Summary of Study ST000586

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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 IDST000586
Study TitleEvaluation of specific concentrations for use in experimental protocol
Study TypeGC-MS non-targeted metabolomic profiling
Study SummaryThis study evaluated specific plasma concentrations and compared the optimal plasma extract volume established in the first study (Effects of dilution on analyte identification and quantification) with the volume previously used in the current institutional protocol. The findings of this study lead to recommendations for experimental design in GC-MS-based metabolomic profiling of human plasma.
Duke University
DepartmentDuke Molecular Physiology Institute
Last NameWang
First NameHanghang
Address300 North Duke Street, Durham, NC, 27701, USA
Phone+1 919 884 0025
Submit Date2017-04-11
Num Groups10
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2018-06-05
Release Version1
Hanghang Wang Hanghang Wang application/zip

Select appropriate tab below to view additional metadata details:


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
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 ID:SU000609
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:60
Human Race:Caucasian
Species Group:Human


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

mb_sample_id local_sample_id Plasma Volume
SA0317860B0 uL
SA0317870A0 uL
SA031788150K150 uL
SA031789150J150 uL
SA031790150L150 uL
SA031791150N150 uL
SA031792150I150 uL
SA031793150M150 uL
SA031794150O150 uL
SA031795150C150 uL
SA031796150B150 uL
SA031797150H150 uL
SA031798150D150 uL
SA031799150A150 uL
SA031800150G150 uL
SA031801150F150 uL
SA031802150E150 uL
SA031803700L700 uL
SA031804700J700 uL
SA031805700K700 uL
SA031806700N700 uL
SA031807700I700 uL
SA031808700O700 uL
SA031809700M700 uL
SA031810700E700 uL
SA031811700B700 uL
SA031812700A700 uL
SA031813700C700 uL
SA031814700D700 uL
SA031815700G700 uL
SA031816700F700 uL
SA031817700H700 uL
Showing results 1 to 32 of 32


Collection ID:CO000603
Collection Summary:Plasma from blood drawn intravenously
Sample Type:Blood
Collection Method:IV
Blood Serum Or Plasma:Plasma


Treatment ID:TR000623
Treatment Summary:no treatment

Sample Preparation:

Sampleprep ID:SP000616
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 AN000901
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Agilent DB5-MS (15m x 0.25mm,0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975B
Units Peak area (Log2 transformed)


Chromatography ID:CH000641
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 x 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 ID:MS000803
Analysis ID:AN000901
Instrument Name:Agilent 5975B
Instrument Type:Single quadrupole
MS Type:EI