Using Non-Target Deconvolution algorithm (NTD) in ChromaTOF software – v5.51.06 [41], overlapped peaks were deconvoluted and the peaks were identified by comparing the mass spectra with NIST library and in-house library database. The minimum signal-to-noise (S/N) ratio and minimum similarity for matching were set to 300 and 500, respectively. An alkane scale retention index method was applied to calculate the retention index of each identified peak. The processed data were then exported to mzML format.
"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["For intracellular metabolite extraction, a 1:1 (v/v) solution of acetonitrile and water, spiked with 1 μM adonitol as an internal standard, was used as the extraction solvent. To the tube containing the dried cell pellet, 100 mg of glass beads (425 - 600 μm) and 1 mL of extraction solvent were added. The tube was tightly sealed and vortexed vigorously for 2 min to disrupt the cell wall and extract intracellular metabolites. Following vortexing, the sample was centrifuged at 12,000 rpm for 2 min at 4 °C, and 800 μL of the resulting supernatant containing intracellular metabolome was transferred to a new microtube. For subsequent derivatization, the metabolite solution was completely dried in a centrifugal evaporator CVE-3000 (Eyela, Japan) at 4 °C for 6 to 8 hours. The dried sample was subjected to two-step derivatization to enhance volatility and improve detection sensitivity prior to GC×GC-TOF/MS system (Pegasus BT 4D, LECO, USA) analysis. For methoximation, 10 μL of methoxyamine hydrochloride in pyridine (20 mg/mL) was added to the sample and incubated at 1,000 rpm for 90 min at 30 °C. This was followed by silylation, achieved by adding 90 μL of N-Methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) and reacting at 1,000 rpm for 30 min at 37 °C. The derivatized samples were transferred to glass vials and analyzed using a GC×GC-TOF/MS system (Pegasus BT 4D, LECO, USA) operated in 1D GC mode for GC×GC setup.
"],"organism":["Megasphaera hexanoica"],"data_transformation_protocol":["The provided dataset corresponds to pre-statistical analysis data, and no data transformation was applied.
"],"study_factor":["Treatment"],"metabolights_link":["https://www.ebi.ac.uk/metabolights/MTBLS14019"],"submitter_email":["psn43@hanyang.ac.kr"],"sample_collection_protocol":["For intracellular metabolite analysis, M. hexanoica KCCM 43214T was cultured in a medium containing fructose and lactate and incubated at 37 °C with 150 rpm. Upon reaching the mid-exponential growth phase, a sample containing 0.5 mg of CDW was used for intracellular metabolome extraction. Immediately after sampling, cellular metabolism was quenched by mixing the sample with an equal volume of prechilled saline solution. The mixture was centrifuged at 12,000 rpm for 2 min under 4 °C, and the supernatant was discarded. The resulting cell pellet was resuspended in saline solution to remove extracellular metabolites, followed by centrifuging again under the same condition and subsequent removal of the supernatant. The cell pellet was dried for 2 hours at 4 °C using a centrifugal evaporator CVE-3000 (Eyela, Japan) and stored at -80 °C until further metabolome extraction.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"omics_type":["Metabolomics"],"instrument_platform":["Gas Chromatography MS - positive"],"study_design":["LECO Pegasus BT TOFMS","gas chromatography-mass spectrometry","untargeted analysis","Megasphaera hexanoica","LECO Pegasus BT 4D GCxGC-TOFMS","targeted metabolite profiling","endometabolome","untargeted metabolite profiling"],"chromatography_protocol":["A DB-5MS UI capillary column (30 m × 0.25 mm i.d., 0.25 μm film thickness; Agilent, USA) was utilized as the primary column, while an Rxi-17Sil MS column (1 m × 0.25 mm i.d., 0.25 μm film thickness; Restek, USA) was employed as the secondary column in the series. Helium was used as the carrier gas at a constant flow rate of 1 mL/min. A volume of 1 μL was injected in splitless mode, with an inlet purge time of 30 seconds. The inlet temperature was set at 250 °C. The oven temperature program began at 50 °C (held for 1 min), increased to 320 °C at a rate of 20 °C/min, and was held at 320 °C for 6.5 min. The secondary oven temperature was maintained at 5 °C above the main oven temperature throughout the analysis, and the transfer line temperature was maintained at 280 °C.
"],"publication":["High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214ᵀ."],"curator_keywords":["gas chromatography-mass spectrometry","LECO Pegasus BT TOFMS","untargeted analysis","Megasphaera hexanoica","targeted metabolite profiling","LECO Pegasus BT 4D GCxGC-TOFMS","endometabolome","untargeted metabolite profiling"],"submitter_affiliation":["Hanyang University"],"submitter_name":["Pranav Sasidharan Nair"],"mass_spectrometry_protocol":["Mass spectra were acquired after a solvent delay of 385 seconds, scanning a mass range of 50 – 500 m/z at an acquisition rate of 20 spectra per second. To establish a retention index reference, a mixture of C7 – C30 saturated alkanes was analyzed under the same conditions. Additionally, various standard compounds, including amino acids, sugars, and organic acids, were derivatized and analyzed to build an in-house spectral library.
"],"additional_accession":[]},"is_claimable":false,"name":"High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214T","description":"Megasphaera hexanoica KCCM 43214T, isolated from cow rumen, is capable of producing medium-chain carboxylic acids such as n-caproate and n-caprylate. In this study, we present a high-quality genome assembly, along with intracellular metabolomic profiling and pangenomic analysis. Illumina sequencing generated 2.3 Mbp from 15,293,634 reads with a GC content of 49.5%, while PacBio HiFi sequencing produced 331.5 Mbp across 45,266 reads, with an average read length of 7,323 bp and a HiFi read N50 of 8,214 bp. Hybrid assembly of short and long reads resulted in a single 2.88 Mbp contig, containing 2,075-2,083 unique genes. A genome-scale metabolic model was constructed, to evaluate its metabolic capabilities under specific growth conditions. Intracellular metabolomic analysis of cells grown in fructose medium and lactate medium revealed key metabolic activities associated with chain elongation. Pangenomic analysis across nine annotated genomes identified 6,721 orthologous gene using OrthoMCL, emphasizing the genetic and functional diversity within the Megasphaera genus. This dataset offers valuable insights into the metabolism and biotechnological potential of M. hexanoica KCCM 43214T.
","dates":{"publication":"2026-04-03","submission":"2026-03-10"},"accession":"MTBLS14019","cross_references":{}}