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.

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

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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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Project:

Project ID:PR000570
Project DOI:doi: 10.21228/M80D5X
Project Title:Metabolomics study of Prostate cancer for African American
Project Type:MS quantitative analysis
Project Summary:Quantitative metabolomics studies on tissues, serum and urine of prostate cancer for African American.
Institute:Baylor College of Medicine
Last Name:Sreekumar
First Name:Arun
Address:One Baylor Plaza, Houston, TX, 77030, USA
Email:Arun.Sreekumar@bcm.edu
Phone:713-798-3305

Subject:

Subject ID:SU000807
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Diagnosis Race
SA04272536673Benign AA
SA04272636916Benign AA
SA04272737687Benign AA
SA04272832871Benign AA
SA04272937654Benign AA
SA04273032595Benign AA
SA04273123979Benign AA
SA04273231703Benign AA
SA04273332567Benign AA
SA04273437976Benign AA
SA04273543779Benign AA
SA04273653247Benign AA
SA04273753983Benign AA
SA04273854182Benign AA
SA04273959701Benign AA
SA04274053131Benign AA
SA04274152012Benign AA
SA04274222693Benign AA
SA04274347605Benign AA
SA04274450742Benign AA
SA0427453609Benign AA
SA04274642957Benign AA
SA04274718476Benign AA
SA04274819338Benign AA
SA04274919051Benign AA
SA04275019205Benign AA
SA04275110188Benign AA
SA0427525050Benign AA
SA04275310506Benign AA
SA04275422346Benign AA
SA04275521274Benign AA
SA0427568678Benign AA
SA04275710524Benign AA
SA04275819567Benign EA
SA04275917626Benign EA
SA04276017637Benign EA
SA04276123868Benign EA
SA04276224070Benign EA
SA04276339117Benign EA
SA04276436361Benign EA
SA04276531630Benign EA
SA04276626163Benign EA
SA04276739907Benign EA
SA04276825793Benign EA
SA04276925923Benign EA
SA04277025944Benign EA
SA04277153248Cancer AA
SA0427723608Cancer AA
SA04277322343Cancer AA
SA0427748680Cancer AA
SA04277554184Cancer AA
SA04277659703Cancer AA
SA0427775057Cancer AA
SA04277853984Cancer AA
SA04277953132Cancer AA
SA04278019204Cancer AA
SA04278132594Cancer AA
SA04278232870Cancer AA
SA04278352014Cancer AA
SA04278419053Cancer AA
SA04278532564Cancer AA
SA04278619337Cancer AA
SA04278722694Cancer AA
SA04278821275Cancer AA
SA04278923977Cancer AA
SA04279031708Cancer AA
SA04279136914Cancer AA
SA04279236668Cancer AA
SA04279343782Cancer AA
SA04279442955Cancer AA
SA04279510512Cancer AA
SA04279647603Cancer AA
SA04279710184Cancer AA
SA04279850739Cancer AA
SA04279937977Cancer AA
SA04280010526Cancer AA
SA04280137653Cancer AA
SA04280218473Cancer AA
SA04280337689Cancer AA
SA04280417627Cancer EA
SA04280536357Cancer EA
SA04280639116Cancer EA
SA04280719564Cancer EA
SA04280839910Cancer EA
SA04280923870Cancer EA
SA04281026166Cancer EA
SA04281125945Cancer EA
SA04281217643Cancer EA
SA04281324068Cancer EA
SA04281426084Cancer EA
SA04281525794Cancer EA
SA04281625922Cancer EA
Showing results 1 to 92 of 92

Collection:

Collection ID:CO000801
Collection Summary:Frozen pathologically-verified prostate tissues were collected and stored at -140°C until analysis
Sample Type:Prostate

Treatment:

Treatment ID:TR000821
Treatment Summary:NA

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.

Combined analysis:

Analysis ID AN001240 AN001241 AN001242 AN001243
Analysis type MS MS MS MS
Chromatography type HILIC HILIC HILIC HILIC
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters XBridge Amide (100 x 4.6mm, 3.5um) Waters XBridge Amide (100 x 4.6mm, 3.5um) Phenomenex Luna NH2 (150 x 2.1mm, 3um) Phenomenex Luna NH2 (150 x 2.1mm, 3um)
MS Type ESI ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name Agilent 6490A QQQ Agilent 6490A QQQ Agilent 6490A QQQ Agilent 6490A QQQ
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units log transform with internal standard normalization log transform with internal standard normalization log transform with internal standard normalization log transform with internal standard normalization

Chromatography:

Chromatography ID:CH000867
Chromatography Summary:Flow rate was 0.3ml/min. Gradients were run starting from 85% buffer B (0.1% formic acid in acetonitrile) to 35% B from 0–3.5 minutes; 35% B to 2% B from 3.5–11.5 minutes; 2% B was held from 11.5–16.5 minutes; 2% B to 85% B from 16.5–17.5 minutes; 85% B was held for 7 minutes to re-equilibrate the column.
Instrument Name:Agilent 1290 Infinity
Column Name:Waters XBridge Amide (100 x 4.6mm, 3.5um)
Flow Rate:0.3ml/min
Solvent A:0.1% formic acid in HPLC grade water
Solvent B:0.1% formic acid in HPLC grade acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH000868
Chromatography Summary:Flow rate was 0.3ml/min. Gradients were run starting from 85% buffer B (HPLC grade acetonitrile ) to 35% B from 0–3.5 minutes; 35% B to 2% B from 3.5–11.5 minutes; 2% B was held from 11.5–16.5 minutes; 2% B to 85% B from 16.5–17.5 minutes; 85% B was held for 7 minutes to re-equilibrate the column
Instrument Name:Agilent 1290 Infinity
Column Name:Phenomenex Luna NH2 (150 x 2.1mm, 3um)
Flow Rate:0.3ml/min
Solvent A:20mM ammonium acetate in water (pH=9)
Solvent B:HPLC grade acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS001134
Analysis ID:AN001240
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001135
Analysis ID:AN001241
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001136
Analysis ID:AN001242
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001137
Analysis ID:AN001243
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
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