Summary of Study ST001265

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 PR000850. The data can be accessed directly via it's Project DOI: 10.21228/M8T98G This work is supported by NIH grant, U2C- DK119886.


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Study IDST001265
Study TitleComparative metabolomics of MCF-7 breast cancer cells using different extraction solvents assessed by mass spectroscopy
Study TypeAnalysing metabolomics using GC Mass Spectroscopy
Study SummaryMetabolic profiling of cancer cells can play a vital role in revealing the molecular bases of cancer development and progression. In this study, gas chromatography coupled with mass spectrometry (GC-MS) was employed for the determination of signatures found in ER+/ PR+ breast cancer cells derived from MCF-7 using different extraction solvents including: A, formic acid in water; B, ammonium hydroxide in water; C, ethyl acetate; D, methanol: water (1:1, v/v); and E, acetonitrile: water (1:1, v/v). The greatest extraction rate and diversity of metabolites occurs with extraction solvents A and E. Extraction solvent D showed moderate extraction efficiency, whereas extraction solvent B and C showed inferior metabolite diversity. Metabolite set enrichment analysis results showed energy production pathways to be key in MCF-7 cell lines. This study showed that mass spectrometry could identify key metabolites associated with cancers. The highest enriched pathways were related to energy production as well as Warburg effect pathways, which may shed light on how energy metabolism has been hijacked to encourage tumour progression and eventually metastasis in breast cancer.
Sharjah Institute for Medical Research
DepartmentClinical Science
Last NameHamoudi
First NameRifat
AddressCollege of Medicine, University of Sharjah
Submit Date2019-07-08
Total SubjectsFive different extractions
Study CommentsMCF-7 cell line
Raw Data AvailableYes
Raw Data File Type(s)gqd
Analysis Type DetailGC-MS
Release Date2019-10-11
Release Version1
Rifat Hamoudi Rifat Hamoudi application/zip

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Combined analysis:

Analysis ID AN002102
Analysis type MS
Chromatography type GC
Chromatography system Shimadzu GCMS-QP2010 Ultra
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Shimadzu QP2010 Ultra
Units Peak Area


Chromatography ID:CH001534
Chromatography Summary:A GC/MS-QP 2010 Ultra System (Shimadzu, Kyoto, Japan) was employed for the metabolomic analysis, along with LabSolutions GC-MS software (ver). A Restek Rtx®-5ms column (30.0 m × 0.25 mm, 0.25 µm) was utilized for separation of the metabolites. Helium (99.9%) was used as the carrier gas at the flow rate of 1.0 mL/min. The initial oven temperature was set at 60 °C and was held at this temperature for 2 minutes, then raised to 310 °C by 50 °C/min and held at this temperature during the analysis. Both the auxiliary temperature at the interface and the ionization temperature were 250 °C. Metabolites were analysed in full scan mode within the range of 50 – 650 amu. Total volume of 10 µL was injected in splitless mode, by employing AOC-20i Auto Injector (Shimadzu, Kyoto, Japan). GC total ion chromatograms (TIC) and fragmentation patterns of the metabolites identified using NIST/EPA/NIH Mass Spectral Library (NIST 14). Run time for each sample was 43.67 min.
Methods Filename:PAH scan
Instrument Name:Shimadzu GCMS-QP2010 Ultra
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Column Pressure:57.4
Column Temperature:60
Flow Rate:1
Injection Temperature:250
Retention Time:many retention time
Sample Injection:1
Solvent A:Pyridine
Analytical Time:43.67
Oven Temperature:60
Time Program:43.67
Transferline Temperature:250
Strong Wash Solvent Name:Acetone
Strong Wash Volume:10 uL
Sample Syringe Size:10 uL
Chromatography Type:GC