Summary of Study ST000448

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 PR000346. The data can be accessed directly via it's Project DOI: 10.21228/M8B301 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 IDST000448
Study TitleEmory University high-resolution metabolomic profiling of ring trial samples
Study TypeUntargeted HRMS for cross-laboratory comparison of metabolomics platforms
Study SummaryUntargeted profiling of blinded plasma samples consisting of 20 females, 20 males, 10 pooled samples and 5 fortified pooled samples was completed using liquid chromatography with high-resolution mass spectrometry. All samples were analyzed using HILIC and C18 chromatography interfaced to a Thermo Scientific Orbitrap Fusion Tribrid high-resolution mass spectrometer operated in positive and negative ESI. Mass spectral data was extracted using adaptive processing algorithms at multiple settings and annotated using xMSannotator. Collected data were uploaded to the Metabolomics Workbench for evaluation of system performance.
Institute
Emory University
DepartmentSchool of Medicine, Division of Pulmonary, Allergy, Critical Care Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameWalker
First NameDouglas
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emaildouglas.walker@emory.edu
Phone4047275984
Submit Date2016-08-08
Num Groups4
Total Subjects55
Num Males20
Num Females20
Study CommentsContained 20 females, 20 males, 10 pooled samples and 5 fortified pooled samples
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2024-12-31
Release Version1
Douglas Walker Douglas Walker
https://dx.doi.org/10.21228/M8B301
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000346
Project DOI:doi: 10.21228/M8B301
Project Title:CHEAR Ring Trial
Project Type:Untargeted HRMS profiling
Project Summary:Blinded, multi-center analysis of plasma from 20 females, 20 males, 10 pools and 5 spiked pools to assess performance of different metabolomics platforms
Institute:Emory University
Department:Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Walker
First Name:Douglas
Address:625 Michael St. Ste 225, Atlanta, GA, 30322, USA
Email:douglas.walker@emory.edu
Phone:4047275984
Funding Source:NIEHS ES026560

Subject:

Subject ID:SU000469
Subject Type:Humans plasma
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Factor
SA022719N027data1
SA022720N024data1
SA022721N046data1
SA022722N048data1
SA022723N008data1
SA022724Std_4data1
SA022725N003data1
SA022726Std_5data1
SA022727N009data1
SA022728N045data1
SA022729N036data1
SA022730N031data1
SA022731N043data1
SA022732N049data1
SA022733N044data1
SA022734N032data1
SA022735N028data1
SA022736Std_3data1
SA022737N039data1
SA022738q3June2014_1cdata1
SA022739NIST_SRM1950_2data1
SA022740q3June2014_1ddata1
SA022741N034data1
SA022742N007data1
SA022743N022data1
SA022744N011data1
SA022745N004data1
SA022746N026data1
SA022747N012data1
SA022748N042data1
SA022749N035data1
SA022750N047data1
SA022751N020data1
SA022752N037data1
SA022753N021data1
SA022754N006data1
SA022755N017data1
SA022756N019data1
SA022757N018data1
SA022758q3June2014_1bdata1
SA022759q3June2014_1adata1
SA022760N025data1
SA022761N038data1
SA022762N002data1
SA022763Std_2data1
SA022764N015data1
SA022765N013data1
SA022766N041data1
SA022767N029data1
SA022768N016data1
SA022769N030data1
SA022770N014data1
SA022771N023data1
SA022772Std_1data1
SA022773N040data1
SA022774N010data1
SA022775N005data1
SA022776N050data1
SA022777N033data1
SA022778N001data1
SA022779NIST_SRM1950_1data1
Showing results 1 to 61 of 61

Collection:

Collection ID:CO000463
Collection Summary:Human plasma collected using lithium heparin were purchased from Bioreclamation by 250 mL/individual from a single point blood draw from 30 men and 30 women, yielding 15L of plasma. Samples were delivered in individual aliquots of 5 mL and include 20 female, 20 male 10 pools and 5 fortified pools spiked with 40 chemicals.
Sample Type:Human plasma
Volumeoramount Collected:250 mL
Additives:Lithium Heparin
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000483
Treatment Summary:Samples were delivered in individual aliquots of 5 mL and include 20 female, 20 male 10 pools and 5 fortified pools spiked with 40 chemicals at varying concentrations.

Sample Preparation:

Sampleprep ID:SP000476
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods (Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80°C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 μL was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 μL of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 μL of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, plasma was equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (16.1 ×g at 4°C for 10 min). The resulting supernatant (100 μL) was removed, added to a low volume autosampler vial and maintained at 4°C until analysis (<22 h).
Sampleprep Protocol ID:HRM_SP_082016_01
Sampleprep Protocol Filename:EmoryUniversity_HRM_SP_082016_01.pdf
Sampleprep Protocol Comments:Date effective: 30 July 2016
Extraction Method:2:1 acetonitrile: sample followed by vortexing and centrifugation
Sample Spiking:2.5 uL [13C6]-D-glucose, [15N,13C5]-L-methionine, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine, [15N]-indole

Combined analysis:

Analysis ID AN000701 AN000702
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column Waters XBridge Amide (50 x 2.1mm,2.5um) Thermo Higgins C18 (50 x 2.1mm,3um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Fusion Orbitrap Thermo Fusion Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak Intensity

Chromatography:

Chromatography ID:CH000507
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 μL of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods ID:2% formic acid in LC-MS grade water
Methods Filename:20160728_HILICpos_c18negwash_FullScan_5min
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters XBridge Amide (50 x 2.1mm,2.5um)
Column Temperature:40C
Flow Gradient:A= water, B= acetontrile, C= 2% formic acid in water; 22.5% A, 75% B, 2.5% C hold for 1.5 min, linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min
Flow Rate:0.35 mL/min for 1.5 min; linear increase to 0.4 mL/min at 4 min, hold for 1 min
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:25 uL
Chromatography Type:HILIC
  
Chromatography ID:CH000508
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods ID:10mM ammonium acetate in LC-MS grade water
Methods Filename:20160728_c18neg_HILICposwash_FullScan_5min
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Thermo Higgins C18 (50 x 2.1mm,3um)
Column Temperature:40C
Flow Gradient:A= water, B= acetontrile, C= 10mM ammonium acetate in water; 60% A, 35% B, 5% C hold for 0.5 min, linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3 min
Flow Rate:0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:25 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS000623
Analysis ID:AN000701
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:300C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:250C
Mass Accuracy:< 3ppm
Spray Voltage:+3500
Activation Parameter:5e5
Activation Time:118ms
Interface Voltage:S-Lens RF level= 69
Resolution Setting:60,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_FusionMS_082016_01.pdf
  
MS ID:MS000624
Analysis ID:AN000702
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:300C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:250C
Mass Accuracy:< 3ppm
Spray Voltage:-4000
Activation Parameter:5e5
Activation Time:118ms
Interface Voltage:S-Lens RF level= 69
Resolution Setting:60,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_FusionMS_082016_01.pdf
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