MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/m_MTBLS14865_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/m_MTBLS14865_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/a_MTBLS14865_LC-MS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/s_MTBLS14865.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865/a_MTBLS14865_LC-MS_positive_reverse-phase.txtprimary200OKftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14865<p>The features detected by the LC-MS platform were matched and annotated using Metabo-Profile's UlibMS database. Compound annotation was performed by comparing the mass-to-charge ratio, retention time, and adduct ion ratios against the database, along with proprietary algorithms based on standard rules. Among the feature peaks corresponding to different adduct forms of the same compound, only one major adduct form was retained to ensure stable and reliable data detection. At this stage, the average retention time and the average measured mass-to-charge ratio across samples within each group were used as the corresponding indices for feature matching.</p>MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phase<p>Chromatographic separation of polar metabolites was performed on an ACQUITY UPLC I-Class system (Waters Corporation, Milford, MA, USA) equipped with an ACQUITY UPLC HSS T3 column (1.8 μm particle size, 100 mm × 2.1 mm i.d., Waters Corporation, Milford, MA, USA). Mobile phase A consisted of 0.1% formic acid in water, and mobile phase B consisted of 0.1% formic acid in acetonitrile. The column temperature was maintained at 40 °C, the flow rate was 0.4 mL/min, and the injection volume was 3 μL. The gradient elution program was as follows: 0–1 min, 1% B; 1–11 min, linear ramp from 1% to 40% B; 11–13 min, 40% to 70% B; 13–15 min, 70% to 99% B; 15–18 min, hold at 99% B; 18–19 min, return to 1% B; 19–22 min, re-equilibration at 1% B. The total run time was 22 min.</p>A Clinical Urine Metabolomics Dataset for Urological Malignancies.Harbin Medical University Cancer HospitalZhenkun Dongurinemass spectrometry assay<p>Cryopreserved samples were thawed at room temperature and vortexed for 30 seconds. A 50 microL aliquot of urine was combined with 700 microL of ice-cold extraction solvent (methyl tert-butyl ether and methanol, 3:1, v/v) containing a mixture of internal standards, namely gibberellic acid A3 (0.45 microg/mL; Sigma-Aldrich, St. Louis, MO, USA), glutaric acid-d4 (0.16 microg/mL; BePure, Beijing, China), glucose-6-13C (2 microg/mL; Scrbio, Shanghai, China), deoxycholic acid-d4 (DCA-d4, 0.16 microg/mL; Isosciences, Ambler, PA, USA) and chenodeoxycholic acid-d4 (CDCA-d4, 1 microg/mL; Isosciences, Ambler, PA, USA). The mixture was vortex-mixed and sonicated in an ice-water bath for 15 min. Subsequently, 350 microL of a water and methanol mixture (3:1, v/v) was added, the sample was vortexed, and centrifuged at 12,700 rpm for 5 minutes. After centrifugation, the liquid naturally separated into two layers. The upper organic phase, enriched in lipophilic components, and the lower aqueous phase, enriched in polar small molecules, were processed separately for LC-MS analysis owing to their markedly different physicochemical properties. A 350 microL aliquot of the upper organic phase was transferred to a new tube and evaporated to dryness in a vacuum concentrator (Speed-Vac, Thermo Fisher Scientific, Waltham, MA, USA). The residue was reconstituted in 200 microL of acetonitrile and isopropanol (7:3, v/v), and the supernatant was used for LC-MS lipid analysis. A 400 microL aliquot of the lower aqueous phase was transferred to another tube, mixed with 1,100 microL of methanol by vortexing, and centrifuged at 12,700 rpm for 10 minutes at 4 degrees C. A 1,000 microL aliquot of the resulting supernatant was transferred to a dedicated Polar tube and evaporated to dryness, then reconstituted in 200 microL of water. The supernatant was used for LC-MS polar metabolite analysis.</p>Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS14865Zhenkun Dong. Harbin Medical University Cancer Hospital. hydfszlyydzk@163.com.<p>The LC-MS data underwent qualitative and quantitative analysis through ProfMet, a proprietary mass spectrometry-based metabolomics data processing workflow developed by Metabo-Profile. The raw mass spectrometry data (Raw files) were subjected to peak extraction, alignment, and filtering to reduce systematic data interference caused by fluctuations in instrument detection time.</p>Treatmenthydfszlyydzk@163.com<p>All urine samples were collected before surgery in patients or during health examinations in healthy individuals, in parallel with routine clinical procedures. Participants were instructed to follow a light diet on the day before sampling, to fast after 8:00 PM, and to refrain from drinking after 9:00 PM. First-void midstream urine (5 to 10 mL) was collected the following morning. Samples were immediately placed at 4 °C and transported to the laboratory within 30 minutes. Samples were processed within 30 minutes of arrival at the laboratory. Samples that could not be centrifuged immediately were temporarily stored at 4 °C. Urine was centrifuged at 1,600 g for 12 minutes at 4 °C, and the supernatant was aliquoted into microcentrifuge tubes (120 μL per tube, 2 tubes) and cryovials (approximately 2 mL per vial, 1 vial), then transferred to a −80 °C freezer. The entire process from sample collection to cryopreservation was completed within one hour.</p>MetabolomicsMetabolomicsThermo Scientific Q Exactiveuntargeted analysisurineWaters ACQUITY UPLC I-Class SystemHomo sapiensexperimental blankUrinary system tumorsclear cell papillary renal cell carcinomauntargeted metabolite profilingMetabolomicsThermo Scientific Q Exactiveurineuntargeted analysisWaters ACQUITY UPLC I-Class SystemHomo sapiensexperimental blankUrinary system tumorsclear cell papillary renal cell carcinomauntargeted metabolite profiling<p>Mass spectrometric detection was performed on a Q Exactive quadrupole-Orbitrap high-resolution mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) equipped with an electrospray ionization (ESI) source. Data were acquired in both positive and negative ionization modes. The full-scan resolution was 70,000 FWHM (at 200 m/z), and the data-dependent acquisition (ddMS2) resolution was 35,000 FWHM (at 200 m/z).</p>falseA Clinical Urine Metabolomics Dataset for Urological MalignanciesRenal cell carcinoma, bladder cancer, and prostate cancer rank among the most common urological malignancies, yet clinically satisfactory non-invasive screening tools for these cancers are still lacking. Here we present an untargeted urine metabolomics dataset generated by liquid chromatography coupled with high-resolution mass spectrometry from 368 clinical urine samples, comprising 249 patients with urological malignancies (194 renal cancer, 39 bladder cancer, and 16 prostate cancer), 62 patients with benign renal , and 57 healthy controls. Clear cell renal cell carcinoma (ccRCC) was the dominant histological subtype in the renal cancer subgroup (170 cases, 87.6%). Chromatographic separation was carried out on an ACQUITY UPLC I-Class system, and detection was performed on a Q Exactive Orbitrap high-resolution mass spectrometer in both positive and negative electrospray ionization modes. Raw data were processed through peak detection, baseline correction, alignment, annotation, and a multi-step normalization pipeline, yielding a final set of 472 metabolic features common to all three groups. The full dataset, along with clinical metadata, data processing scripts, and heatmap visualization code, has been deposited on figshare to support urinary biomarker discovery, diagnostic modeling, and metabolic pathway investigation in urological oncology.2026-06-272026-06-27MTBLS14865