Summary of study ST000784

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 PR000570. The data can be accessed directly via it's Project DOI: 10.21228/M80D5X This work is supported by NIH grant, U2C- DK119886.

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Study IDST000784
Study Titlemetabolome in a group of AA and EA matched pairs of prostate cancer (PCa) and benign adjacent tissues
Study Summary10 µL of suspended samples was injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM) of a total of 240 endogenous water soluble metabolites for steady-state analyses of samples. Those 240 compounds monitored were chosen due to their involvement in central pathways important in a number of malignancies. Source parameters were as follows: Gas temperature was 250 °C; Gas flow was 14 l/min; Nebulizer was 20psi; Sheath gas temperature was 350 °C; Sheath gas flow was 12 l/min; Capillary was 3000 V positive and 3000 V negative; Nozzle voltage was 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. Samples were delivered to the MS via normal phase chromatography using either a 4.6 mm i.d ×10 cm Amide XBridge HILIC column (Waters) or a Luna 3µ NH2 100A (Phenomenex) at 300 µL/min
Institute
Baylor College of Medicine
Last NameSreekumar
First NameArun
AddressOne Baylor Plaza, Houston, TX, 77030, USA
EmailArun.Sreekumar@bcm.edu
Phone713-798-3305
Submit Date2017-05-17
Raw Data AvailableYes
Raw Data File Type(s)excel
Analysis Type DetailLC-MS
Release Date2019-07-17
Release Version1
Arun Sreekumar Arun Sreekumar
https://dx.doi.org/10.21228/M80D5X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP000814
Sampleprep Summary:For extraction of metabolome, 10 mg of tissue was homogenized in 1:4 ice cold water:methanol mixture containing equimolar mixture of 11 standard compounds [Epibrassinolide, [D3] Testosterone (mass difference from endogenous Testosterone = 3 Da), [15N] Anthranilic acid (mass difference from endogenous Anthranilic acid =1 Da), Zeatine, Jasmonic acid, Gibberelic acid, [D4] Estrone (mass difference from endogenous Estrone =4 Da), [15N]-Tryptophan (mass difference from endogenous Tryptophan =1 Da), [D4] Thymine (mass difference from endogenous Thymine =4 Da), [13C] Creatinine (mass difference from endogenous Creatinine =1 Da) and [15N] Arginine (mass difference from endogenous Arginine =1 Da)]. This was followed by sequential addition of ice cold chloroform and water in 3:1 ratio and separation of the organic (methanol and chloroform) and aqueous solvents (water:methanol:chloroform:water; ratio 1:4:3:1). The aqueous extract was de-proteinized using a 3 KDa molecular filter (Amicon Ultracel -3K Membrane, Millipore Corporation, Billerica, MA) and the filtrate containing metabolites was dried under vacuum (Genevac EZ-2plus, Gardiner, NY). Prior to mass spectrometry, the dried extract was resuspended in identical volume of injection solvent composed of water:methanol (50:50) and subjected to liquid chromatography (LC) mass spectrometry.
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