Summary of Study ST002226

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 IDST002226
Study TitleExometabolomics of HK2, 786-O cells cultured in Plasmax media
Study SummaryThe objective of this study is to analyse the exometabolomics of human epithelial renal cell line HK2 and clear cell renal cell carcinoma (ccRCC) cell lines 786-O, 786-M1A, 786-M2A, OS-RC-2, OS-LM1 and RFX-631 that are cultured with the Plasmax media. This is part 3 of the study, and the experimental number is MS51.
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:SU002312
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 Sample type
SA212296MS51-17786-M1A conditioned media
SA212297MS51-18786-M1A conditioned media
SA212298MS51-19786-M1A conditioned media
SA212299MS51-16786-M1A conditioned media
SA212300MS51-20786-M1A conditioned media
SA212301MS51-23786-M2A conditioned media
SA212302MS51-25786-M2A conditioned media
SA212303MS51-21786-M2A conditioned media
SA212304MS51-24786-M2A conditioned media
SA212305MS51-11786-O conditioned media
SA212306MS51-15786-O conditioned media
SA212307MS51-14786-O conditioned media
SA212308MS51-12786-O conditioned media
SA212309MS51-13786-O conditioned media
SA212310MS51-07HK2 conditioned media
SA212311MS51-10HK2 conditioned media
SA212312MS51-08HK2 conditioned media
SA212313MS51-06HK2 conditioned media
SA212314MS51-09HK2 conditioned media
SA212315MS51-02No cell control media
SA212316MS51-01No cell control media
SA212317MS51-04No cell control media
SA212318MS51-05No cell control media
SA212319MS51-03No cell control media
SA212320MS51-31OSLM1B conditioned media
SA212321MS51-33OSLM1B conditioned media
SA212322MS51-35OSLM1B conditioned media
SA212323MS51-32OSLM1B conditioned media
SA212324MS51-34OSLM1B conditioned media
SA212325MS51-26OSRC2 conditioned media
SA212326MS51-30OSRC2 conditioned media
SA212327MS51-27OSRC2 conditioned media
SA212328MS51-28OSRC2 conditioned media
SA212329MS51-29OSRC2 conditioned media
SA212330MS51-40RFX631 conditioned media
SA212331MS51-39RFX631 conditioned media
SA212332MS51-37RFX631 conditioned media
SA212333MS51-36RFX631 conditioned media
SA212334MS51-38RFX631 conditioned media
Showing results 1 to 39 of 39


Collection ID:CO002305
Collection Summary:1.5x105 cells were seeded onto a 6-well plate and cultured in the Plasmax media for 24h. The conditioned medium at 24 hours was analysed for exometabolomics, using media without cells as controls. Quantification of protein content and cell counting was carried using additional plates seeded in parallel.
Sample Type:Cultured cells


Treatment ID:TR002324
Treatment Summary:Cells were cultured in the Plasmax media supplemented with 2.5% FBS for 24 hours.

Sample Preparation:

Sampleprep ID:SP002318
Sampleprep Summary:Media samples collected at t=0 and t=24hrs were centrifuged at 4 °C for 10 min. 50 µl of supernatants was further extracted with 350 µl of metabolite extraction solution (50% methanol, 30% acetonitrile, 20% ultrapure water, 5 µM final concentration valine-d8). The solution was then centrifuged at 4 °C for 10 min at max speed and the supernatant collected onto LC-MS vials.

Combined analysis:

Analysis ID AN003635
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:CH002690
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:MS003386
Analysis ID:AN003635
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.