MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/m_MTBLS14504_LC-MS_alternating_normal-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/m_MTBLS14504_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/s_MTBLS14504.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/a_MTBLS14504_LC-MS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504/a_MTBLS14504_LC-MS_alternating_normal-phase.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14504<p _msttexthash='32273813' _msthash='102868'>Substance identification uses spectral databases such as HMDB, MassBank, Metlin, MoNA, mzVault, KEGG, and self-built metabolite standard databases for search and comparison. All metabolites in the quantitative list are compared and matched with information such as fragment ions in the first and second-level spectra (MS1/MS2) in the databases to achieve metabolite identification and database identification number annotation.</p>MetaboLightsPublicLiquid Chromatography MS - positive - reverse-phaseLiquid Chromatography MS - alternating - normal-phase<p _msttexthash='32273813' _msthash='102673'>The flowrate was 0.3 mL/min, and the injection volumewas 2 L. For positive ion mode (ESI+), the mobile phases were (A2)-0.1% formic acid in waterand (B2) 0.1% formic acid in ACN. For negative ion mode (ESI-), the mobile phases were (A3)-5mM ammonium formate in water and (B3) ACN. The gradient program for both modes was: 0-1min, 8% B; 1-8 min, 8-98% B; 8-10 min, 98% B; 10-10.1 min, 98-8% B; 10.1-12 min, 8% B</p>Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Phallus rugulosus Revealed by Multi-Omics Integration.Northwest A&F UniversityMiao Liusoilmass spectrometry assay<p _msttexthash='32273813' _msthash='103047'>Sample metabolites were extracted using solvent extraction method with LC-MS grade acetonitrile as the main extractant. High-purity formic acid, ammonium formate and Milli-Q ultrapure water were used to prepare extraction solutions. After impurity removal and purification, the prepared sample solutions were suitable for UHPLC separation and ESI-MS detection, and could be directly injected for metabolic profiling analysis in both positive and negative ion modes.</p>composition of soilhttps://www.ebi.ac.uk/metabolights/MTBLS14504Li Minglei. Northwest A&F University. School of Soil and Water Conservation Science and Engineering, Northwest A&F University. liminglei1967@163.com.Miao Liu. lmmiao419@nwafu.edu.cn.<p _msttexthash='32273813' _msthash='102957'>This study used liquid chromatography-tandem mass spectrometry (LC-MS) to collect raw mass spectrometry data. The raw data were first converted to a standardized format using the MSConvert tool. During the conversion process, the peak centroiding function was enabled to centroid the original profile mass spectra, remove baseline noise and invalid signals, and uniformly calibrate mass accuracy and chromatographic retention time information, thereby converting raw data from different types of instruments into the common standard mzML format. After completing format standardization, the converted compliant data were imported into a metabolomics analysis platform to perform data alignment, peak identification, and construction of a quantitative matrix. Finally, they were organized into structured data files that could be used for subsequent bioinformatics analysis, ensuring throughout that no information was lost during the data conversion process and that mass spectrometry signals and chromatographic retention time information were complete and reliable, meeting requirements for data upload and public sharing.</p>Sampling locationlmmiao419@nwafu.edu.cn<p _msttexthash='32273813' _msthash='102620'>LC-MS grade acetonitrile (ACN) was purchased from Fisher Scientific (Loughborough, UK). Formic acid and ammonium formate were obtained from TCI (Shanghai, China) and Sigma-Aldrich (Shanghai, China), respectively. Ultrapure water was produced using a Milli-Q system (Millipore,Bedford, USA). Chromatographic separation was performed on a Vanquish UHPLC System(Thermo Fisher Scientific, USA) equipped with an ACQUITY UPLCR HSS T3 column (2.1 x 100mm, 1.8 um, Waters) maintained at 40-°C</p>MetabolomicsMulti-omics studypooled quality control sampleMetabolomicsBruker maXis II UHR-ToFAgilent 1200 Series HPLC Systemuntargeted analysiscomposition of soilsoilmicrobiomeuntargeted metabolite profilingBruker maXis UHR-ToFexperimental sampleMulti-omics studypooled quality control sampleMetabolomicsBruker maXis II UHR-ToFAgilent 1200 Series HPLC Systemuntargeted analysiscomposition of soilsoilmicrobiomeBruker maXis UHR-ToFuntargeted metabolite profilingexperimental sample<p>Mass spectrometry was performed on a Q Exactive instrument (Thermo Fisher Scientific) with an ESI source operating in Full MS ddMS2 (data dependent MS/MS) mode. Sheath gas pressure was 40 arb, aux gas flow 10 arb, spray voltage ±3.50/–2.50 kV, capillary temperature 325 °C, MS1 scan range m/z 100–1000, MS1 resolution 70,000 FWHM, MS/MS resolution 17,500 FWHM, normalized collision energy 30 eV, and dynamic exclusion automatic. Ten data dependent scans were acquired per cycle .</p>falseRhizosphere Microbiome Assembly and Metabolic Reprogramming in Phallus rugulosus Revealed by Multi-Omics IntegrationWe conducted non-targeted metabolomic analysis on the rhizosphere and non-rhizosphere soils of Phallus rugulosus, using LC-MS to quantify metabolites, and compared the data from both to determine the differences in metabolites between the rhizosphere and non-rhizosphere of Phallus rugulosus.2026-05-172026-05-17MTBLS14504