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.

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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:

Project:

Project ID:PR000964
Project DOI:doi: 10.21228/M83406
Project Title:AS Biomarker Project
Project Type:Biomarker
Project Summary:Metabolomic profiling of baseline plasmas from a longitudinal prospective cohort of 491 active surveillance (AS) participants with the objective of identifying metabolic fingerprints that predict Gleason grade progression.
Institute:University of Texas MD Anderson Cancer Center
Department:Department of Clinical Cancer Prevention
Last Name:Vykoukal
First Name:Jody
Address:1515 Holcombe Boulevard, Houston, Texas, 77030, USA
Email:jody@mdanderson.org
Phone:8327243044

Subject:

Subject ID:SU001482
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id AS participant
SA114205PL25_Lipids_47523AS participant
SA114206PL25_Lipids_44969AS participant
SA114207PL25_Lipids_55162AS participant
SA114208PL25_Lipids_43923AS participant
SA114209PL25_Lipids_49272AS participant
SA114210PL25_Lipids_51376AS participant
SA114211PL25_Lipids_46328AS participant
SA114212PL25_Lipids_48975AS participant
SA114213PL25_Lipids_45971AS participant
SA114214PL25_Lipids_50987AS participant
SA114215PL25_Lipids_46069AS participant
SA114216PL25_Lipids_38976AS participant
SA114217PL25_Lipids_45861AS participant
SA114218PL25_Lipids_47124AS participant
SA114219PL25_Lipids_56908AS participant
SA114220PL25_Lipids_51627AS participant
SA114221PL25_Lipids_55178AS participant
SA114222PL25_Lipids_56459AS participant
SA114223PL25_Lipids_50865AS participant
SA114224PL25_Lipids_51519AS participant
SA114225PL25_Lipids_53051AS participant
SA114226PL25_Lipids_44428AS participant
SA114227PL25_Lipids_55538AS participant
SA114228PL25_Lipids_47157AS participant
SA114229PL25_Lipids_40366AS participant
SA114230PL25_Lipids_44888AS participant
SA114231PL25_Lipids_37813AS participant
SA114232PL25_Lipids_53869AS participant
SA114233PL25_Lipids_50541AS participant
SA114234PL25_Lipids_45298AS participant
SA114235PL25_Lipids_50349AS participant
SA114236PL25_Lipids_51210AS participant
SA114237PL25_Lipids_43599AS participant
SA114238PL25_Lipids_44967AS participant
SA114239PL25_Lipids_50181AS participant
SA114240PL25_Lipids_52820AS participant
SA114241PL25_Lipids_47293AS participant
SA114242PL25_Lipids_41181AS participant
SA114243PL25_Lipids_45578AS participant
SA114244PL25_Lipids_51112AS participant
SA114245PL25_Lipids_56444AS participant
SA114246PL25_Lipids_54825AS participant
SA114247PL25_Lipids_38318AS participant
SA114248PL25_Lipids_44718AS participant
SA114249PL25_Lipids_47407AS participant
SA114250PL24_HA_48104AS participant
SA114251PL24_HA_48177AS participant
SA114252PL24_HA_43477AS participant
SA114253PL24_HA_48334AS participant
SA114254PL24_HA_50199AS participant
SA114255PL25_Lipids_51391AS participant
SA114256PL25_Lipids_52007AS participant
SA114257PL25_Lipids_43921AS participant
SA114258PL25_Lipids_53700AS participant
SA114259PL25_Lipids_50993AS participant
SA114260PL24_HA_53173AS participant
SA114261PL24_HA_39402AS participant
SA114262PL24_HA_50501AS participant
SA114263PL24_HA_46359AS participant
SA114264PL24_HA_55854AS participant
SA114265PL24_HA_47720AS participant
SA114266PL24_HA_47123AS participant
SA114267PL24_HA_41172AS participant
SA114268PL24_HA_54630AS participant
SA114269PL24_HA_56599AS participant
SA114270PL24_HA_54712AS participant
SA114271PL25_Lipids_48485AS participant
SA114272PL25_Lipids_51148AS participant
SA114273PL25_Lipids_53981AS participant
SA114274PL25_Lipids_46665AS participant
SA114275PL25_Lipids_40425AS participant
SA114276PL25_Lipids_47776AS participant
SA114277PL25_Lipids_48125AS participant
SA114278PL25_Lipids_45875AS participant
SA114279PL25_Lipids_54998AS participant
SA114280PL25_Lipids_54743AS participant
SA114281PL25_Lipids_55947AS participant
SA114282PL25_Lipids_43910AS participant
SA114283PL25_Lipids_38418AS participant
SA114284PL25_Lipids_39244AS participant
SA114285PL25_Lipids_39127AS participant
SA114286PL25_Lipids_44418AS participant
SA114287PL25_Lipids_52557AS participant
SA114288PL25_Lipids_48004AS participant
SA114289PL25_Lipids_52086AS participant
SA114290PL25_Lipids_47619AS participant
SA114291PL25_Lipids_52970AS participant
SA114292PL25_Lipids_53530AS participant
SA114293PL25_Lipids_47200AS participant
SA114294PL25_Lipids_56013AS participant
SA114295PL25_Lipids_39665AS participant
SA114296PL25_Lipids_47894AS participant
SA114297PL25_Lipids_51583AS participant
SA114298PL25_Lipids_45728AS participant
SA114299PL25_Lipids_54932AS participant
SA114300PL25_Lipids_40514AS participant
SA114301PL25_Lipids_52819AS participant
SA114302PL25_Lipids_39651AS participant
SA114303PL25_Lipids_54884AS participant
SA114304PL25_Lipids_49746AS participant
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Collection:

Collection ID:CO001477
Collection Summary:Patients in this prospective clinical cohort included men diagnosed with localized prostate cancer and enrolled on an AS trial protocol between February 2006 and February 2014 (n=825). Of these, 616 patients had at least 1 year follow-up and 491 patients had baseline plasma samples, enabling inclusion in the study. The surveillance protocol was conducted by a multidisciplinary team of urologists, radiation oncologists and medical oncologists, was approved by the Institutional Review Board, and is registered on clinicaltrials.gov (NCT00490763). EDTA was used in all plasma collections and all specimens underwent a similar number of freeze/thaw cycles prior to obtaining metabolomics data. Sample ages varied, as the study began accrual in 2006 and continued over a ten year time period. Plasma was not obtained from fasted individuals.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001497
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP001490
Sampleprep Summary:Plasma metabolites were extracted from pre-aliquoted EDTA plasma (10 µL) with 30µL of LCMS grade methanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5 min at 750 rpm, and centrifuged at 2000 × g for 10 minutes at room temperature. The supernatant (10 µL) was carefully transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 10 µL of 100 mM ammonium formate, pH3. For Hydrophilic Interaction Liquid Chromatography (HILIC) analysis, the samples were diluted with 60 µL LCMS grade acetonitrile (ThermoFisher), whereas samples for C18 analysis were diluted with 60 µL water (GenPure ultrapure water system, Thermofisher). Each sample solution was transferred to 384-well microplate (Eppendorf) for LCMS analysis. For lipidomics, Pre-aliquoted EDTA plasma samples (10 µL) were extracted with 30µL of LCMS grade 2-propanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5min at 750 rpm, and centrifuged at 2000 x g for 10 minutes at room temperature. The supernatant (10µL) was carefully transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 90µL of 1:3:2 100mM ammonium formate, pH3 (Fischer Scientific): acetonitrile: 2-propanol and transferred to a 384-well microplate (Eppendorf) for lipids analysis using LCMS.

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

MS:

MS ID:MS002194
Analysis ID:AN002352
Instrument Name:Waters Xevo G2-XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 50-1200 Da range. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units.
Ion Mode:POSITIVE
  
MS ID:MS002195
Analysis ID:AN002353
Instrument Name:Waters Xevo G2-XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 50-1200 Da range. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units.
Ion Mode:POSITIVE
  
MS ID:MS002196
Analysis ID:AN002354
Instrument Name:Waters Xevo G2-XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 100-2000 Da for complex lipids. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units.
Ion Mode:POSITIVE
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