya Samples<p>Sugar contents were detected using GC-MS analysis in ovules at different developmental stages of Zhongbai female and hermaphrodite plants.</p>2026-01-062026-01-05MTBLS13602C00089C01083C00243C00208C00216C10906C01019C00124C00031C00137C00507C00794C00379