Summary of Study ST001639

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 IDST001639
Study TitlePlasma Metabolomic signatures of COPD in a SPIROMICS cohort
Study SummaryThe 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
DepartmentDivision of Pulmonary Medicine
LaboratoryBowler
Last NameBowler
First NameRussell
Address1400 Jackson St. Denver, CO 80206
Emailbowlerr@njhealth.org
Phone303 270 2014
Submit Date2020-12-30
Total Subjects649
Num Males350
Num Females299
Analysis Type DetailLC-MS
Release Date2021-05-30
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:SU001716
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 COPD
SA150531NJHC-01749case
SA150532NJHC-01700case
SA150533NJHC-02023case
SA150534NJHC-01993case
SA150535NJHC-01784case
SA150536NJHC-01810case
SA150537NJHC-01532case
SA150538NJHC-01406case
SA150539NJHC-01540case
SA150540NJHC-01783case
SA150541NJHC-01975case
SA150542NJHC-01976case
SA150543NJHC-01924case
SA150544NJHC-01945case
SA150545NJHC-01953case
SA150546NJHC-02043case
SA150547NJHC-01923case
SA150548NJHC-02041case
SA150549NJHC-01938case
SA150550NJHC-01928case
SA150551NJHC-01929case
SA150552NJHC-01522case
SA150553NJHC-01562case
SA150554NJHC-01912case
SA150555NJHC-01915case
SA150556NJHC-01880case
SA150557NJHC-01881case
SA150558NJHC-01939case
SA150559NJHC-01970case
SA150560NJHC-02019case
SA150561NJHC-02026case
SA150562NJHC-01998case
SA150563NJHC-01497case
SA150564NJHC-01865case
SA150565NJHC-01851case
SA150566NJHC-01583case
SA150567NJHC-01571case
SA150568NJHC-01561case
SA150569NJHC-01524case
SA150570NJHC-01614case
SA150571NJHC-01649case
SA150572NJHC-01864case
SA150573NJHC-01685case
SA150574NJHC-01654case
SA150575NJHC-01926case
SA150576NJHC-01884case
SA150577NJHC-01563case
SA150578NJHC-01508case
SA150579NJHC-01504case
SA150580NJHC-01565case
SA150581NJHC-01529case
SA150582NJHC-01637case
SA150583NJHC-01577case
SA150584NJHC-01621case
SA150585NJHC-01615case
SA150586NJHC-01507case
SA150587NJHC-01479case
SA150588NJHC-01746case
SA150589NJHC-01420case
SA150590NJHC-01419case
SA150591NJHC-01787case
SA150592NJHC-01822case
SA150593NJHC-01445case
SA150594NJHC-01446case
SA150595NJHC-01748case
SA150596NJHC-01442case
SA150597NJHC-01421case
SA150598NJHC-01566case
SA150599NJHC-01601case
SA150600NJHC-01919case
SA150601NJHC-01517case
SA150602NJHC-01663case
SA150603NJHC-01646case
SA150604NJHC-01842case
SA150605NJHC-01455case
SA150606NJHC-01883case
SA150607NJHC-01885case
SA150608NJHC-02034case
SA150609NJHC-01844case
SA150610NJHC-01653case
SA150611NJHC-01674case
SA150612NJHC-01602case
SA150613NJHC-01627case
SA150614NJHC-01610case
SA150615NJHC-01608case
SA150616NJHC-01603case
SA150617NJHC-01622case
SA150618NJHC-01629case
SA150619NJHC-01456case
SA150620NJHC-01747case
SA150621NJHC-01786case
SA150622NJHC-01893case
SA150623NJHC-01462case
SA150624NJHC-01464case
SA150625NJHC-01465case
SA150626NJHC-01818case
SA150627NJHC-01814case
SA150628NJHC-01500case
SA150629NJHC-01587case
SA150630NJHC-01549case
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Collection:

Collection ID:CO001709
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 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.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001729
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 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.

Sample Preparation:

Sampleprep ID:SP001722
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 STARĀ® 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 TurboVapĀ® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.

Combined analysis:

Analysis ID AN002681 AN002682 AN002683 AN002684
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 AU AU AU AU

Chromatography:

Chromatography ID:CH001975
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:CH001976
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:CH001977
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:CH001978
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:MS002480
Analysis ID:AN002681
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:MS002481
Analysis ID:AN002682
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:MS002482
Analysis ID:AN002683
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:MS002483
Analysis ID:AN002684
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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