Summary of Study ST000601

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 PR000438. The data can be accessed directly via it's Project DOI: 10.21228/M8FC7C 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 IDST000601
Study TitleUntargeted LC-MS metabolomics analysis of human COPD plasma, HILIC & C18
Study SummaryIdentify perturbed metabolites and pathways in human plasma collected from 131 COPD subjects. Subjects were either current or former smokers with various COPD phenotypes including emphysema, and exacerbations.
Institute
University of Colorado Denver
Department Anschutz Medical Campus, Pharmaceutical Sciences
Last NameReisdorph
First NameNichole
Address12850 East Montview Blvd, Aurora, CO 80045
EmailNichole.Reisdorph@ucdenver.edu
Phone303-724-9243
Submit Date2017-04-27
Total Subjects131
Num Males56
Num Females75
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2018-10-10
Release Version1
Nichole Reisdorph Nichole Reisdorph
https://dx.doi.org/10.21228/M8FC7C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000438
Project DOI:doi: 10.21228/M8FC7C
Project Title:Chronic Obstructive Pulmonary Disease Human Plasma Metabolomics
Project Type:Untargeted LC-MS Metabolomics
Project Summary:COPD is a very heterogeneous disease comprising multiple phenotypes. Plasma from 131 human subjects was collected as part of the NIH-sponsored COPDGene cohort and analyzed using untargeted LC-MS (C18+) and (HILIC+) metabolomics. The goal was to identify perturbed compounds and pathways associated with COPD.
Institute:University of Colorado Denver
Department:Pharmaceutical Sciences, Anschutz Medical Campus
Last Name:Reisdorph
First Name:Nichole
Address:12850 East Montview Blvd, Aurora, CO 80045
Email:Nichole.Reisdorph@ucdenver.edu
Phone:303-724-9243
Funding Source:NIH P20

Subject:

Subject ID:SU000624
Subject Type:Human Plasma
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:57-70
Gender:Males and Females
Human Race:Non-Hispanic White
Human Smoking Status:Current and Former Smokers
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Smoking Status Gold Stage
SA03324324653Z1 -
SA03324412771P1 -
SA03324524718B1 -
SA03324622363G1 -
SA03324722951X1 -
SA03324823611E1 -
SA03324923744X1 -
SA03325022602Y1 -
SA03325122470H1 -
SA03325224514L1 -
SA03325310104S1 -
SA03325422155Z1 -
SA03325524902U1 2
SA03325624762E1 2
SA03325722986Q1 2
SA03325821305N1 2
SA03325920696X1 2
SA03326020542W1 2
SA03326118468S1 2
SA03326221731E1 2
SA03326322691X1 2
SA03326424513J1 2
SA03326523124T1 2
SA03326624211T1 2
SA03326724670Z1 3
SA03326824706U1 3
SA03326924213X1 3
SA03327021609H1 3
SA03327113959M1 4
SA03327210390T1 4
SA03314222542G- -
SA03314322375N- -
SA03314422569A- -
SA03314522660M- -
SA03314622692Z- -
SA03314722225U- -
SA03314821961V- -
SA03314921711Y- -
SA03315021920H- -
SA03315121929Z- -
SA03315221931M- -
SA03315322753T- -
SA03315423294S- -
SA03315524826E- -
SA03315624716X- -
SA03315725036G- -
SA03315825214E- -
SA03315925229R- -
SA03316024580Y- -
SA03316124394B- -
SA03316212969K- -
SA03316323575A- -
SA03316424344M- -
SA03316524382U- -
SA03316623091E- -
SA03316722545M- -
SA03316810102O- -
SA03316910465Y- -
SA03317010687Q- -
SA03317110136F- -
SA03317221897M- 1
SA03317322723K- 1
SA03317424449A- 1
SA03317522544K- 1
SA03317624931B- 1
SA03317724438V- 1
SA03317822756Z- 1
SA03317923090C- 1
SA03318024739J- 1
SA03318110166O- 1
SA03318212593R- 2
SA03318310473X- 2
SA03318424456X- 2
SA03318510138J- 2
SA03318610544U- 2
SA03318722752R- 2
SA03318810245K- 2
SA03318924063E- 2
SA03319012900A- 2
SA03319124429U- 2
SA03319222754V- 2
SA03319322623G- 2
SA03319410636Z- 2
SA03319520778Z- 2
SA03319620900W- 2
SA03319724673F- 2
SA03319825023X- 2
SA03319910087S- 2
SA03320010071D- 2
SA03320119688L- 2
SA03320221489X- 2
SA03320320777X- 2
SA03320424825C- 2
SA03320510328O- 3
SA03320613686D- 3
SA03320725366B- 3
SA03320824927K- 3
SA03320919370G- 3
SA03321010300S- 3
SA03321124158P- 3
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Collection:

Collection ID:CO000618
Collection Summary:All subjects were from the COPDGene cohort1, an NIH-sponsored multi-centered study of the genetic epidemiology of COPD. Subjects had fresh frozen plasma collected using a p100 tube (BD) at one of the COPDGene sites (National Jewish Health). Additional information on the COPDGene study and the collection of clinical data has been previously described1.” 1 Regan EA, Hokanson JE, Murphy JR, Make B, Lynch DA, Beaty TH et al. Genetic epidemiology of COPD (COPDGene) study design. COPD. 2010;7(1):32-43. doi:10.3109/15412550903499522.
Sample Type:Plasma
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000638
Treatment Summary:n/a

Sample Preparation:

Sampleprep ID:SP000631
Sampleprep Summary:100µL of plasma was prepared using methanol to extract precipitate the proteins into a pellet. A liquid-liquid extraction with water and methyl-tert butyl ether (MTBE) was used to partition the supernatant into an aqueous layer and an organic layer (lipids). The aqueous layer was dried down in a SpeedVac at 45°C, then reconstituted in 100µL of 95:5 water:acetonitrile. The lipid fraction was dried down in a SpeedVac at 45°C, then reconstituted in 200µL of 100% methanol.

Combined analysis:

Analysis ID AN000920 AN000921
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Agilent 6210 Agilent 6520
Column Agilent Zorbax RRHD SB-C18 (100 x 2.1mm, 1.8um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm, 2.6um)
MS Type ESI ESI
MS instrument type TOF QTOF
MS instrument name Agilent Agilent
Ion Mode POSITIVE POSITIVE
Units Count Counts

Chromatography:

Chromatography ID:CH000656
Chromatography Summary:Lipid Fraction (C18)
Instrument Name:Agilent 6210
Column Name:Agilent Zorbax RRHD SB-C18 (100 x 2.1mm, 1.8um)
Column Temperature:60°C
Flow Gradient:0-0.5 minutes 30-70% B, 0.5-7.42 minutes 70-100% B, 7.42-9.9 minutes 100% B, 9.9-10.0 minutes 100-30% B, followed by column re-equilibration
Flow Rate:0.7 mL/min
Injection Temperature:4°C
Sample Injection:4µL
Solvent A:water with 0.1% formic acid
Solvent B:60:36:4 isopropyl alcohol:acetonitrile:water with 0.1% formic acid
Capillary Voltage:4000V
Randomization Order:Excel rand() function
Chromatography Type:Reversed phase
  
Chromatography ID:CH000657
Chromatography Summary:Aqueous Fraction (HILIC)
Instrument Name:Agilent 6520
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm, 2.6um)
Column Temperature:20°C
Flow Gradient:0.2 minutes 100% B, 2-2.1 minutes 100-90% B, 2.1-8.6 minutes 90-50% B, 8.6-8.7 minutes 50-0% B, 8.7-14.7 minutes 0% B, 14.7-14.8 minutes 0-100% B, followed by column re-equilibration
Flow Rate:0.6 mL/min
Injection Temperature:4°C
Sample Injection:1µL
Solvent A:50% ACN with pH 5.8 ammonium acetate
Solvent B:90% ACN with pH 5.8 ammonium acetate
Capillary Voltage:4000V
Randomization Order:Excel rand() function
Chromatography Type:HILIC

MS:

MS ID:MS000819
Analysis ID:AN000920
Instrument Name:Agilent
Instrument Type:TOF
MS Type:ESI
Ion Mode:POSITIVE
Fragment Voltage:120V
Scanning Range:60-1600m/z
Skimmer Voltage:60V
  
MS ID:MS000820
Analysis ID:AN000921
Instrument Name:Agilent
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Fragment Voltage:120V
Scanning Range:50-1700m/z
Skimmer Voltage:60V
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