Summary of study ST000589

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 PR000429. The data can be accessed directly via it's Project DOI: 10.21228/M8M30H This work is supported by NIH grant, U2C- DK119886.

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Study IDST000589
Study TitleEffects of dilution on analyte identification and quantification
Study TypeGC-MS non-targeted metabolomic profiling
Study SummaryThe limiting-dilution study evaluated the effects of sample dilution on the ability to identify and quantify analytes in plasma. The study was divided into 10 batches with identical experimental design spanning over a 16-day period. Each batch consisted of 33 aliquots with 11 different plasma extract volumes (0 – 700 µL) corresponding to 11 plasma concentrations repeated three times.
Institute
Duke University
DepartmentDuke Molecular Physiology Institute
Last NameWang
First NameHanghang
Address300 North Duke Street, Durham, NC, 27701, USA
Emailhanghang.wang@duke.edu
Phone+1 919 884 0025
Submit Date2017-04-04
Num Groups10
Raw Data AvailableYes
Raw Data File Type(s).M, .val, .mth,.pmx,.m,.txt
Analysis Type DetailGC-MS
Release Date2017-07-10
Release Version1
Hanghang Wang Hanghang Wang
https://dx.doi.org/10.21228/M8M30H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000429
Project DOI:doi: 10.21228/M8M30H
Project Title:Methods for improved identification and quantification in GC-MS-based metabolomic profiling of human plasma
Project Type:GC-MS non targeted qualitative analysis
Project Summary:The field of metabolomics as applied to human disease and health is rapidly expanding. However, studies reporting experiences with quality-control and method validation are lacking. In this study, we sought to identify and modify steps in GC-MS-based metabolomic profiling of human plasma that could influence metabolite identification and quantification. Our experimental design included two studies: 1) the limiting-dilution study, which investigated the effects of dilution on analyte identification and quantification, and 2) the concentration-specific study, which compared the optimal plasma extract volume established in the first study with the volume used in the current institutional protocol. We confirmed that contaminants, concentration, intra- and inter-experiment variability are major factors influencing metabolite identification and quantification. In addition, we established methods for improved metabolite identification and quantification, which were summarized to provide recommendations for experimental design of GC-MS-based profiling of human plasma.
Institute:Duke University
Department:Duke Molecular Physiology Institute
Last Name:Wang
First Name:Hanghang
Address:300 North Duke Street, Durham, NC, 27701, USA
Email:hanghang.wang@duke.edu
Phone:+1 919 884 0025
Funding Source:U.S. Department of Health & Human Services, National Institutes of Health (NIH) - T32HL007101; Thoracic Surgery Foundation for Research and Education (TSFRE) - Braunwald Fellowship

Subject:

Subject ID:SU000612
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:60
Gender:male
Human Race:Caucasian
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Plasma Volume Extracted
SA03186511-0A0 uL
SA03186611-0B0 uL
SA03186710-0C0 uL
SA03186810-0B0 uL
SA0318699-0C0 uL
SA03187010-0A0 uL
SA03187112-0A0 uL
SA03187212-0B0 uL
SA0318734-0B0 uL
SA0318744-0A0 uL
SA03187513-0C0 uL
SA03187613-0B0 uL
SA03187712-0C0 uL
SA03187813-0A0 uL
SA0318799-0B0 uL
SA03188011-0C0 uL
SA0318816-0B0 uL
SA0318826-0C0 uL
SA0318835-0C0 uL
SA0318845-0B0 uL
SA0318859-0A0 uL
SA0318865-0A0 uL
SA0318877-0A0 uL
SA0318886-0A0 uL
SA0318898-0B0 uL
SA0318904-0C0 uL
SA0318918-0A0 uL
SA0318928-0C0 uL
SA0318937-0C0 uL
SA0318947-0B0 uL
SA03189510-100C100 uL
SA03189610-100B100 uL
SA03189710-100A100 uL
SA0318989-100B100 uL
SA03189911-100A100 uL
SA0319009-100A100 uL
SA0319019-100C100 uL
SA03190213-100B100 uL
SA03190313-100A100 uL
SA0319048-100C100 uL
SA03190512-100C100 uL
SA03190612-100B100 uL
SA03190711-100C100 uL
SA03190812-100A100 uL
SA03190911-100B100 uL
SA03191013-100C100 uL
SA0319115-100C100 uL
SA0319126-100A100 uL
SA0319135-100B100 uL
SA0319145-100A100 uL
SA0319154-100B100 uL
SA0319164-100C100 uL
SA0319176-100B100 uL
SA0319186-100C100 uL
SA0319198-100A100 uL
SA0319208-100B100 uL
SA0319217-100C100 uL
SA0319227-100B100 uL
SA0319237-100A100 uL
SA0319244-100A100 uL
SA0319259-150B150 uL
SA03192611-150A150 uL
SA03192711-150B150 uL
SA03192810-150C150 uL
SA03192910-150B150 uL
SA0319309-150C150 uL
SA03193110-150A150 uL
SA03193211-150C150 uL
SA03193312-150A150 uL
SA03193413-150B150 uL
SA03193513-150C150 uL
SA03193613-150A150 uL
SA03193712-150C150 uL
SA03193812-150B150 uL
SA0319398-150C150 uL
SA0319408-150B150 uL
SA0319415-150B150 uL
SA0319425-150C150 uL
SA0319435-150A150 uL
SA0319444-150C150 uL
SA0319454-150B150 uL
SA0319466-150A150 uL
SA0319476-150B150 uL
SA0319487-150C150 uL
SA0319498-150A150 uL
SA0319507-150B150 uL
SA0319517-150A150 uL
SA0319526-150C150 uL
SA0319534-150A150 uL
SA0319549-150A150 uL
SA03195510-200C200 uL
SA03195611-200A200 uL
SA03195710-200B200 uL
SA03195810-200A200 uL
SA0319594-200A200 uL
SA0319609-200C200 uL
SA03196111-200B200 uL
SA03196211-200C200 uL
SA03196313-200A200 uL
SA03196413-200B200 uL
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Collection:

Collection ID:CO000606
Collection Summary:Plasma from blood drawn intravenously
Sample Type:Blood
Collection Method:IV
Additives:EDTA
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000626
Treatment Summary:no treatment

Sample Preparation:

Sampleprep ID:SP000619
Sampleprep Summary:Protein precipitation and drying followed by derivatization via methoxyamine and MSTFA
Extraction Method:Protein precipitation
Sample Derivatization:18 mg/mL methoxyamine hydrochloride in pyridine for 30 min at 50°C, followed by trimethylsilylation with N-methyl-N- (trimethylsilyl)trifluoroacetamide (MSTFA) for 30 min at 50°C
Sample Spiking:retention-time-lock internal standard of perdeuterated myristic acid

Combined analysis:

Analysis ID AN000904
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Agilent DB5-MS (15m × 0.25mm, 0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975B
Ion Mode POSITIVE
Units Peak area (Log2 transformed)

Chromatography:

Chromatography ID:CH000642
Chromatography Summary:GC/MS methods follow previous studies using a 6890 N GC connected to a 5975B Inert single quadrupole MS (Agilent Technologies, Santa Clara, CA) (Bonikos et al. 1975; Fiehn 2008; Kind et al. 2009). The two wall-coated, open-tubular GC columns connected in series are both from J&W/Agilent (part 122–5512), DB5-MS, 15 meters in length, 0.25 mm in diameter, with an 0.25-l m luminal film. Positive ions generated with conventional electron-ionization at 70 eV are scanned broadly from 600 to 50 m/z in the detector throughout the 45 min cycle time.
Instrument Name:Agilent 6890N
Column Name:Agilent DB5-MS (15m × 0.25mm, 0.25um)
Flow Rate:2.0 mL/min
Time Program:initial GC oven temperature of 60°C increased at 10°C/min to a final temperature of 325°C
Chromatography Type:GC

MS:

MS ID:MS000804
Analysis ID:AN000904
Instrument Name:Agilent 5975B
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
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