MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/m_MTBLS14441_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/m_MTBLS14441_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/a_MTBLS14441_LC-MS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/a_MTBLS14441_LC-MS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441/s_MTBLS14441.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14441<p>Feature detection and metabolite annotation were performed using Progenesis QI software (Waters Corporation, Milford, USA). The LC-MS/MS data were processed to detect and align metabolic features, including retention time, accurate mass, peak intensity, isotope information, and MS/MS fragmentation spectra. Metabolite annotation was performed by matching the detected features against public and in-house reference databases, including HMDB, METLIN, KEGG, and the Majorbio in-house metabolite database.</p><p>Metabolites were annotated based on accurate mass, isotope distribution, retention behavior, and MS/MS fragmentation patterns when available. KEGG and HMDB were further used for metabolite classification and pathway mapping. Positive and negative ion mode datasets were processed and annotated separately, and the annotated metabolite information was used for downstream statistical and pathway enrichment analyses.</p>MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phase<p>Chromatographic separation was performed on a Vanquish Horizon system (Thermo Fisher Scientific, USA) using an ACQUITY UPLC HSS T3 column (100 mm x 2.1 mm i.d., 1.8 um; Waters, Milford, MA, USA). The column was operated in reverse-phase mode. For negative ion mode analysis, mobile phase A consisted of water containing 5 mM ammonium acetate, and mobile phase B was acetonitrile. The gradient elution program was as follows: 0-1 min, 2% B; 1-9 min, 2-98% B; 9-12 min, 98% B; 12-12.1 min, 98-2% B; 12.1-15 min, 2% B. The column temperature was maintained at 40 C, the flow rate was 0.30 mL/min, and the injection volume was 2 uL.</p>Metabolomic profiling of Streptomyces coelicolor overexpressing the alpha subunit of acyl-CoA carboxylase.Northwest Institute of Eco-Environment and ResourcesShiyu WuWhole Organismmass spectrometry assay<p>Metabolites were extracted from the collected Streptomyces mycelial samples using an organic solvent-based extraction procedure before LC-MS/MS analysis. Briefly, frozen samples were thawed on ice, homogenized, and extracted with pre-cooled extraction solvent. After vortexing, sonication, and centrifugation, the supernatant was collected for metabolomic analysis. The extracts were dried or concentrated when required and then reconstituted in the appropriate solvent prior to LC-MS/MS injection.</p><p>Quality control samples were prepared by pooling equal aliquots from all biological samples and were used to monitor instrument stability and data reproducibility during the analysis. Solvent blank samples were also included to evaluate background signals and potential contamination. Standard or reference samples were used when required for instrument calibration and metabolite identification.</p>Streptomyces ambofacienshttps://www.ebi.ac.uk/metabolights/MTBLS14441Shiyu Wu. Northwest Institute of Eco-Environment and Resources. wushiyu23@mails.ucas.ac.cn.<p>Raw LC-MS/MS data were processed using Progenesis QI software (Waters Corporation, Milford, USA). Peak detection, peak extraction, peak alignment, and peak integration were performed to generate the initial feature matrix. Metabolite annotation was carried out by matching the detected features against public and in-house databases, including HMDB, METLIN, KEGG, and the Majorbio in-house database.</p><p>To reduce technical variation introduced during sample preparation and instrumental analysis, the annotated data were preprocessed before downstream analysis. Features with more than 20% missing values within each group were removed. The remaining missing values were imputed using the minimum value observed across all samples. Peak intensities were normalized using the total sum normalization method to generate a normalized data matrix. Variables with a relative standard deviation greater than 30% in quality control samples were removed, and the data were then log10-transformed to obtain the final matrix for statistical analysis.</p><p>Multivariate statistical analyses, including PCA and OPLS-DA, were performed using the ropls package in R (version 1.6.2). Metabolite annotation and pathway mapping were performed using HMDB and KEGG databases. Pathway enrichment analysis was conducted using the scipy.stats package in Python.</p>Genotypewushiyu23@mails.ucas.ac.cn<p><em>Streptomyces ambofaciens</em> CGMCC 4.1528 and the corresponding accA-overexpressing strain were used in this study. Seed cultures were transferred into fermentation medium and cultivated for 48 h. Samples were collected at the 48 h fermentation time point to investigate metabolite changes associated with overexpression of the alpha subunit of acyl-CoA carboxylase. The mycelial biomass was harvested by centrifugation, rapidly frozen, and stored at -80 ℃ until metabolite extraction and LC-MS/MS analysis.</p>Metabolomicspooled quality control sampleMetabolomicsStreptomyces ambofacienscomparative genome hybridization by array designThermo Scientific Orbitrap Exploris 240untargeted analysisThermo Scientific Vanquish Flex UHPLC Systemexperimental blankgenotype designWhole Organismexperimental sampleuntargeted metabolite profilingpooled quality control sampleMetabolomicsStreptomyces ambofaciensThermo Scientific Orbitrap Exploris 240comparative genome hybridization by array designuntargeted analysisThermo Scientific Vanquish Flex UHPLC Systemexperimental blankgenotype designWhole Organismuntargeted metabolite profilingexperimental sample<p>Mass spectrometric analysis was performed on an Orbitrap Exploris 240 mass spectrometer (Thermo Fisher Scientific, USA) equipped with an electrospray ionization source. Data were acquired in positive ion mode over an m/z range of 50-1050. Standard electrospray ionization settings were used for untargeted metabolomic profiling, including optimized spray voltage, ion transfer tube temperature, vaporizer temperature, sheath gas flow, auxiliary gas flow, and collision energy settings.</p>falseMetabolomic profiling of Streptomyces ambofaciens overexpressing the alpha subunit of acyl-CoA carboxylase<p>This study contains metabolomics data from Streptomyces ambofaciens CGMCC 4.1528 overexpressing the alpha subunit of acyl-CoA carboxylase. The data were generated to investigate metabolite changes associated with alpha subunit overexpression and to explore its effects on primary metabolism, acyl-CoA precursor supply, and polyketide biosynthesis.</p>2026-05-062026-05-06MTBLS14441