Summary of Study ST001167

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 PR000779. The data can be accessed directly via it's Project DOI: 10.21228/M8097N This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST001167
Study Title	Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry
Study Summary	We developed a stable-isotope tracing capillary electrophoresis (CE)-MS metabolomics approach to cover polar metabolites as well as isotopologues in a non-targeted way. An in-house developed software enables high throughput processing of complex multi-dimensional data. The practicability is demonstrated analysing 13C-U-glucose exposed prostate cancer and non-cancer cells.
Institute	Dalian Institute Of Chemical Physics
Last Name	Wang
First Name	Zhichao
Address	457, Zhongshan Road
Email	wangzc05@dicp.ac.cn
Phone	+86-15998625250
Submit Date	2019-01-06
Study Comments	Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry - A Novel Tool Complementing Metabolomics Analyses of Polar Metabolites
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2020-01-06
Release Version	1

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Project:

Project ID:	PR000779
Project DOI:	doi: 10.21228/M8097N
Project Title:	Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry
Project Summary:	Prostate cell RWPE1 and prostate cancer cell VCaP were labeled with 13C6-Glucose for 6 time points 0h, 0.25h, 4h, 12h, 24h and 6 days. Then CE-MS based metabolomics analysis were peformed.
Institute:	Dalian Institute Of Chemical Physics, Chinese Academy Of Sciences
Department:	Group, 1808
Last Name:	Wang
First Name:	Zhichao
Address:	457, Zhongshan Road, Dalian, Shenyang
Email:	wangzc05@dicp.ac.cn
Phone:	+86-15998625250
Project Comments:	A Novel Tool Complementing Metabolomics Analyses of Polar Metabolites

Subject:

Subject ID:	SU001232
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	Cell lines	Time points
SA080688	13RWPE1_0.25-4	RWPE1	0.25h
SA080689	13RWPE1_0.25-3	RWPE1	0.25h
SA080690	13RWPE1_0.25-2	RWPE1	0.25h
SA080691	12RWPE1_0-2	RWPE1	0h
SA080692	12RWPE1_0-1	RWPE1	0h
SA080693	12RWPE1_0-3	RWPE1	0h
SA080694	12RWPE1_0-4	RWPE1	0h
SA080695	13RWPE1_12-3	RWPE1	12h
SA080696	13RWPE1_12-2	RWPE1	12h
SA080697	13RWPE1_12-4	RWPE1	12h
SA080698	13RWPE1_12-1	RWPE1	12h
SA080699	13RWPE1_24-4	RWPE1	24h
SA080700	13RWPE1_24-3	RWPE1	24h
SA080701	13RWPE1_24-2	RWPE1	24h
SA080702	13RWPE1_24-1	RWPE1	24h
SA080703	13RWPE1_4-3	RWPE1	4h
SA080704	13RWPE1_4-4	RWPE1	4h
SA080705	13RWPE1_4-2	RWPE1	4h
SA080706	13RWPE1_P3-4	RWPE1	6days
SA080707	13RWPE1_P3-1	RWPE1	6days
SA080708	13RWPE1_P3-3	RWPE1	6days
SA080709	13RWPE1_P3-2	RWPE1	6days
SA080710	13VCaP_0.25-1	VCaP	0.25h
SA080711	13VCaP_0.25-3	VCaP	0.25h
SA080712	13VCaP_0.25-2	VCaP	0.25h
SA080713	13VCaP_0.25-4	VCaP	0.25h
SA080714	12VCaP_0-2	VCaP	0h
SA080715	12VCaP_0-4	VCaP	0h
SA080716	12VCaP_0-1	VCaP	0h
SA080717	12VCaP_0-3	VCaP	0h
SA080718	13VCaP_12-2	VCaP	12h
SA080719	13VCaP_12-3	VCaP	12h
SA080720	13VCaP_12-1	VCaP	12h
SA080721	13VCaP_12-4	VCaP	12h
SA080722	13VCaP_24-2	VCaP	24h
SA080723	13VCaP_24-4	VCaP	24h
SA080724	13VCaP_24-1	VCaP	24h
SA080725	13VCaP_24-3	VCaP	24h
SA080726	13VCaP_4-1	VCaP	4h
SA080727	13VCaP_4-2	VCaP	4h
SA080728	13VCaP_4-3	VCaP	4h
SA080729	13VCaP_4-4	VCaP	4h
SA080730	13VCaP_P3-4	VCaP	6days
SA080731	13VCaP_P3-1	VCaP	6days
SA080732	13VCaP_P3-2	VCaP	6days
SA080733	13VCaP_P3-3	VCaP	6days

Showing results 1 to 46 of 46

Showing results 1 to 46 of 46

Collection:

Collection ID:	CO001226
Collection Summary:	cells were grown in RPMI 1640 medium containing 2 g/L glucose with 10% dFBS, and were harvested at 80% confluence. One hour before the isotope switch, the medium was aspirated and replaced with fresh unlabeled medium[1]. Subsequently, VCaP and RWPE-1 were cultured in RPMI 1640 medium with 2 g/L [U−13C]-glucose and 10% dFBS for 0 h, 0.25 h, 4 h, 12 h, 24 h and long-term for 6 days performing thereby 3 passages. 10 cm petri dish with 10 mL of media was used for each sample, and 4 independent biological replicates were prepared for the labeling experiments. Unlabeled samples were treated in the same way with medium containing unlabeled glucose. After the cultures have been grown for the targeted amount of time, the medium was aspirated completely, then cells were washed thrice with 5% D-mannitol solution, followed by inactivation with liquid nitrogen immediately.
Sample Type:	Cultured cells

Treatment:

Treatment ID:	TR001247
Treatment Summary:	One hour before the isotope switch, the medium was aspirated and replaced with fresh unlabeled medium[1]. Subsequently, VCaP and RWPE-1 were cultured in RPMI 1640 medium with 2 g/L [U−13C]-glucose and 10% dFBS for 0 h, 0.25 h, 4 h, 12 h, 24 h and long-term for 6 days performing thereby 3 passages. 10 cm petri dish with 10 mL of media was used for each sample, and 4 independent biological replicates were prepared for the labeling experiments. Unlabeled samples were treated in the same way with medium containing unlabeled glucose.

Treatment ID:

TR001247

Treatment Summary:

One hour before the isotope switch, the medium was aspirated and replaced with fresh unlabeled medium[1]. Subsequently, VCaP and RWPE-1 were cultured in RPMI 1640 medium with 2 g/L [U−13C]-glucose and 10% dFBS for 0 h, 0.25 h, 4 h, 12 h, 24 h and long-term for 6 days performing thereby 3 passages. 10 cm petri dish with 10 mL of media was used for each sample, and 4 independent biological replicates were prepared for the labeling experiments. Unlabeled samples were treated in the same way with medium containing unlabeled glucose.

Sample Preparation:

Sampleprep ID:	SP001240
Sampleprep Summary:	After the cultures have been grown for the targeted amount of time, the medium was aspirated completely, then cells were washed thrice with 5% D-mannitol solution, followed by inactivation with liquid nitrogen immediately. Cells were handled on ice during the preparation. 1 mL of precooled methanol, containing 13.3 μM of MetS and CSA, was added to each cell culture dish. Cells were harvested using a cell scraper, and transferred into a 5 mL tube. Then, 1 mL of chloroform was added and vortexed for 5 min, followed by 400 μL of Milli-Q water and 10 min of vortexing. After 5 min of standing, the mixture was centrifuged to form a two-phase system (10,000 g, 4 °C, 15 min). The upper layer was transferred and centrifugally filtered through a Millipore 5-kDa cutoff filter (USA) (13,000 g, 3h at 4°C). The filtrate was dried and stored at -80 °C. Finally, the upper extract was dissolved in Milli-Q water containing 50 μM of 3-AP, DPA, DHD and TMA for capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS) analysis.

Sampleprep ID:

SP001240

Sampleprep Summary:

After the cultures have been grown for the targeted amount of time, the medium was aspirated completely, then cells were washed thrice with 5% D-mannitol solution, followed by inactivation with liquid nitrogen immediately. Cells were handled on ice during the preparation. 1 mL of precooled methanol, containing 13.3 μM of MetS and CSA, was added to each cell culture dish. Cells were harvested using a cell scraper, and transferred into a 5 mL tube. Then, 1 mL of chloroform was added and vortexed for 5 min, followed by 400 μL of Milli-Q water and 10 min of vortexing. After 5 min of standing, the mixture was centrifuged to form a two-phase system (10,000 g, 4 °C, 15 min). The upper layer was transferred and centrifugally filtered through a Millipore 5-kDa cutoff filter (USA) (13,000 g, 3h at 4°C). The filtrate was dried and stored at -80 °C. Finally, the upper extract was dissolved in Milli-Q water containing 50 μM of 3-AP, DPA, DHD and TMA for capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS) analysis.

Combined analysis:

Analysis ID	AN001929	AN001930
Analysis type	MS	MS
Chromatography type	CE	CE
Chromatography system	Agilent 1290 Infinity II	Agilent 1290 Infinity II
Column	a fused silica capillary (50 μm i.d. × 80 cm)	a fused silica capillary (50 μm i.d. × 80 cm)
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	Agilent 6224 TOF	Agilent 6224 TOF
Ion Mode	POSITIVE	NEGATIVE
Units	Relative intensity after normalization	Relative intensity after normalization

Chromatography:

Chromatography ID:	CH001400
Instrument Name:	Agilent 1290 Infinity II
Column Name:	a fused silica capillary (50 μm i.d. × 80 cm)
Column Temperature:	20
Flow Rate:	a positive voltage of 27 kV
Injection Temperature:	20
Solvent A:	1 M formic acid
Chromatography Type:	CE

Chromatography ID:	CH001401
Instrument Name:	Agilent 1290 Infinity II
Column Name:	a fused silica capillary (50 μm i.d. × 80 cm)
Column Temperature:	20
Flow Rate:	internal pressure of 15 mbar and positive voltage of 30 kV
Injection Temperature:	20
Solvent A:	100% water; 25 mM ammonium acetate; 75 mM ammonium phosphate, pH 8.5
Chromatography Type:	CE

MS:

MS ID:	MS001785
Analysis ID:	AN001929
Instrument Name:	Agilent 6224 TOF
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	nebulizer pressure of 5 psig, dry gas temperature of 300 °C, nitrogen flow of 7 L/min, capillary voltage of 4 kV, fragmentor of 105 V, skimmer of 50 V, Oct RFV of 650 V, acquisition rate of 1.5 spectra/s and mass range of 60-1,000 were utilized.
Ion Mode:	POSITIVE

MS ID:	MS001786
Analysis ID:	AN001930
Instrument Name:	Agilent 6224 TOF
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	capillary voltage of 3.5 kV, fragmentor of 125 V and mass range of 50-1,000 were set in the TOF/MS analysis. During sample analysis, reference masses were applied to ensure the real-time calibration of exact mass measurement.
Ion Mode:	NEGATIVE