Summary of Study ST002224

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 IDST002224
Study TitleIntracellular metabolic profile of renal cells cultured in Plasmax
Study SummaryThe objective of this experiment is to analyse the metabolic profiles of human renal epithelial cells HK2 and ccRCC cell lines 786-O, 786-M1A and 786-M2A in Plasmax media. The experiment was conducted on three different days using cells with different passage numbers. This is Part 5 of a study and the experimental number is MS55.
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:SU002310
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606


Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Cell line Treatment
SA212140MS55_27786-M1A Plasmax + 2.5% FBS
SA212141MS55_26786-M1A Plasmax + 2.5% FBS
SA212142MS55_12786-M1A Plasmax + 2.5% FBS
SA212143MS55_28786-M1A Plasmax + 2.5% FBS
SA212144MS55_42786-M1A Plasmax + 2.5% FBS
SA212145MS55_44786-M1A Plasmax + 2.5% FBS
SA212146MS55_43786-M1A Plasmax + 2.5% FBS
SA212147MS55_11786-M1A Plasmax + 2.5% FBS
SA212148MS55_41786-M1A Plasmax + 2.5% FBS
SA212149MS55_25786-M1A Plasmax + 2.5% FBS
SA212150MS55_09786-M1A Plasmax + 2.5% FBS
SA212151MS55_10786-M1A Plasmax + 2.5% FBS
SA212152MS55_29786-M2A Plasmax + 2.5% FBS
SA212153MS55_31786-M2A Plasmax + 2.5% FBS
SA212154MS55_32786-M2A Plasmax + 2.5% FBS
SA212155MS55_45786-M2A Plasmax + 2.5% FBS
SA212156MS55_48786-M2A Plasmax + 2.5% FBS
SA212157MS55_47786-M2A Plasmax + 2.5% FBS
SA212158MS55_46786-M2A Plasmax + 2.5% FBS
SA212159MS55_30786-M2A Plasmax + 2.5% FBS
SA212160MS55_14786-M2A Plasmax + 2.5% FBS
SA212161MS55_16786-M2A Plasmax + 2.5% FBS
SA212162MS55_13786-M2A Plasmax + 2.5% FBS
SA212163MS55_15786-M2A Plasmax + 2.5% FBS
SA212164MS55_39786-O Plasmax + 2.5% FBS
SA212165MS55_21786-O Plasmax + 2.5% FBS
SA212166MS55_22786-O Plasmax + 2.5% FBS
SA212167MS55_05786-O Plasmax + 2.5% FBS
SA212168MS55_37786-O Plasmax + 2.5% FBS
SA212169MS55_23786-O Plasmax + 2.5% FBS
SA212170MS55_06786-O Plasmax + 2.5% FBS
SA212171MS55_08786-O Plasmax + 2.5% FBS
SA212172MS55_07786-O Plasmax + 2.5% FBS
SA212173MS55_40786-O Plasmax + 2.5% FBS
SA212174MS55_24786-O Plasmax + 2.5% FBS
SA212175MS55_38786-O Plasmax + 2.5% FBS
SA212176MS55_03HK2 Plasmax + 2.5% FBS
SA212177MS55_02HK2 Plasmax + 2.5% FBS
SA212178MS55_04HK2 Plasmax + 2.5% FBS
SA212179MS55_35HK2 Plasmax + 2.5% FBS
SA212180MS55_19HK2 Plasmax + 2.5% FBS
SA212181MS55_20HK2 Plasmax + 2.5% FBS
SA212182MS55_01HK2 Plasmax + 2.5% FBS
SA212183MS55_18HK2 Plasmax + 2.5% FBS
SA212184MS55_17HK2 Plasmax + 2.5% FBS
SA212185MS55_34HK2 Plasmax + 2.5% FBS
SA212186MS55_33HK2 Plasmax + 2.5% FBS
SA212187MS55_36HK2 Plasmax + 2.5% FBS
Showing results 1 to 48 of 48


Collection ID:CO002303
Collection Summary:2x105 cells were plated the day before onto 6-well plates (5 or 6 replicates for each cell type) and extracted the day after. The experiment was repeated 3 times (N=3). Before extraction, cells were counted using CASY cell counter (Omni Life Sciences) using a separate counting plate. After that, cells were washed at room temperature with PBS twice and then kept in a cold bath with dry ice and methanol before adding the metabolite extraction solution.
Sample Type:Cultured cells


Treatment ID:TR002322
Treatment Summary:Cells were cultured in Plasmax supplemented with 2.5% FBS. No further treatments were carried out.

Sample Preparation:

Sampleprep ID:SP002316
Sampleprep Summary:Metabolite extraction solution (50% methanol, 30% acetonitrile, 20% ultrapure water, 5 µM final concentration valine-d8) was added to each well after the washes in PBS following the proportion of 1ml of extraction solution per million cells. The extracts were scraped and mixed at 4°C for 15 min. After final centrifugation at max speed for 15 min at 4°C, the supernatants were transferred into LC-MS vials.

Combined analysis:

Analysis ID AN003633
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:CH002688
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:MS003384
Analysis ID:AN003633
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.