Summary of Study ST001408

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 PR000964. The data can be accessed directly via it's Project DOI: 10.21228/M83406 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.

Show all samples  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001408
Study TitleMetabolomic profiling of baseline plasmas from a longitudinal prospective cohort of 491 active surveillance (AS) participants
Study TypeBiomarker study
Study SummaryUntargeted metabolomics analyses were performed on clinically matched baseline plasma samples (n = 16 per group) prospectively collected from patients with clinically low-risk early stage prostate cancer undergoing AS who exhibited early disease progression (DP) (defined as upgrading of Gleason score (GS) and/or increased tumor volume on surveillance biopsy within 18 months after start of AS) or indolent disease (no progression for five or more years after start of AS) as well as 459 baseline plasma samples prospectively collected from patients with early-stage prostate cancer undergoing AS.
Institute
University of Texas MD Anderson Cancer Center
DepartmentDepartment of Clinical Cancer Prevention
Last NameVykoukal
First NameJody
Address6767 Bertner Ave, Houston, TX 77030
Emailjvykouka@mdanderson.org
Phone713-834-6095
Submit Date2020-05-19
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2020-07-02
Release Version1
Jody Vykoukal Jody Vykoukal
https://dx.doi.org/10.21228/M83406
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Combined analysis:

Analysis ID AN002352 AN002353 AN002354
Analysis type MS MS MS
Chromatography type HILIC Reversed phase Reversed phase
Chromatography system Waters Acquity UPLC Waters Acquity UPLC Waters Acquity UPLC
Column Waters Acquity UPLC BEH amide,(100 x 2.1mm,1.7um,100 Å) Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å) Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å)
MS Type ESI ESI ESI
MS instrument type QTOF QTOF QTOF
MS instrument name Waters Xevo G2-XS Waters Xevo G2-XS Waters Xevo G2-XS
Ion Mode POSITIVE POSITIVE POSITIVE
Units normalized ion abundance normalized ion abundance normalized ion abundance

Chromatography:

Chromatography ID:CH001724
Chromatography Summary:Chromatographic separation was performed using HILIC (Acquity™ UPLC BEH amide, 100 Å, 1.7 µm 2.1× 100mm, Waters Corporation, Milford, U.S.A). Quaternary solvent system mobile phases were (A) 0.1% formic acid in water, (B) 0.1% formic acid in acetonitrile and (D) 100mM ammonium formate, pH 3. For HILIC separation, a starting gradient of 95% B and 5% D was increase linearly to 70% A, 25% B and 5% D over a 5min period at 0.4mL/min flow rate, followed by 1 min isocratic gradient at 100 % A at 0.4mL/min flow rate.Waters Acquity™ UPLC system with 2D column regeneration configuration
Instrument Name:Waters Acquity UPLC
Column Name:Waters Acquity UPLC BEH amide,(100 x 2.1mm,1.7um,100 Å)
Flow Gradient:a starting gradient of 95% B and 5% D was increase linearly to 70% A, 25% B and 5% D over a 5min period followed by 1 min isocratic gradient at 100% A
Flow Rate:0.4ml/min
Solvent A:100% water; 0.1% formic acid(A), 100% acetonitrile; 0.1% formic acid(B), 100% water; 100 mM ammonium formate, pH 3(D)
Solvent B:100% water; 0.1% formic acid(A), 100% acetonitrile; 0.1% formic acid(B), 100% water; 100 mM ammonium formate, pH 3(D)
Chromatography Type:HILIC
  
Chromatography ID:CH001725
Chromatography Summary:Chromatographic separation was performed using C18 (Acquity™ UPLC HSS T3, 100 Å, 1.8 µm,, 2.1×100mm, Water Corporation, Milford, U.S.A) columns at 45°C. Quaternary solvent system mobile phases were (A) 0.1% formic acid in water, (B) 0.1% formic acid in acetonitrile and (D) 100mM ammonium formate, pH 3. For C18 separation, a chromatography gradient of was as follows: starting conditions, 100% A, with linear increase to final conditions of 5% A, 95% B followed by isocratic gradient at 95% B, 5% D for 1 min.Waters Acquity™ UPLC system with 2D column regeneration configuration
Instrument Name:Waters Acquity UPLC
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å)
Column Temperature:45
Flow Gradient:starting conditions, 100% A, with linear increase to final conditions of 5% A, 95% B followed by isocratic gradient at 95% B, 5% C for 1 min.
Solvent A:100% water; 0.1% formic acid(A); 100% acetonitrile; 0.1% formic acid(B); 100 mM ammonium formate, pH 3(C)
Solvent B:100% water; 0.1% formic acid(A); 100% acetonitrile; 0.1% formic acid(B); 100 mM ammonium formate, pH 3(C)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001726
Chromatography Summary:Chromatographic separation was performed using a C18 (Acquity™ UPLC HSS T3, 100 Å, 1.8 µm, 2.1×100mm, Water Corporation, Milford, U.S.A) column at 55°C. The mobile phases were (A) water, (B) Acetonitrile, (C) 2-propanol and (D) 500mM ammonium formate, pH 3. A starting elution gradient of 20% A, 30% B, 49% C and 1% D was increased linearly to 10% B, 89% C and 1 % D for 5.5 min, followed by isocratic elution at 10% B, 89%C and 1%D for 1.5 min and column equilibration with initial conditions for 1min. Waters Acquity™ UPLC system with 2D column regeneration configuration
Instrument Name:Waters Acquity UPLC
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å)
Column Temperature:55
Flow Gradient:A starting elution gradient of 20% A, 30% B, 49% C and 1% D was increased linearly to 10% B, 89% C and 1 % D for 5.5 min, followed by isocratic elution at 10% B, 89%C and 1%D for 1.5 min and column equilibration with initial conditions for 1min.
Solvent A:100% water(A), 100% acetonitrile(B), 100% isopropanol(C), 500 mM ammonium formate, pH 3(D)
Solvent B:100% water(A), 100% acetonitrile(B), 100% isopropanol(C), 500 mM ammonium formate, pH 3(D)
Chromatography Type:Reversed phase
  logo