Summary of Study ST000626

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 IDST000626
Study TitleNon targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Lipid(-) experiment (part II)
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 Subjects36
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:SU000649
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
SA03514717800V_BALF_neg_BHuman Smoker COPD
SA03514817800V_BALF_neg_AHuman Smoker COPD
SA03514917800V_BALF_neg_CHuman Smoker COPD
SA03515014442G_BALF_neg_BHuman Smoker Healthy
SA03515114442G_BALF_neg_CHuman Smoker Healthy
SA03515214442G_BALF_neg_AHuman Smoker Healthy
SA035153BALF_MET141_2x_BMouse Non-Smoker Healthy
SA035154BALF_MET142_4x_AMouse Non-Smoker Healthy
SA035155BALF_MET141_2x_CMouse Non-Smoker Healthy
SA035156BALF_MET133_1x_AMouse Non-Smoker Healthy
SA035157BALF_MET142_4x_BMouse Non-Smoker Healthy
SA035158BALF_MET133_1x_CMouse Non-Smoker Healthy
SA035159BALF_MET141_2x_AMouse Non-Smoker Healthy
SA035160BALF_MET143_1x_CMouse Non-Smoker Healthy
SA035161BALF_MET144_2x_BMouse Non-Smoker Healthy
SA035162BALF_MET144_2x_CMouse Non-Smoker Healthy
SA035163BALF_MET144_2x_AMouse Non-Smoker Healthy
SA035164BALF_MET133_1x_BMouse Non-Smoker Healthy
SA035165BALF_MET143_1x_AMouse Non-Smoker Healthy
SA035166BALF_MET143_1x_BMouse Non-Smoker Healthy
SA035167BALF_MET142_4x_CMouse Non-Smoker Healthy
SA035168BALF_MET128_1x_AMouse Smoker Emphysema
SA035169BALF_MET107_1x_BMouse Smoker Emphysema
SA035170BALF_MET107_1x_CMouse Smoker Emphysema
SA035171BALF_MET107_1x_AMouse Smoker Emphysema
SA035172BALF_MET106_4x_CMouse Smoker Emphysema
SA035173BALF_MET106_4x_AMouse Smoker Emphysema
SA035174BALF_MET106_4x_BMouse Smoker Emphysema
SA035175BALF_MET108_2x_AMouse Smoker Emphysema
SA035176BALF_MET108_2x_BMouse Smoker Emphysema
SA035177BALF_MET126_4x_CMouse Smoker Emphysema
SA035178BALF_MET128_1x_BMouse Smoker Emphysema
SA035179BALF_MET126_4x_BMouse Smoker Emphysema
SA035180BALF_MET126_4x_AMouse Smoker Emphysema
SA035181BALF_MET108_2x_CMouse Smoker Emphysema
SA035182BALF_MET128_1x_CMouse Smoker Emphysema
Showing results 1 to 36 of 36

Collection:

Collection ID:CO000643
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:TR000663
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000656
Sampleprep Summary:100uL of BALF were prepared using methanol assisted protein precipitation followed by methyl-tert butyl ether (MTBE) liquid-liquid extraction. Both liquid and aqueous fractions were preserved for analysis. The lipid fraction was reconstituted in 200µL of methanol. The lipid fraction was dried down in a SpeedVac at 45°C for reconstitution in 50 µL of 95:5 water:acetonitrile.

Combined analysis:

Analysis ID AN000958
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290
Column Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6510 QTOF
Ion Mode NEGATIVE
Units peak intensity

Chromatography:

Chromatography ID:CH000683
Chromatography Summary:The BALF samples were separated using C18 reverse phase chromatography. The separations used an Agilent Zorbax Rapid Resolution HD (RRHD) SB-C18, 1.8 micron (2.1 x 100 mm) analytical column with an Agilent Zorbax SB-C18, 1.8 micron (2.1 x 5 mm) guard column and used an Agilent 1290 series high performance liquid chromatography (HPLC) pump. Injection volumes were 4µL for mouse BALF and 15µL for human BALF. Flow rate was 0.7 mL/min using the following mobile phases: mobile phase A was water with 0.1% formic acid, and mobile phase B was 60:36:4 isopropyl alcohol:acetonitrile:water with 0.1% formic acid. Gradients were 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, 10-14.6 minutes 30% B for the positive mode injections. For negative mode the following eluant profile was used: 0-1 minutes 30-70% B, 1-7.92 minutes 70-100% B, 7.92-10.4 minutes 100% B, 10.4-10.5 minutes 100-30% B, 10.5-15.1 minutes 30% B.
Instrument Name:Agilent 1290
Column Name:Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)
Flow Gradient:0-1 minutes 30-70% B, 1-7.92 minutes 70-100% B, 7.92-10.4 minutes 100% B, 10.4-10.5 minutes 100-30% B, 10.5-15.1 minutes 30% B.
Flow Rate:0.7 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:60% isopropanol/36% acetonitrile/4% water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS000853
Analysis ID:AN000958
Instrument Name:Agilent 6510 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:4000V
Fragment Voltage:120
Desolvation Gas Flow:12mL/min
Desolvation Temperature:300C
Nebulizer:30psi
Scan Range Moverz:60-1600
Scanning:2.02 spectra/second
Skimmer Voltage:60V
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