Convert the original mass spectrometry raw files to mzXML file format using the MSConvert tool in the Proteowizard software package. Then, using the RXCMS software package, adjust the parameters to bw = 2, ppm = 15, peakwidth = c(5, 30), mzwid = 0.015, mzdiff = 0.01, method = centWave, and subsequently perform peak detection, peak filtering, and peak alignment to obtain the quantitative results of substances. Then, perform substance identification, set ppm < 30 ppm, and use databases such as HMDB, MassBank, LipidMaps, mzCloud, and KEGG for substance identification.
"],"disease":[""],"extraction_protocol":["Sample Extraction:
(1) Accurately weigh 0.1 g of seeds, mix with 600 μL of methanol (containing 2-chloro-L-phenylalanine at 4 ppm) in a 2 mL centrifuge tube, and shake for 30 s;
(2) Add glass beads, place in an ultrasonic grinder, and grind at 60 Hz for 90 s;
(3) Treat at 40 Hz in an ultrasonic instrument for 15 min;
(4) Remove and place in a centrifuge, centrifuge at 12,000 rpm, 4°C for 10 min, collect the supernatant, filter through a 0.22 μm membrane, place in a detection vial, and wait for analysis.
"],"organism":["Polygonatum sibiricum"],"data_transformation_protocol":["Convert the original mass spectrometry raw files to mzXML file format using the MSConvert tool in the Proteowizard software package. Then, using the RXCMS software package, adjust the parameters to bw = 2, ppm = 15, peakwidth = c(5, 30), mzwid = 0.015, mzdiff = 0.01, method = centWave, and subsequently perform peak detection, peak filtering, and peak alignment to obtain the quantitative results of substances. Then, perform substance identification, set ppm < 30 ppm, and use databases such as HMDB, MassBank, LipidMaps, mzCloud, and KEGG for substance identification.
"],"study_factor":["Germination stage"],"submitter_email":["2077655532@qq.com"],"metabolights_link":["https://www.ebi.ac.uk/metabolights/MTBLS14022"],"sample_collection_protocol":["The experimental material was Polygonatum from the experimental base in Lüyang County of the National Engineering Laboratory for the Development of Endangered Medicinal Resources in Northwest China (33°31′25″ N, 106°11′38″ E, 955.4 m elevation). Seeds with optimal sand storage conditions (GA3 concentration 129 mg/L, temperature 4°C, sand storage substrate a volumetric mixture of yellow ginger soil and sand) were sampled at 0, 30, 60, 90, and 105 days and then stored in a -80°C freezer. They were used for RNA-seq analysis and LC-MS analysis. Three biological replicates were collected at each stage.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"omics_type":["Metabolomics"],"instrument_platform":["Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - negative - hilic"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","Multi-omics study","untargeted metabolite profiling"],"chromatography_protocol":["The liquid chromatography system used was the Thermo Vanquish (Thermo Fisher Scientific, USA) ultra-high performance liquid chromatography system. The column used was ACQUITY UPLC® HSS T3 (2.1×150 mm, 1.8 µm) (Waters, Milford, MA, USA), with an injection volume of 2 μL, column temperature of 40 ℃, and flow rate of 0.25 mL/min. In positive ion mode, mobile phase C was 0.1% formic acid in acetonitrile and D was 0.1% formic acid in water, with the gradient elution program as follows: 0–1 min, 2% C; 1–9 min, 2%–50% C; 9–12 min, 50%–98% C; 12–13.5 min, 98% C; 13.5–14 min, 98%–2% C; 14–20 min, 2% C. In negative ion mode, mobile phase A was acetonitrile and B was 5 mM ammonium formate in water, with the program as follows: 0–1 min, 2% A; 1–9 min, 2%–50% A; 9–12 min, 50%–98% A; 12–13.5 min, 98% A; 13.5–14 min, 98%–2% A; 14–17 min, 2% A.
"],"publication":["Analysis of seed germination attributes and kinetics of Polygonatum sibiricum Red. through metabolomics and transcriptomics."],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","Multi-omics study","untargeted metabolite profiling"],"submitter_name":["Xiaoqi Zhang"],"submitter_affiliation":["Shaanxi Normal University"],"mass_spectrometry_protocol":["The instrument used was the Thermo Q Exactive HF-X mass spectrometer (Thermo Fisher Scientific, USA) with an electrospray ionization source, operating in both positive and negative ionization modes. The positive ion spray voltage was 3.50 kV, and the negative ion spray voltage was -2.50 kV. The capillary temperature was set at 325 ℃, with auxiliary and sheath gases at 10 arb and 30 arb, respectively. The resolution for full MS scan was 60,000, with an ion scan range of m/z 81~1000. Through HCD secondary fragmentation, the resolution was 15,000 with a voltage of 30%, and the top eight ions based on signal were selected for fragmentation, with dynamic background exclusion.
"],"additional_accession":[]},"is_claimable":false,"name":"Analysis of seed germination attributes and kinetics of Polygonatum sibiricum Red. through metabolomics and transcriptomics","description":"Polygonatum sibiricum Red. (P. sibiricum) seeds exhibit strong dormancy, which prolongs germination period, reduces germination rate, and thus hinders its production. Research on breaking seed dormancy via optimized sand storage and clarifying germination-related mechanisms is insufficient. This study focused on optimizing sand storage conditions of P. sibiricum seeds and analyzing their biological traits, enzyme gene expressions, and metabolic changes to elucidate germination kinetics.
","dates":{"publication":"2026-03-24","submission":"2026-03-11"},"accession":"MTBLS14022","cross_references":{}}