Summary of Study ST002318

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 PR001485. The data can be accessed directly via it's Project DOI: 10.21228/M8S41S This work is supported by NIH grant, U2C- DK119886.


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Study IDST002318
Study TitleMass spectroscopy‑based proteomics and metabolomics analysis of triple‑positive breast cancer cells treated with trastuzumab
Study SummaryHER2-enriched breast cancer with high levels of hormone receptor expression, known as triple positive breast cancer, may represent a new entity with a relatively favourable prognosis against which the combination of chemotherapy, HER-2 inhibition, and endocrine treatment may be considered overtreatment. We explored the effect of the anticancer drugs tamoxifen and trastuzumab, both separately and in combination, on the integrated proteomic and metabolic profile of triple positive breast cancer cells (BT-474). Method We employed ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry using a Bruker timsTOF to investigate changes in BT-474 cell line treated with either tamoxifen, trastuzumab or a combination. Differentially abundant metabolites were identified using the Bruker Human Metabolome Database metabolite library and proteins using the Uniprot proteome for Homo sapiens using MetaboScape and MaxQuant, respectively, for identification and quantitation. Results A total of 77 proteins and 85 metabolites were found to significantly differ in abundance in BT-474 treated cells with tamoxifen 5 μM/and or trastuzumab 2.5 μM. Findings suggest that by targeting important cellular signalling pathways which regulate cell growth, apoptosis, proliferation, and chemoresistance, these medicines have a considerable anti-growth effect in BT-474 cells. Pathways enriched for dysregulation include RNA splicing, neutrophil degranulation and activation, cellular redox homeostasis, mitochondrial transmembrane transport, ferroptosis and necroptosis, ABC transporters and central carbon metabolism. Conclusion Our findings in protein and metabolite level research revealed that anti-cancer drug therapy had a significant impact on the key signalling pathways and molecular processes in triple positive BT-474 cell lines.
University of Sharjah
DepartmentSharjah Institute for Medical Research
LaboratoryBiomarker Discovery Group
Last NameSoares
First NameNelson
AddressM32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah
Submit Date2022-10-18
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-11-21
Release Version1
Nelson Soares Nelson Soares application/zip

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Combined analysis:

Analysis ID AN003785
Analysis type MS
Chromatography type Reversed phase
Chromatography system Bruker Elute HPG 1300
Column Hamilton Intensity Solo 2 C18
MS instrument type QTOF
MS instrument name Bruker timsTOF
Units AU


Chromatography ID:CH002799
Chromatography Summary:Samples were chromatographically separated by inline reversed-phase chromatography using the Elute HPG 1300 pumps and Elute Autosampler (Bruker, Darmstadt, Germany) with solvent A 0.1% FA in HPLC grade water and solvent B 0.1% FA in ACN. A Hamilton Intensity Solo 2 C18 column (100 mm × 2.1 mm, 1.8 μm beads) was maintained at 35 ℃ (metabolomics analyses).
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Instrument Name:Bruker Elute HPG 1300
Column Name:Hamilton Intensity Solo 2 C18
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Column Temperature:35
Flow Gradient:1%B to 99%B in 15 min
Flow Rate:250 uL/min
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Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
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Oven Temperature:35C
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Chromatography Type:Reversed phase