Summary of Study ST000346

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 PR000278. The data can be accessed directly via it's Project DOI: 10.21228/M8030X This work is supported by NIH grant, U2C- DK119886.

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Study IDST000346
Study TitleMetabolites detected from human bronchoalveolar lavage
Study SummaryThis is a preliminary trial to determine how viable this system will be to use on a much larger number of samples (up to 150). We would like to determine the range, number of metabolite species, and relative concentrations than can be detected in human bronchoalveolar lavage. We would also like to determine how clear the distinction is between the 3 patient groups as this will inform us as to how many of the 150 samples we need to run in the study proper.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-02-11
Num Groups8
Total Subjects32
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-03-03
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8030X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000278
Project DOI:doi: 10.21228/M8030X
Project Title:Metabolites detected from human bronchoalveolar lavage
Project Summary:This is a preliminary trial to determine how viable this system will be to use on a much larger number of samples (up to 150). We would like to determine the range, number of metabolite species, and relative concentrations than can be detected in human bronchoalveolar lavage. We would also like to determine how clear the distinction is between the 3 patient groups as this will inform us as to how many of the 150 samples we need to run in the study proper.
Institute:University of California, Davis
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154

Subject:

Subject ID:SU000366
Subject Type:Animal
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Condition
SA015294BAL_Mild_5148_009Mild Asthma
SA015295BAL_Mild_7693_006Mild Asthma
SA015296BAL_Mild_7223_007Mild Asthma
SA015297BAL_Mild_5965_010Mild Asthma
SA015298BAL_Mild_6816_008Mild Asthma
SA015299BAL_Normal_7230_013No Asthma
SA015300BAL_Normal_7376_011No Asthma
SA015301BAL_Normal_7042_014No Asthma
SA015302BAL_Normal_7295_012No Asthma
SA015303BAL_Normal_6880_015No Asthma
SA015304Kailko_Biorec01Quality Control
SA015305Kailko_Biorec01_1Quality Control
SA015306BAL_Severe_7747_007Severe Asthma
SA015307BAL_Severe_7277_002Severe Asthma
SA015308BAL_Severe_5842_005Severe Asthma
SA015309BAL_Severe_6247_004Severe Asthma
SA015310BAL_Severe_6339_003Severe Asthma
SA015311BAL_Severe_7747_001Severe Asthma
Showing results 1 to 18 of 18

Collection:

Collection ID:CO000360
Collection Summary:50ml of hospital grade sterile saline was instilled into the lungs of human volunteers. As much liquid as possible is then gently suctioned out. The sample is then centrifuged to remove cellular material and debris, and supernatant collected and frozen at -80C
Collection Protocol Filename:StudyDesign-GerardKaiko10202015.pdf
Sample Type:Bronchoalveolar lavage supernatant

Treatment:

Treatment ID:TR000380
Treatment Summary:The 3 groups are as follows: 1. Healthy controls (5) 2. Subjects with mild asthma (5) 3. Subjects with severe asthma (5)
Treatment Protocol Filename:StudyDesign-GerardKaiko10202015.pdf

Sample Preparation:

Sampleprep ID:SP000373
Sampleprep Summary:None

Combined analysis:

Analysis ID AN000561 AN000562
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6530 Agilent 6550
Column Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak height Peak height

Chromatography:

Chromatography ID:CH000398
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Sample Injection:1.67 uL
Solvent A:60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase
  
Chromatography ID:CH000399
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6550
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Sample Injection:5.0 uL
Solvent A:60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000497
Analysis ID:AN000561
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:200
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000498
Analysis ID:AN000562
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 l/min
Dry Gas Temp:325
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:200
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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