Summary of Study ST002089

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 PR000907. The data can be accessed directly via it's Project DOI: 10.21228/M8FQ2X This work is supported by NIH grant, U2C- DK119886.

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Study IDST002089
Study TitlePlasma metabolomic signatures of COPD: A metabolomic severity score for airflow obstruction and emphysema.
Study TypeMS qualitative analysis
Study SummaryThe NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2. This study is a duplicate of ST001443 (https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=ST001443&StudyType=MS&ResultType=5) but differs in analysis and contains batch normalized data using median metabolite values.
Institute
National Jewish Health
DepartmentDivision of Pulmonary Medicine
LaboratoryBowler
Last NameBowler
First NameRussell
Address1400 Jackson St. Denver, CO 80206
Emailbowlerr@njhealth.org
Phone303 270 2014
Submit Date2022-02-08
Total Subjects1120
Analysis Type DetailLC-MS
Release Date2022-03-09
Release Version1
Russell Bowler Russell Bowler
https://dx.doi.org/10.21228/M8FQ2X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000907
Project DOI:doi: 10.21228/M8FQ2X
Project Title:Plasma metabolomic signatures of COPD
Institute:National Jewish Health
Department:Division of Pulmonary Medicine
Last Name:Bowler
First Name:Russell
Address:1400 Jackson St. Denver, CO 80206
Email:bowlerr@njhealth.org
Phone:303 270 2014
Funding Source:NHLBI R21 HL140376, R01HL129937, R01HL 095432, R01 HL089856, R01 HL089897); and UL1 RR025680 from NCRR/HIH

Subject:

Subject ID:SU002173
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:40-80
Gender:Male and female
Human Race:Non-hispanic White and African-American
Human Smoking Status:Current/Former/Never

Factors:

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

mb_sample_id local_sample_id gender race.eth smoking_status ccenter
SA19945216854NFemale Black/Africian American Current Smoker NJC
SA19945311239UFemale Black/Africian American Current Smoker NJC
SA19945416930DFemale Black/Africian American Current Smoker NJC
SA19945513730GFemale Black/Africian American Current Smoker NJC
SA19945611358CFemale Black/Africian American Current Smoker NJC
SA19945711059SFemale Black/Africian American Current Smoker NJC
SA19945810934HFemale Black/Africian American Current Smoker NJC
SA19945914353HFemale Black/Africian American Current Smoker NJC
SA19946014442GFemale Black/Africian American Current Smoker NJC
SA19946115900PFemale Black/Africian American Current Smoker NJC
SA19946215975UFemale Black/Africian American Current Smoker NJC
SA19946314121MFemale Black/Africian American Current Smoker NJC
SA19946417419AFemale Black/Africian American Current Smoker NJC
SA19946513688HFemale Black/Africian American Current Smoker NJC
SA19946612330LFemale Black/Africian American Current Smoker NJC
SA19946712309UFemale Black/Africian American Current Smoker NJC
SA19946812558PFemale Black/Africian American Current Smoker NJC
SA19946919068HFemale Black/Africian American Current Smoker NJC
SA19947018968MFemale Black/Africian American Current Smoker NJC
SA19947125571CFemale Black/Africian American Current Smoker NJC
SA19947220749SFemale Black/Africian American Current Smoker NJC
SA19947312032DFemale Black/Africian American Current Smoker NJC
SA19947425537CFemale Black/Africian American Current Smoker NJC
SA19947520894BFemale Black/Africian American Current Smoker NJC
SA19947620863QFemale Black/Africian American Current Smoker NJC
SA19947720810VFemale Black/Africian American Current Smoker NJC
SA19947810298FFemale Black/Africian American Current Smoker NJC
SA19947925477KFemale Black/Africian American Current Smoker NJC
SA19948025361RFemale Black/Africian American Current Smoker NJC
SA19948115116YFemale Black/Africian American Current Smoker NJC
SA19948214493XFemale Black/Africian American Current Smoker NJC
SA19948314492VFemale Black/Africian American Current Smoker NJC
SA19948415163HFemale Black/Africian American Current Smoker NJC
SA19948515177SFemale Black/Africian American Current Smoker NJC
SA19948615841ZFemale Black/Africian American Former Smoker NJC
SA19948716557HFemale Black/Africian American Former Smoker NJC
SA19948820885AFemale Black/Africian American Former Smoker NJC
SA19948920787AFemale Black/Africian American Former Smoker NJC
SA19949020784UFemale Black/Africian American Former Smoker NJC
SA19949117562FFemale Black/Africian American Former Smoker NJC
SA19949221074UFemale Black/Africian American Former Smoker NJC
SA19949315798YFemale Black/Africian American Former Smoker NJC
SA19949420317PFemale Black/Africian American Former Smoker NJC
SA19949521697EFemale Black/Africian American Former Smoker NJC
SA19949610725YFemale Black/Africian American Former Smoker NJC
SA19949710137HFemale Black/Africian American Former Smoker NJC
SA19949813840NFemale Black/Africian American Former Smoker NJC
SA19949917882XFemale Black/Africian American Former Smoker NJC
SA19950022489CFemale Black/Africian American NA NJC
SA19950130527GFemale Black/Africian American Never Smoked NJC
SA19950230476PFemale Black/Africian American Never Smoked NJC
SA19950330491LFemale Black/Africian American Never Smoked NJC
SA19950430483MFemale Black/Africian American Never Smoked NJC
SA19950516839RFemale Non-Hispanic, White Current Smoker NJC
SA19950621128RFemale Non-Hispanic, White Current Smoker NJC
SA19950721910EFemale Non-Hispanic, White Current Smoker NJC
SA19950811126HFemale Non-Hispanic, White Current Smoker NJC
SA19950918377PFemale Non-Hispanic, White Current Smoker NJC
SA19951014571RFemale Non-Hispanic, White Current Smoker NJC
SA19951111648LFemale Non-Hispanic, White Current Smoker NJC
SA19951210104SFemale Non-Hispanic, White Current Smoker NJC
SA19951321704BFemale Non-Hispanic, White Current Smoker NJC
SA19951417008FFemale Non-Hispanic, White Current Smoker NJC
SA19951521731EFemale Non-Hispanic, White Current Smoker NJC
SA19951611522PFemale Non-Hispanic, White Current Smoker NJC
SA19951711531QFemale Non-Hispanic, White Current Smoker NJC
SA19951811785VFemale Non-Hispanic, White Current Smoker NJC
SA19951910180IFemale Non-Hispanic, White Current Smoker NJC
SA19952021809PFemale Non-Hispanic, White Current Smoker NJC
SA19952123668HFemale Non-Hispanic, White Current Smoker NJC
SA19952217566NFemale Non-Hispanic, White Current Smoker NJC
SA19952319464PFemale Non-Hispanic, White Current Smoker NJC
SA19952412900AFemale Non-Hispanic, White Current Smoker NJC
SA19952519843XFemale Non-Hispanic, White Current Smoker NJC
SA19952620023YFemale Non-Hispanic, White Current Smoker NJC
SA19952720218NFemale Non-Hispanic, White Current Smoker NJC
SA19952817850KFemale Non-Hispanic, White Current Smoker NJC
SA19952913272CFemale Non-Hispanic, White Current Smoker NJC
SA19953013261XFemale Non-Hispanic, White Current Smoker NJC
SA19953124779VFemale Non-Hispanic, White Current Smoker NJC
SA19953218282EFemale Non-Hispanic, White Current Smoker NJC
SA19953313252WFemale Non-Hispanic, White Current Smoker NJC
SA19953413090WFemale Non-Hispanic, White Current Smoker NJC
SA19953524739JFemale Non-Hispanic, White Current Smoker NJC
SA19953620256VFemale Non-Hispanic, White Current Smoker NJC
SA19953712585SFemale Non-Hispanic, White Current Smoker NJC
SA19953812229WFemale Non-Hispanic, White Current Smoker NJC
SA19953923959SFemale Non-Hispanic, White Current Smoker NJC
SA19954016650XFemale Non-Hispanic, White Current Smoker NJC
SA19954112173VFemale Non-Hispanic, White Current Smoker NJC
SA19954223867NFemale Non-Hispanic, White Current Smoker NJC
SA19954323989BFemale Non-Hispanic, White Current Smoker NJC
SA19954412313LFemale Non-Hispanic, White Current Smoker NJC
SA19954517800VFemale Non-Hispanic, White Current Smoker NJC
SA19954614881GFemale Non-Hispanic, White Current Smoker NJC
SA19954720271RFemale Non-Hispanic, White Current Smoker NJC
SA19954824811RFemale Non-Hispanic, White Current Smoker NJC
SA19954924812TFemale Non-Hispanic, White Current Smoker NJC
SA19955023860ZFemale Non-Hispanic, White Current Smoker NJC
SA19955121710WFemale Non-Hispanic, White Current Smoker NJC
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Collection:

Collection ID:CO002166
Collection Summary:The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2. Subject data includes: gender(Male/Female); race.eth (Non-Hispanic, White/Black African American/Other); smoking_status (Never smoked/Former Smoker/Current Smoker); ccenter (Clinical center); FEV1_post.2 (Post-bronchodilator, FEV1); adj_density_mesa (MESA-adjusted lung density), age_visit (Age years); BMI (Body Mass Index); ATS_PackYears (pack-years of smoking)
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002185
Treatment Summary:The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling.

Sample Preparation:

Sampleprep ID:SP002179
Sampleprep Summary:P100 plasma was profiled using the Metabolon (Durham, USA) Global Metabolomics Platform, as described (2-4). Briefly, samples were extracted with methanol under vigorous shaking for two minutes (Glen Mills GenoGrinder 2000) followed by centrifugation to remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase/ultrahigh performance liquid chromatography/tandem mass spectrometry (RP/UPLC-MS/MS) methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by hydrophilic interaction chromatography (HILIC)/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup.

Combined analysis:

Analysis ID AN003410 AN003411 AN003412 AN003413
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo LTQ Thermo LTQ Thermo LTQ Thermo LTQ
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units relativeMedian relativeMedian relativeMedian relativeMedian

Chromatography:

Chromatography ID:CH002521
Chromatography Summary:Low pH polar
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002522
Chromatography Summary:Low pH Lipophilic
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002523
Chromatography Summary:High pH
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002524
Chromatography Summary:HILIC
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS003175
Analysis ID:AN003410
Instrument Name:Thermo LTQ
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Proprietary analytical software for integration and peak picking
Ion Mode:POSITIVE
  
MS ID:MS003176
Analysis ID:AN003411
Instrument Name:Thermo LTQ
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Proprietary analytical software for integration and peak picking
Ion Mode:POSITIVE
  
MS ID:MS003177
Analysis ID:AN003412
Instrument Name:Thermo LTQ
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Proprietary analytical software for integration and peak picking
Ion Mode:NEGATIVE
  
MS ID:MS003178
Analysis ID:AN003413
Instrument Name:Thermo LTQ
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Proprietary analytical software for integration and peak picking
Ion Mode:NEGATIVE
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