Metabolite annotation was performed by matching accurate mass and MS/MS spectra against public databases, including HMDB, MassBank, LipidMaps, mzClou, and KEGG, together with an in-house spectral library.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["For polar metabolite analysis, a Vanquish ultra-high-performance liquid chromatography (UHPLC) system (Thermo Fisher Scientific) was used. Chromatographic separation of target compounds was performed on a Waters ACQUITY UPLC BEH Amide column (2.1 mm × 50 mm, 1.7 μm). The mobile phase consisted of 25 mmol L-1 ammonium acetate and 25 mmol L-1 ammonium hydroxide in water as solvent A, and acetonitrile as solvent B.The autosampler was maintained at 4 °C, and the injection volume was 2 μL.
"],"publication":["Process-integrated engineered resting cells for biocatalytic production of rare natural sugars from sole methanol molecules."],"submitter_name":["Yujie Wang"],"submitter_affiliation":["University of Science and Technology of China"],"organism_part":["cell"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["The bacteria pellets (about 10^7 bacteria) were taken, mixed with 1000 μ L of extraction solution (MeOH:ACN:H2O, 2:2:1 (v/v)), the extraction solution contain deuterated internal standards, the mixed solution were vortexed for 30 s. Add 2 homogenization beads and homogenize for 4 min (35 Hz), then transferred to an ice-water bath to sonicate for 5 min. (Repeat 3 times) The samples were then allowed to thaw at room temperature and vortexed for 30 s. This freeze–thaw cycle was repeated three times.Then the samples were sonicated for 10 min in 4 ℃ water bath, and incubated for 1 h at -40 ℃ to precipitate proteins. The samples were centrifuged at 12000 rpm (RCF=13800(×g), R = 8.6cm) for 15 min at 4 ℃ . The supernatant was transferred to a fresh glass vial for analysis. The quality control (QC) sample was prepared by mixing an equal aliquot of the supernatant of samples.
"],"organism":["Escherichia coli"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14812"],"author":["Yujie Xiong. University of Science and Technology of China. yjxiong@ustc.edu.cn.","Yujie Wang. wangy9974@mail.ustc.edu.cn."],"data_transformation_protocol":["Raw mass spectrometry data files were converted to the mzXML format using the MSConvert tool in the ProteoWizard package (v3.0.8789). Peak detection, peak filtering, and retention time alignment were performed using the XCMS package in R, generating a quantitative metabolite feature table. To minimize batch effects and instrumental drift, signal intensities were corrected using a quality control (QC)-based locally weighted scatterplot smoothing (LOESS) normalization approach. Metabolite features with a relative standard deviation (RSD) greater than 30% in QC samples were excluded from further analysis.
"],"study_factor":["Methanol","Biological replicate"],"submitter_email":["wangy9974@mail.ustc.edu.cn"],"sample_collection_protocol":["To verify the effect of methanol to cellular metabolism of E. coli BL21(DE3) resting cells, resting cells were treated with 500 mM methanol at 30℃ for 2 h.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Orbitrap Exploris 122","Thermo Scientific Orbitrap Exploris 123","Metabolomics","Thermo Scientific Orbitrap Exploris 124","Thermo Scientific Orbitrap Exploris 125","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","Escherichia coli","Thermo Scientific Orbitrap Exploris 121","cell","untargeted metabolite profiling","Methanol treatment","Escherichia coli metabolism","Thermo Scientific Vaqn uish","experimental blank"],"curator_keywords":["Thermo Scientific Orbitrap Exploris 122","Thermo Scientific Orbitrap Exploris 123","Metabolomics","Thermo Scientific Orbitrap Exploris 124","Thermo Scientific Orbitrap Exploris 125","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","Escherichia coli","Thermo Scientific Orbitrap Exploris 121","cell","untargeted metabolite profiling","Methanol treatment","Thermo Scientific Vaqn uish","Escherichia coli metabolism","experimental blank"],"mass_spectrometry_protocol":["Mass spectrometry data were acquired using an Orbitrap Exploris 120 mass spectrometer operating under the control of Xcalibur software (version 4.4, Thermo Fisher Scientific) in both MS and MS/MS modes. The detailed instrument parameters were as follows: sheath gas flow rate, 50 Arb; auxiliary gas flow rate, 15 Arb; capillary temperature, 320 °C; full MS resolution, 60,000; MS/MS resolution, 15,000; stepped normalized collision energy (SNCE), 20/30/40; and spray voltage, 3.8 kV in positive ion mode and -3.4 kV in negative ion mode.
"],"additional_accession":[]},"is_claimable":false,"name":"Process-integrated engineered resting cells for biocatalytic production of rare natural sugars from sole methanol molecules","description":"The biocatalytic conversion of green methanol, a promising feedstock, into high value-added products is seen as an attractive way to establish sustainable biomanufacturing. Although natural and engineered microorganisms can utilize methanol, efficiently converting C1 carbon into valuable chemicals remains challenging because non-native pathways often suffer from low carbon utilization and limited catalytic stability. Here we show the integration of an engineered enzyme cascade into resting cells and its coupling with a screened alcohol oxidase enzyme to develop an efficient and stable enzyme-resting cell cascade system for methanol conversion, achieving customizable production of L-erythrulose (C4 sugar) or L-sorbose (C6 sugar).","dates":{"publication":"2026-06-22","submission":"2026-06-22"},"accession":"MTBLS14812","cross_references":{}}