Summary of Study ST003154
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001960. The data can be accessed directly via it's Project DOI: 10.21228/M8CF0S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST003154 |
| Study Title | Nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer |
| Study Summary | The experiment focus on the nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer. Briefly, KPC FC1245 cells were genetically engineered using doxycycline inducible CRISPR/Cas9 system platform to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT were then orthotopically injected in the head of the pancreas of 8-10 weeks old C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice were sacrificed and tumor interstitial fluid was collected as reported in the Collection section of this study. Standard curves for glutamine, cytidine, uridine, glucose, UTP and UDP were prepared and extracted along with the interstitial fluid samples. The concentrations of glutamine, cytidine, uridine, UDP and UTP were measured by LC-MS, and glucose was measured by GC-MS. A decrease in uridine content, and accordingly in UDP and UTP, and a concomitant accumulation of cytidine was observed in sgCda tumors. On the other hand, no differences were observed in glucose and glutamine abundance. |
| Institute | VIB-KU Leuven Center for Cancer Biology |
| Last Name | Mazzone |
| First Name | Massimiliano |
| Address | Herestraat 49, box 912, Leuven, Flemish Brabant, 3000, Belgium |
| massimiliano.mazzone@kuleuven.be | |
| Phone | +32-16-37.32.13 |
| Submit Date | 2024-03-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC/LC-MS |
| Release Date | 2024-04-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005174 | AN005175 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | GC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Agilent 8860 |
| Column | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Agilent J&W DB-35ms (30 m x 0.25 mm, 0.25 µm) |
| MS Type | ESI | EI |
| MS instrument type | Orbitrap | Single quadrupole |
| MS instrument name | Thermo Q Exactive Orbitrap | Agilent 5977C |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Ion Counts (AUC) | Ion Counts (AUC) |
MS:
| MS ID: | MS004909 |
| Analysis ID: | AN005174 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The MS was operated in negative full scan mode (m/z range: 70–900 and 400-500) using a spray voltage of 4.0 kV, capillary temperature of 350 °C, sheath gas at 50.0, auxiliary gas at 10.0. The AGC target was set at 3.0E6 using a resolution if 140000, with a maximum IT fill time of 512 ms. Data was collected and analyzed using the Xcalibur software (Thermo Scientific) considering a 5 ppm error. The chromatographic peaks for UDP, UTP, cytidine, uridine and glutamine were normalized to the internal standard glutaric acid. Tumor interstitial fluid samples were interpolated to the standard curve and normalized for tumor interstitial fluid volume in order to quantify metabolite concentration. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004910 |
| Analysis ID: | AN005175 |
| Instrument Name: | Agilent 5977C |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | 5977C quipped with EI inert source. Mass spectrometry was performed at 70 eV and a mass range of 150-650 atomic mass units was measured. The chromatographic peaks were extracted from raw chromatograms with a custom MATLAB Script. The chromatographic peaks for 12C-Glucose were normalized to the internal standard 13C6-glucose. Tumor interstitial fluid samples were interpolated to the standard curve and normalized for tumor interstitial fluid volume to quantify metabolite concentration. |
| Ion Mode: | POSITIVE |
