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data were exploratively annotated using MSDIAL and its lipidomics database. For data integration and relative quantitation we used Lipid Data Analyzer 2.8.3_2</p>MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phase<p>Samples were analyzed with reversed phase-UHPLC (BEH-C18, 2.1x 150 mm, 1.7 µm, Waters, Milford, USA) QTOF-MS (1290 Infinity II and 6560 IM-QTOF-MS, Agilent, Waldbronn, Germany) in positive/negative ESI QTOF-only mode. For the gradient elution, an aqueous eluent A and a 2-propanol eluent B were used, both with the following additives: Ammonium acetate (10 mM), phosphoric acid (8 μM), and formic acid (0.1 vol%). The gradient started with 60% eluent A for 0.5 min, followed by a linear decrease over 8.5 min to 20% and within 13 min to 0% A. This composition was held constant for 2.5 min and then returned to initial conditions for 5 min prior to the next injection. Eluent flow was constant 150 µl/min. </p>Urinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma. 10.1101/2024.08.12.607453.Gustav JonssonMedical University of Grazurinemass spectrometry assay<p>Lipids were extracted according to the Matyash protocol [31] using 3 ml of Urinary supernatant. Internal standard mix (PE 34:0, 830456P; PS 34:0, 840028P; LPC 17:1, 855677C; SM d35:1, 860585; purchased form Avanti Polar Lipids, USA, and PC 34:0, 37-1700-7; TG 54:0, 33-1835-9; purchased from Larodan, Sweden) was added to the samples before extraction. The organic phase of the final extraction was dried in a vacuum centrifuge and resolved in 500 µl 2-propanol:MeOH:H2O (70:25:10, v:v:v) before injection. </p>Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS14671Gustav Jonsson. Institute of Molecular Biotechnology. gustav.jonsson@medunigraz.at.Züllig Thomas. thomas.zuellig@uni-graz.at.Rechberger Gerald. gerald.rechberger@uni-graz.at.<p>The data were exploratively annotated using MSDIAL and its lipidomics database. For data integration and relative quantitation we used Lipid Data Analyzer 2.8.3_2</p>Diseasegustav.jonsson@medunigraz.at<p>The study was approved by the ethical commission at the Medical University of Vienna (EthikKommission Medizinische Universität Wien), study number 2224/2021, project title: Urinproteomik zur Validierung von Biomarkern für das klarzellige Nierenkarzinom – Pilotstudie (UrineProt).</p><p>Urine was collected from 40 patients who presented with a suspected primary renal mass at the Department of Urology of the Medical University of Vienna. Out of the 40 patients, 9 were excluded due to the renal mass being identified as something other than a renal cell carcinoma, such as oncocytomas, cysts, angiomyolipoma, papillary adenoma or a kidney-lodged metastasis. From the remaining 31 patients, 22 patients were characterized as ccRCC, 8 as pRCC and 1 as chromophobe RCC through histological assessment by a trained pathologist. </p><p>For lipidomics, the 22 ccRCC samples and 12 controls were used for downstream analysis.</p>MetabolomicsLipid Data Analyzerurineuntargeted analysisClear Cell Renal Cell CarcinomaAgilent 1290 Infinity II UHPLCHealthy ControlLipidomicsHomo sapiensMS-DIALAgilent 6560 Ion Mobility Q-TOFclear cell renal carcinomaexperimental sampleLipid Data Analyzerurineuntargeted analysisClear Cell Renal Cell CarcinomaAgilent 1290 Infinity II UHPLCHealthy ControlLipidomicsHomo sapiensMS-DIALAgilent 6560 Ion Mobility Q-TOFclear cell renal carcinomaexperimental sample<p>In positive mode 1 µl and in negative ion mode 5 µl were injected. Column temperature was 50°C. The ESI instrument parameters were in positive mode: Gas temp 300°C, flow 10 l/min, Nebulizer 50 psi, sheath gas temp 400°C, flow 12 l/min), and in negative mode: Gas temp 300°C, flow 5 l/min, Nebulizer 30 psi, sheath gas temp 350°C, flow 12 l/min). The scan source parameters in pos and neg mode were (VCap 3500, Nozzle Voltage 500 V, Fragmentor 360, Skimmer 1 and OctopoleRFPeak 750). </p>falseUrinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma (Lipidomics)<p>Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy. Yet, no rapid, non-invasive biomarkers are available for diagnosis or screening. Urine represents an ideal analyte matrix due to its accessibility, low invasiveness, longitudinal sampling and the kidney’s central role in filtration. Here, we integrated proteomic, lipidomic, and metabolomic analyses of urine from ccRCC patients and controls to identify diagnostic biomarkers. Multi-omics profiling revealed urogenital metabolic dysregulation in ccRCC, including increased lipid metabolism, altered mitochondrial respiration signatures, and elevated urinary lipid content. We identified three urinary protein biomarkers: serum amyloid A1 (SAA1), haptoglobin (HP), and lipocalin 15 (LCN15). Using a parallel reaction monitoring mass spectrometry workflow, we developed a rapid and sensitive assay and combined these markers into a diagnostic UrineScore. The UrineScore achieved 96% accuracy in receiver operating characteristic analysis in the discovery cohort and 95% accuracy in an independent validation cohort. Together, these results support the feasibility of multi-omics-guided urinary biomarker discovery and represent a step toward accessible diagnostic platforms for ccRCC.</p>2026-07-152026-06-05MTBLS14671