Summary of Study ST004282

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 PR002706. The data can be accessed directly via it's Project DOI: 10.21228/M8W25J 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	ST004282
Study Title	Multiomics analysis of Peptide-Functionalized Zin Oxide Nanoparticles for the selective Targeting of Breast Cancer Expressing Placenta-Specific Protein 1
Study Type	LC/MS/MS
Study Summary	Metabolomics analysis is a powerful tool in biomedical research that allows to analyze in detail the small molecules metabolites present in biological systems. These metabolites provide crucial information about the metabolic pathways and processes found inside tissues, cells, and living things. In the context of nanoparticle studies, when zinc oxide nanoparticles with peptide (ZnOPs) were used, metabolicomics caused the changes in metabolism caused by nanoparticles. When zinc oxide nanoparticles (ZnO) were used to treat breast cancer, metabolomics studies revealed a distinct metabolic pattern when compared to untreated samples. These alterations might be due to abnormalities in signaling pathways, stress responses, and cellular metabolism brought on by exposure to nanoparticles. The potential of the metabolomics data to distinguish between several groups suggests that ZnO nanoparticles significantly affect the metabolomics of treated cells. L-norleucine is a prospective candidate for cancer therapy because of its ability to disrupt cancer cell metabolism, growth signaling pathways, and angiogenesis . Continued research into L-norleucine's anticancer characteristics could lead to the development of new therapeutic options for various cancers.6-Diazo-5-oxo-l-norleucine is a glutamine antagonist with anticancer activity proven in numerous preclinical trials. L-norleucine metabolite is present abundantly when treated with ZnOPs. Higher level of L-phenyl alanine was found when treated with ZnOPs compared to control. Previous research has demonstrated that l-phenylalanine acts as a transporter for anticancer medicines, delivering medication molecules straight into the tumor site . This can not only prevent cancer cell multiplication, but also lessen drug side effects. Oxaloacetic acid (OAA) is an important step in the citric acid cycle (also known as the Krebs cycle or tricarboxylic acid cycle), a critical route in cellular metabolism. While OAA has not been thoroughly explored in the context of cancer, changes in the citric acid cycle and other metabolic pathways have been linked to cancer biology.Oxaloacetate has the potential to directly affect the Warburg effect in cancer cells. Oxaloacetate (OAA) competitively inhibits human lactate dehydrogenase A (LDHA), preventing it from working in cancer cells. OAA promotes a favorable (alkaline) cellular environment that enables the success of other treatments. Quinaldic acid is thought to be a byproduct of kynurenic acid, a tryptophan metabolite that has antiproliferative capabilities against cancer. Quinaldic acid altered the phosphorylation levels of ERK 1/2, p38, cAMP response element-binding protein (CREB), and Akt (protein kinase B) kinases .Quinaldic acid was shown abundantly when treated with ZNOPs.
Institute	University of Sharjah
Last Name	Facility
First Name	Core
Address	Sharjah
Email	tims-tof@sharjah.ac.ae
Phone	0562075273
Submit Date	2025-10-10
Raw Data Available	Yes
Raw Data File Type(s)	mzML, d
Analysis Type Detail	LC-MS
Release Date	2025-11-03
Release Version	1

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Project:

Project ID:	PR002706
Project DOI:	doi: 10.21228/M8W25J
Project Title:	Multiomics analysis of Peptide-Functionalized Zin Oxide Nanoparticles for the selective Targeting of Breast Cancer Expressing Placenta-Specific Protein 1
Project Type:	LC-MS/MS
Project Summary:	Metabolomics analysis is a powerful tool in biomedical research that allows to analyze in detail the small molecules metabolites present in biological systems. These metabolites provide crucial information about the metabolic pathways and processes found inside tissues, cells, and living things. In the context of nanoparticle studies, when zinc oxide nanoparticles with peptide (ZnOPs) were used, metabolicomics caused the changes in metabolism caused by nanoparticles. When zinc oxide nanoparticles (ZnO) were used to treat breast cancer, metabolomics studies revealed a distinct metabolic pattern when compared to untreated samples. These alterations might be due to abnormalities in signaling pathways, stress responses, and cellular metabolism brought on by exposure to nanoparticles. The potential of the metabolomics data to distinguish between several groups suggests that ZnO nanoparticles significantly affect the metabolomics of treated cells. L-norleucine is a prospective candidate for cancer therapy because of its ability to disrupt cancer cell metabolism, growth signaling pathways, and angiogenesis . Continued research into L-norleucine's anticancer characteristics could lead to the development of new therapeutic options for various cancers.6-Diazo-5-oxo-l-norleucine is a glutamine antagonist with anticancer activity proven in numerous preclinical trials. L-norleucine metabolite is present abundantly when treated with ZnOPs. Higher level of L-phenyl alanine was found when treated with ZnOPs compared to control. Previous research has demonstrated that l-phenylalanine acts as a transporter for anticancer medicines, delivering medication molecules straight into the tumor site . This can not only prevent cancer cell multiplication, but also lessen drug side effects. Oxaloacetic acid (OAA) is an important step in the citric acid cycle (also known as the Krebs cycle or tricarboxylic acid cycle), a critical route in cellular metabolism. While OAA has not been thoroughly explored in the context of cancer, changes in the citric acid cycle and other metabolic pathways have been linked to cancer biology.Oxaloacetate has the potential to directly affect the Warburg effect in cancer cells. Oxaloacetate (OAA) competitively inhibits human lactate dehydrogenase A (LDHA), preventing it from working in cancer cells. OAA promotes a favorable (alkaline) cellular environment that enables the success of other treatments. Quinaldic acid is thought to be a byproduct of kynurenic acid, a tryptophan metabolite that has antiproliferative capabilities against cancer. Quinaldic acid altered the phosphorylation levels of ERK 1/2, p38, cAMP response element-binding protein (CREB), and Akt (protein kinase B) kinases .Quinaldic acid was shown abundantly when treated with ZNOPs.
Institute:	Sharjah Institute for Medical Research
Last Name:	Facility
First Name:	Core
Address:	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email:	tims-tof@sharjah.ac.ae
Phone:	+971 6 5057656

Subject:

Subject ID:	SU004435
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Sample source
SA498356	C4-01-11115	Control	breast cancer cell line (MDA-MB 231)
SA498357	C1-02-11110	Control	breast cancer cell line (MDA-MB 231)
SA498358	C4-02-11116	Control	breast cancer cell line (MDA-MB 231)
SA498359	C1-01-11109	Control	breast cancer cell line (MDA-MB 231)
SA498360	C3-02-11114	Control	breast cancer cell line (MDA-MB 231)
SA498361	C2-02-11112	Control	breast cancer cell line (MDA-MB 231)
SA498362	C2-01-11111	Control	breast cancer cell line (MDA-MB 231)
SA498363	C3-01-11113	Control	breast cancer cell line (MDA-MB 231)
SA498380	P4-02-11125	peptide solution	breast cancer cell line (MDA-MB 231)
SA498381	P4-01-11124	peptide solution	breast cancer cell line (MDA-MB 231)
SA498382	P3-02-11123	peptide solution	breast cancer cell line (MDA-MB 231)
SA498383	P3-01-11122	peptide solution	breast cancer cell line (MDA-MB 231)
SA498384	P2-02-11121	peptide solution	breast cancer cell line (MDA-MB 231)
SA498385	P2-01-11120	peptide solution	breast cancer cell line (MDA-MB 231)
SA498386	P1-02-11119	peptide solution	breast cancer cell line (MDA-MB 231)
SA498387	P1-01-11118	peptide solution	breast cancer cell line (MDA-MB 231)
SA498364	ZNOP4-02-11143	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498365	ZNOP4-01-11142	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498366	ZNOP3-02-11141	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498367	ZNOP3-01-11140	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498368	ZNOP2-02-11139	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498369	ZNOP2-01-11138	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498370	ZNOP1-02-11137	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498371	ZNOP1-01-11136	ZnOPs	breast cancer cell line (MDA-MB 231)
SA498372	ZNO3-02-11132	ZnO	breast cancer cell line (MDA-MB 231)
SA498373	ZNO4-02-11134	ZnO	breast cancer cell line (MDA-MB 231)
SA498374	ZNO4-01-11133	ZnO	breast cancer cell line (MDA-MB 231)
SA498375	ZNO2-02-11130	ZnO	breast cancer cell line (MDA-MB 231)
SA498376	ZNO3-01-11131	ZnO	breast cancer cell line (MDA-MB 231)
SA498377	ZNO2-01-11129	ZnO	breast cancer cell line (MDA-MB 231)
SA498378	ZNO1-02-11128	ZnO	breast cancer cell line (MDA-MB 231)
SA498379	ZNO1-01-11127	ZnO	breast cancer cell line (MDA-MB 231)

Showing results 1 to 32 of 32

Showing results 1 to 32 of 32

Collection:

Collection ID:	CO004428
Collection Summary:	The human metastatic breast cancer cell line (MDA-MB 231) was acquired from ATCC (Manassas, VA, USA). The MDA-MB 231 cells were cultivated in RPMI media supplemented with 10% fetal bovine serum, 100 units/mL of penicillin, and 100 μg/mL of streptomycin. Cell lines were cultured in a controlled environment with specific humidity and 5% CO2 at a temperature of 37 °C for further investigations.
Sample Type:	Cultured cells

Treatment:

Treatment ID:	TR004444
Treatment Summary:	Zinc oxide-p nanoparticles (ZnOPs) were synthesized by dispersing 2 mig of zinc oxide nanoparticles (ZnO) in 4 mL of water using sonication for 10 minutes. A peptide solution was created by dissolving 9 mg of GILGFVFTL peptide in a mixture of ACN and water (91:9) until the final concentration reached 562 µg/mL. The peptide solution was thereafter introduced gradually to the suspension of ZnO while being agitated at a speed of 600 rpm for of 2 hours at ambient temperature. The ZnOPs were rinsed with distilled water and then subjected to ultracentrifugation at 16,000 rpm for 24 minutes at a temperature of 4 °C. The washing phase was performed twice in order to eliminate any peptides that was not bonded. An equal number of MDA-MB 231 cells (5 × 103 ) were seeded and treated with ZnO or ZnOPs at concentrations of 73.73 µg/mL and 47.72 µg/mL, respectively, for 6 hours. After treatment, the cells were collected from the culture dishes using cell scrapers. The detached cell pellets were then collected by centrifugation at 15000 rpm for 10 min at 4oC to remove excess PBS.

Treatment ID:

TR004444

Treatment Summary:

Zinc oxide-p nanoparticles (ZnOPs) were synthesized by dispersing 2 mig of zinc oxide nanoparticles (ZnO) in 4 mL of water using sonication for 10 minutes. A peptide solution was created by dissolving 9 mg of GILGFVFTL peptide in a mixture of ACN and water (91:9) until the final concentration reached 562 µg/mL. The peptide solution was thereafter introduced gradually to the suspension of ZnO while being agitated at a speed of 600 rpm for of 2 hours at ambient temperature. The ZnOPs were rinsed with distilled water and then subjected to ultracentrifugation at 16,000 rpm for 24 minutes at a temperature of 4 °C. The washing phase was performed twice in order to eliminate any peptides that was not bonded. An equal number of MDA-MB 231 cells (5 × 103 ) were seeded and treated with ZnO or ZnOPs at concentrations of 73.73 µg/mL and 47.72 µg/mL, respectively, for 6 hours. After treatment, the cells were collected from the culture dishes using cell scrapers. The detached cell pellets were then collected by centrifugation at 15000 rpm for 10 min at 4oC to remove excess PBS.

Sample Preparation:

Sampleprep ID:	SP004441
Sampleprep Summary:	The cells were treated with 1 mL of the extraction solvent (methanol + 0.1% FA), which inhibited metabolic activity. To ensure that metabolites were extracted quantitatively, the cells were vortexed for two minutes before being placed on ice for one hour. Subsequently, intermittent ultrasonication was applied to the insoluble cell matrices using the COPLEY sonicator (Qsonica Sonicator, USA) with a 30% amplifier and for 30 seconds while a cold bath was utilized. The cell debris was subjected to centrifugation at 15,000 rpm for 10 minutes at -4°C. The supernatants were collected and evaporated using a speed vac (Genevac EZ-2 plus, Ipswich, UK). The extract samples were resuspended with 200uL of 0.1% formic acid in deionized water-LC-MS CHROMASOLV from Honeywell (Wunstorfer Strasse, Seelze, Germany) and vortexed for 2 min to be mixed totally. Finally, the samples were filtered using a hydrophilic nylon syringe filter of 0.45 µm pore size and returned to the glass insert within LC glass vials. The quality control (QC) sample was prepared by pooling the same volume (10 μL) of each sample, and all samples were placed in the autosampler at a temperature set at 4℃ and analyzed with UHPLC-QTOF-MS.
Processing Storage Conditions:	On ice

Combined analysis:

Analysis ID	AN007122
Chromatography ID	CH005412
MS ID	MS006818
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Bruker Elute
Column	Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Bruker timsTOF
Ion Mode	POSITIVE
Units	AU

Chromatography:

Chromatography ID:	CH005412
Chromatography Summary:	The Elute UHPLC and Q-TOF Mass Spectrometer (Bruker, Bremen, Germany) were utilized for metabolite detection. The Elute HPG 1300 pumps, Elute Au-tosampler (Bruker, Bremen, Germany), and Hamilton® Intensity Solo 2 C18 column (100 mm x 2.1 mm, 1.8 μm) were employed using reversed-phase chromatography. Solvents used for separation were 0.1 % FA in LC grade water (solvent A) and 0.1 % FA in ACN (solvent B). The column was kept at 35°C, and each sample was injected twice with an injection volume of 10 µL. Sample elution was performed in 30 min gradient starting with 1% ACN for 2 min and then ramped to 99% ACN within 15 min. After that, 99% ACN was kept for 3 min, and then the re-equilibration to 1% ACN was done for 10 min. The flow rate was 0.25 mL/min for 20 min and then 0.35 mL/min for 8.3 min and then the flow rate set at 0.25 mL/min for 1.7 min.
Instrument Name:	Bruker Elute
Column Name:	Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8um)
Column Temperature:	35°C
Flow Gradient:	Sample elution was performed in 30 min gradient starting with 1% B for 2 min and then ramped to 99% B within 15 min. After that, 99% B was kept for 3 min, and then the re-equilibration to 1% B was done for 10 min.
Flow Rate:	The flow rate was 0.25 mL/min for 20 min and then 0.35 mL/min for 8.3 min and then the flow rate set at 0.25 mL/min for 1.7 min.
Solvent A:	100% water; 0.1 % Formic acid
Solvent B:	100% acetonitrile; 0.1 % Formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS006818
Analysis ID:	AN007122
Instrument Name:	Bruker timsTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	A timsTOF (Bruker, Bremen, Germany) with an Apollo II electrospray ionization (ESI) source was utilized for the MS analysis with the following parameters: the nebulizer pressure was 2.2 bar, the drying gas flow rate was 10 L/min, the drying temperature was 220°C, and the capillary voltage was 4500 V. In the first 0.3 min of each LC-MS/MS run, the external calibrant, sodium formate, was injected. The acquisition was in two sections: auto MS scan for the calibrant sodium formate in 0-0.3 min, and auto MS/MS for fragmentation, in 0.3 to 30 min. Positive mode at 12 Hz was performed in both acquisition sections. The scan range was 20 to 1300 m/z, the precursor ion’s width of ±0.5, the cycle time of 0.5 seconds, and the threshold of 400 counts. After three spectra, active exclusion was performed and released after 0.2 min. For MS2 acquisition, the collision energy was fluctuated between 100-250% of 20 eV and end plate offset of 500V Mass calibration was done prior to analysis according to the manufacturer’s recommendations using external mass calibration (10 mM sodium formate calibrant solution). The performance of the column and the mass spectrometer was tested using a test mixture of (TRX-2101/RT-28-calibrants for Bruker T-ReX LC-QTOF solution from Nova Medical Testing Inc.) to check the performance of reversed-phase liquid chromatography (RPLC) separation and perform multipoint re-tention time calibration, and (TRX-3112-R/MS Certified Human serum for Bruker T-ReX LC-QTOF solution from Nova Medical Testing Inc.) to check the performance of sample preparation protocols as well as LC-MS instruments.
Ion Mode:	POSITIVE