Summary of Study ST002223

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001418. The data can be accessed directly via it's Project DOI: 10.21228/M8F409 This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002223
Study TitleMetabolic profiling of mouse tissues and tissue interstitial fluids
Study SummaryTissue and tissue interstitial fluids was collected from mice of a hybrid C57BL/6J;129/SvJ background of about 12 weeks of age (8 in total) and used to profile the metabolic content. This is Part 6 of a study and the experimental number is MS56.
CECAD Research Center
Last NameYang
First NameMing
AddressJoseph-Stelzmann-Straße 26, Köln, Koeln, 50931, Germany
Submit Date2022-07-15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-08-03
Release Version1
Ming Yang Ming Yang application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001418
Project DOI:doi: 10.21228/M8F409
Project Title:Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression
Project Summary:Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally related clear cell renal cancer cells (ccRCC) grown in physiological media to identify key stage-specific metabolic vulnerabilities. We show that a VHL loss-dependent reprogramming of branched-chain amino acid catabolism sustains the de novo biosynthesis of aspartate and arginine enabling tumor cells with the flexibility of partitioning the nitrogen of the amino acids depending on their needs. Importantly, we identify the epigenetic reactivation of argininosuccinate synthase (ASS1), a urea cycle enzyme suppressed in primary ccRCC, as a crucial event for metastatic renal cancer cells to acquire the capability to generate arginine, invade in vitro and metastasize in vivo. Overall, our study uncovers a novel mechanism of metabolic flexibility occurring during ccRCC progression, paving the way for the development of novel stage-specific therapies.
Institute:CECAD Research Center, University Hospital Cologne
Last Name:Yang
First Name:Ming
Address:Joseph-Stelzmann-Straße 26, CECAD Research Center, Köln, Koeln, 50931, Germany


Subject ID:SU002309
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Species Organ Matrix
SA212077MS56-042mouse heart interstitial fluid
SA212078MS56-062mouse heart interstitial fluid
SA212079MS56-064mouse heart interstitial fluid
SA212080MS56-035mouse heart interstitial fluid
SA212081MS56-063mouse heart interstitial fluid
SA212082MS56-044mouse heart interstitial fluid
SA212083MS56-053mouse heart interstitial fluid
SA212084MS56-055mouse heart interstitial fluid
SA212085MS56-004mouse heart tissue
SA212086MS56-021mouse heart tissue
SA212087MS56-017mouse heart tissue
SA212088MS56-014mouse heart tissue
SA212089MS56-023mouse heart tissue
SA212090MS56-008mouse heart tissue
SA212091MS56-011mouse heart tissue
SA212092MS56-006mouse heart tissue
SA212093MS56-061mouse kidney interstitial fluid
SA212094MS56-034mouse kidney interstitial fluid
SA212095MS56-039mouse kidney interstitial fluid
SA212096MS56-050mouse kidney interstitial fluid
SA212097MS56-057mouse kidney interstitial fluid
SA212098MS56-036mouse kidney interstitial fluid
SA212099MS56-038mouse kidney interstitial fluid
SA212100MS56-054mouse kidney interstitial fluid
SA212101MS56-001mouse kidney tissue
SA212102MS56-026mouse kidney tissue
SA212103MS56-016mouse kidney tissue
SA212104MS56-010mouse kidney tissue
SA212105MS56-012mouse kidney tissue
SA212106MS56-007mouse kidney tissue
SA212107MS56-025mouse kidney tissue
SA212108MS56-003mouse kidney tissue
SA212109MS56-043mouse liver interstitial fluid
SA212110MS56-052mouse liver interstitial fluid
SA212111MS56-049mouse liver interstitial fluid
SA212112MS56-056mouse liver interstitial fluid
SA212113MS56-041mouse liver interstitial fluid
SA212114MS56-040mouse liver interstitial fluid
SA212115MS56-037mouse liver interstitial fluid
SA212116MS56-059mouse liver interstitial fluid
SA212117MS56-031mouse liver tissue
SA212118MS56-002mouse liver tissue
SA212119MS56-030mouse liver tissue
SA212120MS56-027mouse liver tissue
SA212121MS56-009mouse liver tissue
SA212122MS56-019mouse liver tissue
SA212123MS56-013mouse liver tissue
SA212124MS56-015mouse liver tissue
SA212125MS56-058mouse lung interstitial fluid
SA212126MS56-060mouse lung interstitial fluid
SA212127MS56-033mouse lung interstitial fluid
SA212128MS56-051mouse lung interstitial fluid
SA212129MS56-045mouse lung interstitial fluid
SA212130MS56-046mouse lung interstitial fluid
SA212131MS56-047mouse lung interstitial fluid
SA212132MS56-048mouse lung interstitial fluid
SA212133MS56-018mouse lung tissue
SA212134MS56-005mouse lung tissue
SA212135MS56-020mouse lung tissue
SA212136MS56-032mouse lung tissue
SA212137MS56-029mouse lung tissue
SA212138MS56-024mouse lung tissue
SA212139MS56-022mouse lung tissue
Showing results 1 to 63 of 63


Collection ID:CO002302
Collection Summary:Mice were culled by cervical dislocation and tissue samples from hearts, livers, kidneys, and lungs were collected and split into two halves. One half was snap frozen in liquid nitrogen and stored at -80°C until further processing. The second half was used for interstitial fluid extraction using a protocol adapted from Sullivan et al. 2019 (
Sample Type:Mouse tissues and interstitial fluids


Treatment ID:TR002321
Treatment Summary:No further treatment was carried out.

Sample Preparation:

Sampleprep ID:SP002315
Sampleprep Summary:For tissue extraction, samples were homogenized in metabolite extraction buffer using the proportion 25 μl/mg of buffer with Precellys Lysing tubes (Bertin Instruments). After that, extracts were kept in the freezer overnight and the following day centrifuged twice at max speed at 4C˚ to remove the protein precipitates. Equal volumes of supernatants were spiked in with 13C arginine (Cambridge Isotopes) for quantification of arginine content. For extraction of the tissue interstitial for interstitial fluid extraction, the organ was washed in saline solution and then a portion was centrifuged at for 10 min at 4°C at 106 x g using 20 µm nylon filters (Spectrum Labs, Waltham, MA, 148134) affixed on top of 2 ml Eppendorf tubes. 1μl of the eluate was extracted in 45μl of extraction buffer and frozen overnight. The following day, all extracted were centrifuged twice at max speed at 4C˚to remove the protein precipitates. Supernatants were finally spiked in with 13C arginine (Cambridge Isotopes) for arginine quantification.

Combined analysis:

Analysis ID AN003632
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000
Column SeQuant ZIC-pHILIC
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units peak area


Chromatography ID:CH002687
Chromatography Summary:Chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A was 20 mM ammonium carbonate, 0.05% ammonium hydroxide; Solvent B was acetonitrile. The column oven and autosampler tray were held at 40 °C and 4 °C, respectively. The chromatographic gradient was run at a flow rate of 0.200 mL/min as follows: 0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B. Samples were randomized and the injection volume was 5 µl. A pooled quality control (QC) sample was generated from an equal mixture of all individual samples and analysed interspersed at regular intervals.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC-pHILIC
Column Temperature:40
Flow Gradient:0-2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B
Flow Rate:0.200 mL/min
Solvent A:100% water; 20 mM ammonium carbonate; 0.05% ammonium hydroxide
Solvent B:100% acetonitrile
Chromatography Type:HILIC


MS ID:MS003383
Analysis ID:AN003632
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Comments:Metabolites were measured with a Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (HRMS) coupled to a Dionex Ultimate 3000 UHPLC. The mass spectrometer was operated in full-scan, polarity-switching mode, with the spray voltage set to +4.5 kV/-3.5 kV, the heated capillary held at 320 °C, and the auxiliary gas heater held at 280 °C. The sheath gas flow was set to 55 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 0 unit. HRMS data acquisition was performed in a range of m/z = 70–900, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 120 ms. Metabolite identities were confirmed using two parameters: (1) precursor ion m/z was matched within 5 ppm of theoretical mass predicted by the chemical formula; (2) the retention time of metabolites was within 5% of the retention time of a purified standard run with the same chromatographic method. Chromatogram review and peak area integration were performed using the Thermo Fisher software Tracefinder 5.0 and the peak area for each detected metabolite was normalized against the total ion count (TIC) of that sample to correct any variations introduced from sample handling through instrument analysis. The normalized areas were used as variables for further statistical data analysis.