Summary of Study ST002088

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 PR001048. The data can be accessed directly via it's Project DOI: 10.21228/M87D6G This work is supported by NIH grant, U2C- DK119886.

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Study IDST002088
Study TitlePlasma Metabolomic signatures of COPD in a SPIROMICS cohort: A metabolomic severity score for airflow obstructions and emphysema
Study TypeObservational Cohort
Study SummaryPlasma Metabolomic signatures of COPD in a SPIROMICS cohort The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 648 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit. This study is a duplicate of ST001639 (https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=ST001639) 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 Date2022-02-14
Num Groups1
Total Subjects648
Analysis Type DetailLC-MS
Release Date2022-03-04
Release Version1
Russell Bowler Russell Bowler
https://dx.doi.org/10.21228/M87D6G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001048
Project DOI:doi: 10.21228/M87D6G
Project Title:Plasma Metabolomic signatures of COPD in a SPIROMICS cohort
Project Summary:The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 649 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit.
Institute:National Jewish Health
Department:Division of Pulmonary Medicine
Laboratory:Bowler
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:SU002172
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:40-80
Gender:Male and female
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 smokStatus SITE_cat
SA198804CU101030Female Black/Africian American Current Smoker Columbia
SA198805CU101007Female Black/Africian American Current Smoker Columbia
SA198806CU101469Female Black/Africian American Current Smoker Columbia
SA198807CU102687Female Black/Africian American Current Smoker Columbia
SA198808CU103987Female Black/Africian American Current Smoker Columbia
SA198809CU100598Female Black/Africian American Current Smoker Columbia
SA198810CU102586Female Black/Africian American Current Smoker Columbia
SA198811CU105046Female Black/Africian American Current Smoker Columbia
SA198812CU100195Female Black/Africian American Current Smoker Columbia
SA198813JH112826Female Black/Africian American Current Smoker Johns Hopkins
SA198814JH112675Female Black/Africian American Current Smoker Johns Hopkins
SA198815JH112762Female Black/Africian American Current Smoker Johns Hopkins
SA198816JH112785Female Black/Africian American Current Smoker Johns Hopkins
SA198817JH112757Female Black/Africian American Current Smoker Johns Hopkins
SA198818JH112291Female Black/Africian American Current Smoker Johns Hopkins
SA198819JH110070Female Black/Africian American Current Smoker Johns Hopkins
SA198820JH110704Female Black/Africian American Current Smoker Johns Hopkins
SA198821JH110753Female Black/Africian American Current Smoker Johns Hopkins
SA198822UI250716Female Black/Africian American Current Smoker Other
SA198823UI250636Female Black/Africian American Current Smoker Other
SA198824UI250537Female Black/Africian American Current Smoker Other
SA198825UI250152Female Black/Africian American Current Smoker Other
SA198826NJ220276Female Black/Africian American Current Smoker Other
SA198827UI250139Female Black/Africian American Current Smoker Other
SA198828UI250274Female Black/Africian American Current Smoker Other
SA198829UI250394Female Black/Africian American Current Smoker Other
SA198830UI250195Female Black/Africian American Current Smoker Other
SA198831LA190249Female Black/Africian American Current Smoker UCLA
SA198832LA190477Female Black/Africian American Current Smoker UCLA
SA198833LA190919Female Black/Africian American Current Smoker UCLA
SA198834LV200353Female Black/Africian American Current Smoker UCLA
SA198835SF180993Female Black/Africian American Current Smoker UCSF
SA198836WF121956Female Black/Africian American Current Smoker Wake Forest University
SA198837WF125272Female Black/Africian American Current Smoker Wake Forest University
SA198838CU102313Female Black/Africian American Former Smoker Columbia
SA198839CU102278Female Black/Africian American Former Smoker Columbia
SA198840CU100103Female Black/Africian American Former Smoker Columbia
SA198841CU103303Female Black/Africian American Former Smoker Columbia
SA198842CU103543Female Black/Africian American Former Smoker Columbia
SA198843CU103194Female Black/Africian American Former Smoker Columbia
SA198844CU100708Female Black/Africian American Former Smoker Columbia
SA198845CU102189Female Black/Africian American Former Smoker Columbia
SA198846JH110321Female Black/Africian American Former Smoker Johns Hopkins
SA198847JH113053Female Black/Africian American Former Smoker Johns Hopkins
SA198848JH112697Female Black/Africian American Former Smoker Johns Hopkins
SA198849JH110693Female Black/Africian American Former Smoker Johns Hopkins
SA198850JH113969Female Black/Africian American Former Smoker Johns Hopkins
SA198851UI250614Female Black/Africian American Former Smoker Other
SA198852UI250068Female Black/Africian American Former Smoker Other
SA198853UI250124Female Black/Africian American Former Smoker Other
SA198854UA240863Female Black/Africian American Former Smoker Other
SA198858LA190453Female Black/Africian American Former Smoker UCLA
SA198859SF182098Female Black/Africian American Former Smoker UCSF
SA198855MU161423Female Black/Africian American Former Smoker U of Michigan
SA198856MU160949Female Black/Africian American Former Smoker U of Michigan
SA198857MU160575Female Black/Africian American Former Smoker U of Michigan
SA198860WF123814Female Black/Africian American Former Smoker Wake Forest University
SA198861CU100826Female Black/Africian American Never Smoked Columbia
SA198862CU100734Female Black/Africian American Never Smoked Columbia
SA198863JH110130Female Black/Africian American Never Smoked Johns Hopkins
SA198864MU161128Female Black/Africian American Never Smoked U of Michigan
SA198865MU160460Female Black/Africian American Never Smoked U of Michigan
SA198866MU160954Female Black/Africian American Never Smoked U of Michigan
SA198867MU162562Female Black/Africian American Never Smoked U of Michigan
SA198868MU160610Female Black/Africian American Never Smoked U of Michigan
SA198869MU161435Female Black/Africian American Never Smoked U of Michigan
SA198870CU103944Female Non-Hispanic, White Current Smoker Columbia
SA198871CU103346Female Non-Hispanic, White Current Smoker Columbia
SA198872CU102850Female Non-Hispanic, White Current Smoker Columbia
SA198873CU101849Female Non-Hispanic, White Current Smoker Columbia
SA198874CU101837Female Non-Hispanic, White Current Smoker Columbia
SA198875CU102704Female Non-Hispanic, White Current Smoker Columbia
SA198876CU102382Female Non-Hispanic, White Current Smoker Columbia
SA198877CU102659Female Non-Hispanic, White Current Smoker Columbia
SA198878JH112431Female Non-Hispanic, White Current Smoker Johns Hopkins
SA198879JH113099Female Non-Hispanic, White Current Smoker Johns Hopkins
SA198880JH110934Female Non-Hispanic, White Current Smoker Johns Hopkins
SA198881JH110875Female Non-Hispanic, White Current Smoker Johns Hopkins
SA198882JH110687Female Non-Hispanic, White Current Smoker Johns Hopkins
SA198883IA210208Female Non-Hispanic, White Current Smoker Other
SA198884IA210229Female Non-Hispanic, White Current Smoker Other
SA198885IA210123Female Non-Hispanic, White Current Smoker Other
SA198886UI250178Female Non-Hispanic, White Current Smoker Other
SA198907LA190171Female Non-Hispanic, White Current Smoker UCLA
SA198908LA190351Female Non-Hispanic, White Current Smoker UCLA
SA198909LA191364Female Non-Hispanic, White Current Smoker UCLA
SA198910LA190641Female Non-Hispanic, White Current Smoker UCLA
SA198911SF182364Female Non-Hispanic, White Current Smoker UCSF
SA198912SF183492Female Non-Hispanic, White Current Smoker UCSF
SA198887MU160316Female Non-Hispanic, White Current Smoker U of Michigan
SA198888MU161985Female Non-Hispanic, White Current Smoker U of Michigan
SA198889MU162446Female Non-Hispanic, White Current Smoker U of Michigan
SA198890MU163475Female Non-Hispanic, White Current Smoker U of Michigan
SA198891MU162369Female Non-Hispanic, White Current Smoker U of Michigan
SA198892MU163210Female Non-Hispanic, White Current Smoker U of Michigan
SA198893MU161704Female Non-Hispanic, White Current Smoker U of Michigan
SA198894MU161916Female Non-Hispanic, White Current Smoker U of Michigan
SA198895MU161211Female Non-Hispanic, White Current Smoker U of Michigan
SA198896MU162963Female Non-Hispanic, White Current Smoker U of Michigan
SA198897MU162439Female Non-Hispanic, White Current Smoker U of Michigan
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Collection:

Collection ID:CO002165
Collection Summary:The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 648 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit. Subject data includes: GENDER (Male/Female); RACE.ETH (Non-Hispanic, White/Black, African American/Other); smokStatus (Never Smoked/Former Smoker/Current Smoker); SITE_cat (Clinical center); POST_FEV1_DERV_V1 (Post-bronchodilator FEV1 (L)); adj_density_mesa (MESA-adjusted Lung Density); AGE_DERV_V1 (Age years); BMI_CM_V1 (Body Mass Index); SMOKING_PACK_YEARS_V1 (pack-years of smoking at baseline).
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002184
Treatment Summary:The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 648 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit.
Human Fasting:Fasting

Sample Preparation:

Sampleprep ID:SP002178
Sampleprep Summary:Following receipt, samples were inventoried and immediately stored at -80oC. Each sample received was accessioned into the Metabolon LIMS system and was assigned by the LIMS a unique identifier that was associated with the original source identifier only. This identifier was used to track all sample handling, tasks, results, etc. The samples (and all derived aliquots) were tracked by the LIMS system. All portions of any sample were automatically assigned their own unique identifiers by the LIMS when a new task was created; the relationship of these samples was also tracked. All samples were maintained at -80oC until processed. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (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 HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.

Combined analysis:

Analysis ID AN003406 AN003407 AN003408 AN003409
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:CH002517
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:CH002518
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:CH002519
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:CH002520
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:MS003171
Analysis ID:AN003406
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:MS003172
Analysis ID:AN003407
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:MS003173
Analysis ID:AN003408
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:MS003174
Analysis ID:AN003409
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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