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.
Study ID | ST000448 |
Study Title | Emory University high-resolution metabolomic profiling of ring trial samples |
Study Type | Untargeted HRMS for cross-laboratory comparison of metabolomics platforms |
Study Summary | Untargeted 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 |
Department | School of Medicine, Division of Pulmonary, Allergy, Critical Care Medicine |
Laboratory | Clincal Biomarkers Laboratory |
Last Name | Walker |
First Name | Douglas |
Address | 615 Michael St. Ste 225, Atlanta, GA, 30322, USA |
douglas.walker@emory.edu | |
Phone | 4047275984 |
Submit Date | 2016-08-08 |
Num Groups | 4 |
Total Subjects | 55 |
Num Males | 20 |
Num Females | 20 |
Study Comments | Contained 20 females, 20 males, 10 pooled samples and 5 fortified pooled samples |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Chear Study | Yes |
Analysis Type Detail | LC-MS |
Release Date | 2024-12-31 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|
SA022719 | N027 | data1 |
SA022720 | N024 | data1 |
SA022721 | N046 | data1 |
SA022722 | N048 | data1 |
SA022723 | N008 | data1 |
SA022724 | Std_4 | data1 |
SA022725 | N003 | data1 |
SA022726 | Std_5 | data1 |
SA022727 | N009 | data1 |
SA022728 | N045 | data1 |
SA022729 | N036 | data1 |
SA022730 | N031 | data1 |
SA022731 | N043 | data1 |
SA022732 | N049 | data1 |
SA022733 | N044 | data1 |
SA022734 | N032 | data1 |
SA022735 | N028 | data1 |
SA022736 | Std_3 | data1 |
SA022737 | N039 | data1 |
SA022738 | q3June2014_1c | data1 |
SA022739 | NIST_SRM1950_2 | data1 |
SA022740 | q3June2014_1d | data1 |
SA022741 | N034 | data1 |
SA022742 | N007 | data1 |
SA022743 | N022 | data1 |
SA022744 | N011 | data1 |
SA022745 | N004 | data1 |
SA022746 | N026 | data1 |
SA022747 | N012 | data1 |
SA022748 | N042 | data1 |
SA022749 | N035 | data1 |
SA022750 | N047 | data1 |
SA022751 | N020 | data1 |
SA022752 | N037 | data1 |
SA022753 | N021 | data1 |
SA022754 | N006 | data1 |
SA022755 | N017 | data1 |
SA022756 | N019 | data1 |
SA022757 | N018 | data1 |
SA022758 | q3June2014_1b | data1 |
SA022759 | q3June2014_1a | data1 |
SA022760 | N025 | data1 |
SA022761 | N038 | data1 |
SA022762 | N002 | data1 |
SA022763 | Std_2 | data1 |
SA022764 | N015 | data1 |
SA022765 | N013 | data1 |
SA022766 | N041 | data1 |
SA022767 | N029 | data1 |
SA022768 | N016 | data1 |
SA022769 | N030 | data1 |
SA022770 | N014 | data1 |
SA022771 | N023 | data1 |
SA022772 | Std_1 | data1 |
SA022773 | N040 | data1 |
SA022774 | N010 | data1 |
SA022775 | N005 | data1 |
SA022776 | N050 | data1 |
SA022777 | N033 | data1 |
SA022778 | N001 | data1 |
SA022779 | NIST_SRM1950_1 | data1 |
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 |