Summary of Study ST003362
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 PR002088. The data can be accessed directly via it's Project DOI: 10.21228/M8QJ9B 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 | ST003362 |
| Study Title | Metabolomics analysis of Glioblastoma (GBM) cell line U251 labeled by 13C-glutamine after treatment with pimozide |
| Study Summary | Glioblastoma (GBM) cell line U251 was treated with antipsychotic drug pimozide (3 uM) for 24 hr, and then labeled with 13C-glutamine (2 mM) for 1 hr. Cells were collected and extracted for metabolites and analyzed by LC-MS. Our data showed that pimozide treatment significantly increased 13C-labeled glutamine uptake and subsequent consumption, including anaplerosis of metabolites for tricarboxylic acid (TCA) cycle and de novo fatty acid synthesis derived from glutamine-mediated reductive carboxylation process. |
| Institute | The Ohio State University |
| Last Name | Guo |
| First Name | Deliang |
| Address | Department of Radiation Oncology, Ohio State Comprehensive Cancer Center, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, and College of Medicine at The Ohio State University, Columbus, OH 43210, USA. |
| deliang.guo@osumc.edu | |
| Phone | 6143663774 |
| Submit Date | 2024-07-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002088 |
| Project DOI: | doi: 10.21228/M8QJ9B |
| Project Title: | Metabolomics analysis of Glioblastoma (GBM) cell line U251 labeled by 13C-glutamine after treatment with pimozide |
| Project Summary: | Glioblastoma (GBM) cell line U251 was treated with antipsychotic drug pimozide (3 uM) for 24 hr, and then labeled with 13C-glutamine (2 mM) for 1 hr. Cells were collected and extracted for metabolites and analyzed by LC-MS. Our data showed that pimozide treatment significantly increased 13C-labeled glutamine uptake and subsequent consumption, including anaplerosis of metabolites for tricarboxylic acid (TCA) cycle and de novo fatty acid synthesis derived from glutamine-mediated reductive carboxylation process. |
| Institute: | The Ohio State University |
| Department: | Radiation Oncology |
| Last Name: | Guo |
| First Name: | Deliang |
| Address: | Department of Radiation Oncology, Ohio State Comprehensive Cancer Center, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, and College of Medicine at The Ohio State University, Columbus, OH 43210, USA. |
| Email: | deliang.guo@osumc.edu |
| Phone: | 6143663774 |
Subject:
| Subject ID: | SU003483 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA365913 | U251_Control_1_POS | Human glioblastoma U251 cell line | Control |
| SA365914 | U251_Control_4_POS | Human glioblastoma U251 cell line | Control |
| SA365915 | LCFA_Control_2 | Human glioblastoma U251 cell line | Control |
| SA365916 | U251_Control_3_POS | Human glioblastoma U251 cell line | Control |
| SA365917 | U251_Control_3_NEG | Human glioblastoma U251 cell line | Control |
| SA365918 | U251_Control_2_POS | Human glioblastoma U251 cell line | Control |
| SA365919 | U251_Control_2_NEG | Human glioblastoma U251 cell line | Control |
| SA365920 | LCFA_Control_1 | Human glioblastoma U251 cell line | Control |
| SA365921 | U251_Control_1_NEG | Human glioblastoma U251 cell line | Control |
| SA365922 | LCFA_Control_4 | Human glioblastoma U251 cell line | Control |
| SA365923 | LCFA_Control_3 | Human glioblastoma U251 cell line | Control |
| SA365924 | U251_Control_4_NEG | Human glioblastoma U251 cell line | Control |
| SA365925 | U251_UNLABELED_NEG_2 | Human glioblastoma U251 cell line | NA |
| SA365926 | U251_UNLABELED_NEG | Human glioblastoma U251 cell line | NA |
| SA365927 | U251_UNLABELED_POS | Human glioblastoma U251 cell line | NA |
| SA365928 | U251_UNLABELED_POS_2 | Human glioblastoma U251 cell line | NA |
| SA365929 | LCFA_Pimozide_1 | Human glioblastoma U251 cell line | Pimozide |
| SA365930 | LCFA_Pimozide_2 | Human glioblastoma U251 cell line | Pimozide |
| SA365931 | LCFA_Pimozide_3 | Human glioblastoma U251 cell line | Pimozide |
| SA365932 | U251_Pimozide_1_NEG | Human glioblastoma U251 cell line | Pimozide |
| SA365933 | U251_Pimozide_1_POS | Human glioblastoma U251 cell line | Pimozide |
| SA365934 | U251_Pimozide_2_NEG | Human glioblastoma U251 cell line | Pimozide |
| SA365935 | LCFA_Pimozide_4 | Human glioblastoma U251 cell line | Pimozide |
| SA365936 | U251_Pimozide_3_NEG | Human glioblastoma U251 cell line | Pimozide |
| SA365937 | U251_Pimozide_3_POS | Human glioblastoma U251 cell line | Pimozide |
| SA365938 | U251_Pimozide_4_NEG | Human glioblastoma U251 cell line | Pimozide |
| SA365939 | U251_Pimozide_4_POS | Human glioblastoma U251 cell line | Pimozide |
| SA365940 | U251_Pimozide_2_POS | Human glioblastoma U251 cell line | Pimozide |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO003476 |
| Collection Summary: | 1) For labelled Group: 3 million U251 cells were seeded in a 15-cm dish for 24 hr, then treated with/without the drug (Pimozide: 3 µM) in a fresh medium containing 1% FBS, 5 mM glucose, 4 mM glutamine for another 24 hr. After drug treatment, cells were deprived for 1 hr with a serum-free medium containing 5 mM glucose, 0 mM glutamine, and 1 mM pyruvate. 2 mM 13C(U)-glutamine was added to the media and incubated for 1 hr. The cells were washed twice with cold PBS and quenched with cold acetonitrile and ultrapure water (4:3, v:v) for 5 min, and metabolites were extracted for subsequent LC-MS analysis. Long chain fatty acid Control: U251 cells without pimozide treatment. Long chain fatty acid Pimozide: U251 cells with pimozide treatment. |
| Sample Type: | Glioma cells |
Treatment:
| Treatment ID: | TR003492 |
| Treatment Summary: | 3 million U251 cells were seeded in a 15-cm dish for 24 hr, then treated with/without Pimozide (3 µM) in a fresh medium containing 1% FBS, 5 mM glucose, 4 mM glutamine for another 24 hr |
Sample Preparation:
| Sampleprep ID: | SP003490 |
| Sampleprep Summary: | After treatment, the cells were washed twice with cold PBS and quenched with cold acetonitrile and ultrapure water (4:3, v:v) for 5 min. Metabolites were then extracted for subsequent LC-MS analysis. |
Combined analysis:
| Analysis ID | AN005504 | AN005505 | AN005506 | AN005507 | AN005508 |
|---|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) | SeQuant ZIC-cHILIC (150 x 2.1mm, 3 um) | SeQuant ZIC-cHILIC (150 x 2.1mm, 3 um) | Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Counts | Counts | Counts | Counts | Counts |
Chromatography:
| Chromatography ID: | CH004186 |
| Chromatography Summary: | Parallel 2D-LC for polar profiling |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0 min, 5% B; 0 to 5 min, 5% B; 5 to 6.1 min, 5 to 15% B; 6.1 to 10 min, 15 to 60% B; 10 to 12 min, 60% B; 12 to 14 min, 60% to 100% B; 14 to 27.0 min, 100% to 100% B; 27.0 to 27.1 min, 5% B |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004187 |
| Chromatography Summary: | Parallel 2D-LC for polar profiling |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-cHILIC (150 x 2.1mm, 3 um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0 min, 95% B; 0 to 5 min, 95% B to 35% B; 5 to 6 min, 35% B; 6.0 to 6.1 min, 35% B to 5% B; 6.1 to 23 min, 5% B; 23.0 to 23.1 min, 5% to 95% B. |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 10 mM ammonium acetate (pH 3.25) |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004188 |
| Chromatography Summary: | LC method for long-chain fatty acid detection |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | started with 30% B, hold for 3 min, then increased to 99% B at 20 min, hold for 5 min; then hold at 30% B from 25.1 to 28 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% acetic acid |
| Solvent B: | 100% acetonitrile; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005230 |
| Analysis ID: | AN005504 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FullMS data was collected under both positive and negative mode. XCMS software was used for spectrum deconvolution and MetSign software for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis.To identify metabolites, 2DLC-MS/MS data was first matched to our in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards. Threshold for spectral similarity was set ≥ 0.4, while thresholds of retention time difference and m/z variation window were respectively set ≤ 0.15 min and ≤ 5 ppm. 2DLC-MS/MS data without a match with the metabolites in the in-house database were further analyzed using Compound Discoverer software (v 2.0, Thermo Fisher Scientific, Germany), where MS/MS spectra similarity score threshold was set ≥ 40 with a maximum score of 100. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005231 |
| Analysis ID: | AN005505 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FullMS data was collected under both positive and negative mode. XCMS software was used for spectrum deconvolution and MetSign software for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis.To identify metabolites, 2DLC-MS/MS data was first matched to our in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards. Threshold for spectral similarity was set ≥ 0.4, while thresholds of retention time difference and m/z variation window were respectively set ≤ 0.15 min and ≤ 5 ppm. 2DLC-MS/MS data without a match with the metabolites in the in-house database were further analyzed using Compound Discoverer software (v 2.0, Thermo Fisher Scientific, Germany), where MS/MS spectra similarity score threshold was set ≥ 40 with a maximum score of 100. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005232 |
| Analysis ID: | AN005506 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FullMS data was collected under negative mode. XCMS software was used for spectrum deconvolution and MetSign software for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis.To identify metabolites, 2DLC-MS/MS data was first matched to our in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards. Threshold for spectral similarity was set ≥ 0.4, while thresholds of retention time difference and m/z variation window were respectively set ≤ 0.15 min and ≤ 5 ppm. 2DLC-MS/MS data without a match with the metabolites in the in-house database were further analyzed using Compound Discoverer software (v 2.0, Thermo Fisher Scientific, Germany), where MS/MS spectra similarity score threshold was set ≥ 40 with a maximum score of 100. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005233 |
| Analysis ID: | AN005507 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FullMS data was collected under negative mode. XCMS software was used for spectrum deconvolution and MetSign software for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis.To identify metabolites, 2DLC-MS/MS data was first matched to our in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards. Threshold for spectral similarity was set ≥ 0.4, while thresholds of retention time difference and m/z variation window were respectively set ≤ 0.15 min and ≤ 5 ppm. 2DLC-MS/MS data without a match with the metabolites in the in-house database were further analyzed using Compound Discoverer software (v 2.0, Thermo Fisher Scientific, Germany), where MS/MS spectra similarity score threshold was set ≥ 40 with a maximum score of 100. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005234 |
| Analysis ID: | AN005508 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FullMS data was collected under negative mode. XCMS software was used for spectrum deconvolution and MetSign software for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis.To identify metabolites, 2DLC-MS/MS data was first matched to our in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards. Threshold for spectral similarity was set ≥ 0.4, while thresholds of retention time difference and m/z variation window were respectively set ≤ 0.15 min and ≤ 5 ppm. 2DLC-MS/MS data without a match with the metabolites in the in-house database were further analyzed using Compound Discoverer software (v 2.0, Thermo Fisher Scientific, Germany), where MS/MS spectra similarity score threshold was set ≥ 40 with a maximum score of 100. |
| Ion Mode: | NEGATIVE |
