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

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Study IDST001167
Study TitleComprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry
Study SummaryWe 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, Chinese Academy Of Sciences
Last NameWang
First NameZhichao
Address457, Zhongshan Road
Emailwangzc05@dicp.ac.cn
Phone+86-15998625250
Submit Date2019-01-06
Study CommentsComprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry - A Novel Tool Complementing Metabolomics Analyses of Polar Metabolites
Raw Data AvailableYes
Raw Data File Type(s).cd,.cg, .xml, .bin, .stg
Analysis Type DetailLC-MS
Release Date2020-01-06
Release Version1
Zhichao Wang Zhichao Wang
https://dx.doi.org/10.21228/M8097N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA08068813RWPE1_0.25-4RWPE1 0.25h
SA08068913RWPE1_0.25-3RWPE1 0.25h
SA08069013RWPE1_0.25-2RWPE1 0.25h
SA08069112RWPE1_0-2RWPE1 0h
SA08069212RWPE1_0-1RWPE1 0h
SA08069312RWPE1_0-3RWPE1 0h
SA08069412RWPE1_0-4RWPE1 0h
SA08069513RWPE1_12-3RWPE1 12h
SA08069613RWPE1_12-2RWPE1 12h
SA08069713RWPE1_12-4RWPE1 12h
SA08069813RWPE1_12-1RWPE1 12h
SA08069913RWPE1_24-4RWPE1 24h
SA08070013RWPE1_24-3RWPE1 24h
SA08070113RWPE1_24-2RWPE1 24h
SA08070213RWPE1_24-1RWPE1 24h
SA08070313RWPE1_4-3RWPE1 4h
SA08070413RWPE1_4-4RWPE1 4h
SA08070513RWPE1_4-2RWPE1 4h
SA08070613RWPE1_P3-4RWPE1 6days
SA08070713RWPE1_P3-1RWPE1 6days
SA08070813RWPE1_P3-3RWPE1 6days
SA08070913RWPE1_P3-2RWPE1 6days
SA08071013VCaP_0.25-1VCaP 0.25h
SA08071113VCaP_0.25-3VCaP 0.25h
SA08071213VCaP_0.25-2VCaP 0.25h
SA08071313VCaP_0.25-4VCaP 0.25h
SA08071412VCaP_0-2VCaP 0h
SA08071512VCaP_0-4VCaP 0h
SA08071612VCaP_0-1VCaP 0h
SA08071712VCaP_0-3VCaP 0h
SA08071813VCaP_12-2VCaP 12h
SA08071913VCaP_12-3VCaP 12h
SA08072013VCaP_12-1VCaP 12h
SA08072113VCaP_12-4VCaP 12h
SA08072213VCaP_24-2VCaP 24h
SA08072313VCaP_24-4VCaP 24h
SA08072413VCaP_24-1VCaP 24h
SA08072513VCaP_24-3VCaP 24h
SA08072613VCaP_4-1VCaP 4h
SA08072713VCaP_4-2VCaP 4h
SA08072813VCaP_4-3VCaP 4h
SA08072913VCaP_4-4VCaP 4h
SA08073013VCaP_P3-4VCaP 6days
SA08073113VCaP_P3-1VCaP 6days
SA08073213VCaP_P3-2VCaP 6days
SA08073313VCaP_P3-3VCaP 6days
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.

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.

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:solution of 25 mM ammonium acetate and 75 mM diammonium hydrogen 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
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