Summary of Study ST000625

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 PR000456. The data can be accessed directly via it's Project DOI: 10.21228/M83W49 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 IDST000625
Study TitleNon targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Aqueous(+) experiment (part I)
Study TypeComprehensive profile
Study SummaryMouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64).
Institute
University of Colorado Denver
Department Anschutz Medical Campus, Pharmaceutical Sciences
LaboratoryMetabolomics and Mass Spectrometry
Last NameReisdorph
First NameNichole
Address12850 East Montview Blvd, Denver, CO 80204
Emailnichole.reisdorph@ucdenver.edu
Phone-
Submit Date2017-04-21
Num Groups2
Total Subjects15
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Nichole Reisdorph Nichole Reisdorph
https://dx.doi.org/10.21228/M83W49
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000456
Project DOI:doi: 10.21228/M83W49
Project Title:A strategy for producing a searchable bronchoalveolar lavage fluid compound database
Project Type:MS
Project Summary:Comprehensive metabolomic databases for Lipid(+/-) and Aqueous(+) fractions of BALF assembled from a mouse and human COPD experiment.
Institute:University of Colorado Denver
Department:Pharmaceutical Sciences, Anschutz Medical Campus
Laboratory:Metabolomics and Mass Spectrometry
Last Name:Reisdorph
First Name:Nichole
Address:12850 East Montview Blvd, Denver, CO 80204
Email:nichole.reisdorph@ucdenver.edu
Phone:-
Funding Source:P20-HL113445 Metabolic Profiles of COPD phenotypes

Subject:

Subject ID:SU000648
Subject Type:Human | Animal
Subject Species:Homo sapiens;Mus musculus
Taxonomy ID:9606;10090
Genotype Strain:Animal: C57BL/6
Species Group:Mammal

Factors:

Subject type: Human | Animal; Subject species: Homo sapiens;Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Species SmokingStatus Phenotype
SA035132HBAL_11833GHuman Former smoker Moderate
SA035133HBAL_10031RHuman Smoker COPD
SA035134HBAL_17800VHuman Smoker COPD
SA035135HBAL_12558PHuman Smoker Healthy
SA035136HBAL_14442GHuman Smoker Healthy
SA035137MBAL_MET142Mouse Non-Smoker Healthy
SA035138MBAL_MET133Mouse Non-Smoker Healthy
SA035139MBAL_MET141Mouse Non-Smoker Healthy
SA035140MBAL_MET144Mouse Non-Smoker Healthy
SA035141MBAL_MET143Mouse Non-Smoker Healthy
SA035142MBAL_MET108Mouse Smoker Emphysema
SA035143MBAL_MET106Mouse Smoker Emphysema
SA035144MBAL_MET107Mouse Smoker Emphysema
SA035145MBAL_MET126Mouse Smoker Emphysema
SA035146MBAL_MET128Mouse Smoker Emphysema
Showing results 1 to 15 of 15

Collection:

Collection ID:CO000642
Collection Summary:Mouse BALF collection was performed using a total of 1.0 mL PBS divided into three washes and stored at -80°C until analysis. Human BALF was collected in the right middle lobe and lingual by instilling two aliquots of 40 mL and one aliquot of 50 mL of sterile saline per lobe (i.e., 130 mL per lobe, total volume = 260 mL per subject), which is withdrawn by gentle manual suction and immediately placed on ice. Aliquots for metabolomics analysis were frozen at -80 °C and stored until sample preparation and MS analysis.
Sample Type:BALF
Collection Method:Broncheoalveolar lavage

Treatment:

Treatment ID:TR000662
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000655
Sampleprep Summary:200uL of BALF was prepared using methanol assisted protein precipitation followed by methyl-tert butyl ether (MTBE) liquid-liquid extraction. The aqueous fraction was dried down in a SpeedVac at 45°C, then reconstituted in 50 µL of 95:5 water:acetonitrile.

Combined analysis:

Analysis ID AN000957
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1200
Column Agilent Zorbax Narrow Bore RRHT RRHD SB-AQ (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6520 QTOF
Ion Mode POSITIVE
Units peak intensity

Chromatography:

Chromatography ID:CH000682
Chromatography Summary:Analysis of the aqueous fraction was by reversed-phase chromatography using an Agilent 1200 series pump with an Agilent Zorbax Narrow Bore RRHT SB-AQ (1.8 micron, 2.1 x 100 mm, 80Å) analytical column and an Agilent Zorbax SB-AQ (5 micron, 2.1 x 12.5 mm) guard column. Sample injection volumes were 10 µL. A flow rate of 0.3ml/min was used with the following mobile phases: mobile phase A was water with 0.1% formic acid, and mobile phase B was 90:10 acetonitrile:water with 0.1% formic acid. Gradient elution was as follows: 0-3 minutes 2% B, 3-5 minutes 2-40% B, 5-20 minutes 40-100% B, 20-30 minutes 100% B, 30-30.01 100-2% B, 30.01-40 minutes 2% B.
Instrument Name:Agilent 1200
Column Name:Agilent Zorbax Narrow Bore RRHT RRHD SB-AQ (100 x 2.1mm,1.8um)
Flow Gradient:0-3 minutes 2% B, 3-5 minutes 2-40% B, 5-20 minutes 40-100% B, 20-30 minutes 100% B, 30-30.01 100-2% B, 30.01-40 minutes 2% B
Flow Rate:0.3ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:90% acetonitrile/10% water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS000852
Analysis ID:AN000957
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:4000V
Desolvation Gas Flow:10L/min
Desolvation Temperature:300C
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