Untargeted Metabolomics Data Analysis. Data were processed using Progenesis QI (Nonlinear Dynamics, Waters). Ion intensity maps were aligned to a reference dataset, and peak picking was performed on an aggregated map. Ions were identified by comparing accurate mass, adduct patterns, and isotope distributions with the Human Metabolome Database (HMDB) using a mass accuracy tolerance of 5 mDa; fragmentation patterns were also considered. All biological samples were analyzed in triplicate, with quality controls run on pooled samples and reference compound mixtures. Finally, pathway analysis of significantly altered metabolites in cells and urine samples was performed using MetaboAnalyst (http://www.metaboanalyst.ca) with default settings.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - capillary-hilic-/-beh-amide"],"chromatography_protocol":["Cellular metabolites were separated on a Waters nanoAcquity UPLC using a BEH Amide capillary column (150 μm × 50 μm × 1.7 μm). Mobile phase A was 5 mM ammonium acetate in water and mobile phase B was 5 mM ammonium acetate in acetonitrile. The gradient ran from 5% A to 50% A over 12 min. Injection volume was 1 μL with a flow rate adjusted from 3 to 2 μL/min.
"],"publication":["Autophagy regulator ATG7 links lipid metabolism to proximal tubule cell-fate decisions in health and disease."],"submitter_name":["Mikhail Korzinkin","Martina Zanella"],"submitter_affiliation":["FGCZ","Insilico Medicine"],"organism_part":["renal proximal tubule"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Sample Preparation. Cellular metabolism was quenched by adding 80% pre-cooled methanol to the cells. After vortexing, samples were incubated at –20°C for 1.5 h. Proteins were precipitated by centrifuging at 10,000 rpm for 20 min at 4°C, and the clear supernatant was transferred to a new vial. The supernatant was then dried under a nitrogen stream and reconstituted in 20 μL water mixed with 80 μL injection buffer (90% acetonitrile, 8.8% methanol, 50 mM ammonium acetate, pH 7). Following another round of vortexing and centrifugation (10,000 rpm, 4°C, 10 min), the clear supernatant was transferred to Total Recovery Vials (Waters) for LC-MS injection. Method blanks, standard mixes, and pooled samples were prepared identically for quality control.
"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15857"],"author":["Alessandro Luciani. Institute of Physiology, University of Zurich. University of Zurich, 8057 Zurich, Switzerland. alessandro.luciani@physiol.uzh.ch.","Mikhail Korzinkin. Insilico Medicine. mike@insilicomedicine.com.","Martina Zanella. martina.zanella@fgcz.ethz.ch."],"data_transformation_protocol":["Raw data were processed in Progenesis QI (Nonlinear Dynamics, Waters). Ion intensity maps were aligned to a reference dataset prior to peak picking on an aggregated map. Metabolite identification was conducted by matching accurate mass (tolerance 5 mDa), adduct patterns, isotope distribution, and fragmentation patterns against the Human Metabolome Database (HMDB). Secondary pathway analysis was performed using MetaboAnalyst.
"],"study_factor":["Atg7 PT-KO","WT"],"submitter_email":["martina.zanella@fgcz.ethz.ch","mike@insilicomedicine.com"],"sample_collection_protocol":["The mouse lines were used: Fip200fl/fl, Atg7fl/fl and γGt1-Cre. The Fip200fl/fl mouse line was kindly provided by C. Münz (University of Zurich). The Atg7fl/fl mice10 (C57BL/6J background) were obtained from the RIKEN repository (National BioResource Project, started by the Ministry for Education, Culture Sports, Science and Technology, Japan). The Atg7fl/fl mice were generated by inserting two Lox P sites around exon 14, which encodes the active site cysteine essential for activation of the conjugation substrates. The Cre-expressing mouse line was obtained from The Jackson Laboratory (RRID: IMSR_JAX:012841). The rat proximal promoter to γGt1 was used in a transgene construct to drive Cre recombinase expression.23 The γGt1-Cre promoter becomes active around postpartum day 14, coinciding with the completion of nephrogenesis and thus targeting cortical tubular epithelium in mature kidneys.23 The Cre-expressing mice (C57BL/6 x SJL background) were backcrossed (>10 times) into the C57BL/6 background. The PT-specific Atg7KO mice were generated by crossing mice carrying the respective LoxP-flanked alleles with γGt1-Cre transgenic mice. All mice were housed at the animal service centre of the University of Zurich under specific pathogen-free conditions and maintained under controlled temperature (22-25°C) and humidity (50-60%), with a 12-h dark/light cycle and ad libitum access to tap water and standard chow (Diet AO3, SAFE). Kidneys were collected for analysis at the time of sacrifice. Both female and male mice at 4, 12, and 24 weeks of age were used for kidney function studies, whereas the other experiments were performed using mice at 12 and 24 weeks of age. Littermates not carrying the γGt1-Cre transgenes were used as controls in all experiments.
"],"omics_type":["Metabolomics"],"study_design":["hydrophilic interaction chromatography","ultra-performance liquid chromatography-mass spectrometry","Metabolomics","Mus musculus","untargeted analysis","Progenesis QI","experimental sample","Time-of-Flight Mass Spectrometry","renal proximal tubule","ultra high-performance liquid chromatography","Waters SYNAPT G2-Si","cell culture","Waters nanoACQUITY UPLC system"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","hydrophilic interaction chromatography","Metabolomics","Mus musculus","untargeted analysis","Progenesis QI","experimental sample","Time-of-Flight Mass Spectrometry","renal proximal tubule","ultra high-performance liquid chromatography","Waters SYNAPT G2-Si","cell culture","Waters nanoACQUITY UPLC system"],"mass_spectrometry_protocol":["LC-MS analysis was conducted on a Waters Synapt G2-Si mass spectrometer equipped with a nanoESI source operating in negative ion mode. Data acquisition was performed in MSE mode over an m/z range of 50–1200 at a resolution >20,000.
"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomic profiling of primary mouse proximal tubule cells (mPTCs) derived from 24-week-old CTR and Atg7 PT-KO kidneys","description":"To explore the role of ATG7 in the kidney PT, we crossed mice homozygous for floxed alleles of Atg7 with Ggt1-Cre mice expressing Cre recombinase under the rat Ggt1 (gamma-glutamyltransferase 1) gene promoter. This generated Atg7fl/fl; γGt1cre/cre mice (hereafter referred to as Atg7 PT-KO), in which exon 14 of Atg7 was efficiently excised, and control littermates (Atg7fl/fl; γGt1wt/wt, referred to as CTR). Sample Preparation. Cellular metabolism was quenched by adding 80% pre-cooled methanol to the cells. After vortexing, samples were incubated at –20°C for 1.5 h. Proteins were precipitated by centrifuging at 10,000 rpm for 20 min at 4°C, and the clear supernatant was transferred to a new vial. The supernatant was then dried under a nitrogen stream and reconstituted in 20 μL water mixed with 80 μL injection buffer (90% acetonitrile, 8.8% methanol, 50 mM ammonium acetate, pH 7). Following another round of vortexing and centrifugation (10,000 rpm, 4°C, 10 min), the clear supernatant was transferred to Total Recovery Vials (Waters) for LC-MS injection. Method blanks, standard mixes, and pooled samples were prepared identically for quality control. LC-MS Data Acquisition. Cell metabolites were separated using a Waters nanoAcquity UPLC with a BEH Amide capillary column (150 μm × 50 μm × 1.7 μm). A gradient was applied using solvent A (5 mM ammonium acetate in water) and solvent B (5 mM ammonium acetate in acetonitrile), transitioning from 5% A to 50% A over 12 min. The injection volume was 1 μL, with the flow rate adjusted from 3 to 2 μL/min. The UPLC was coupled to a Waters Synapt G2Si mass spectrometer via a nanoESI source. MS1 and MS2 data were acquired in negative ion mode using MSE over a mass range of 50 to 1200 m/z at resolutions greater than 20,000. Species: Mus musculus Samples list: Supernatant_0529_WT_Fed Supernatant_0530_WT_Fed Supernatant_0221_WT_Fed Supernatant_0222_WT_Fed Supernatant_0491_cKO_Fed Supernatant_0435_cKO_Fed Supernatant_0436_cKO_Fed Supernatant_0438_cKO_Fed","dates":{"publication":"2026-09-30","submission":"2026-09-29"},"accession":"MTBLS15857","cross_references":{}}