Summary of Study ST003193
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 PR001989. The data can be accessed directly via it's Project DOI: 10.21228/M8MT61 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 | ST003193 |
| Study Title | Metabolomics study on frozen tissue derived from the tumor and adjacent non-malignant liver tissue (NML) of patient afflicted with fibrolamellar carinoma (FLC) |
| Study Type | LC-MS quantitative analysis |
| Study Summary | Fibrolamellar carcinoma (FLC) is a rare, early-onset liver cancer. The five-year survival rate is low, and there is a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets. To date, only one study has attempted to characterize the FLC proteome and metabolome, but with modest sample size (proteomics—n = 16 patient samples; metabolomics—n = 10 patient samples) and protein detection (n = 4620 proteins). We have performed the most comprehensive characterization of FLC in both proteomics (n = 23 patient samples; n = 8485 proteins) and metabolomics (n = 26 patient samples; n = 135 metabolites). Targeted metabolomics on central carbon metabolism (polar metabolite extraction) was performed followed by extensive quantitative and qualitative assessment of its relationship with the proteome of FLC to gain insight on how the metabolic network is constructed in this cancer. Frozen patient tissue was derived from both primary and metastatic tumors as well as adjacent non-malignant liver tissue (NML). Primary and metastatic tumors served as our FLC cohort while NMLs served as our control cohort. |
| Institute | Cornell University |
| Department | Biomedical Sciences |
| Laboratory | Praveen Sethupathy |
| Last Name | Long Jr. |
| First Name | Donald |
| Address | 618 Tower Road, Ithaca, New York, 14853, USA |
| dl964@cornell.edu | |
| Phone | 4355312013 |
| Submit Date | 2024-05-06 |
| Num Groups | 2 |
| Total Subjects | 26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005241 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | normalized-BatchCorrected-Imputed-log2transformed Intensity |
Chromatography:
| Chromatography ID: | CH003968 |
| Chromatography Summary: | Metabolites were measured on a Q Exactive Orbitrap mass spectrometer (Thermo Scientific), which was coupled to a Vanquish UPLC system (Thermo Scientific) via an Ion Max ion source with a HESI II probe (Thermo Scientific). A Sequant ZIC-pHILIC column (2.1 mm i.d. × 150 mm, particle size of 5 µm, Millipore Sigma) was used for separation of metabolites. A 2.1 × 20 mm guard column with the same packing material was used for protection of the analytical column. Flow rate was set at 150 μL/min. Buffers consisted of 100% acetonitrile for mobile phase A, and 0.1% NH 4 OH/20 mM CH 3 COONH 4 in water for mobile phase B. The chromatographic gradient ran from 85% to 30% A in 20 min followed by a wash with 30% A and re-equilibration at 85% A. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | - |
| Flow Gradient: | 85% to 30% A in 20 minutes |
| Flow Rate: | 150uL/min |
| Solvent A: | 100% acetonitrile |
| Solvent B: | 100% water; 0.1% ammonium hydroxide; 20mM ammonium acetate |
| Chromatography Type: | HILIC |
