Summary of study ST000450

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 PR000348. The data can be accessed directly via it's Project DOI: 10.21228/M82K58 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000450
Study TitleMetabolic features of chronic fatigue syndrome
Study TypePlasma metabolomic profiling
Study SummaryThis targeted metabolomic analysis was performed on plasma samples from 39 normal controls (n=18 men and 21 women) and 45 subjects ((n = 22 men and 23 women) who met diagnostic criteria for ME/CFS by Institute of Medicine, Canadian, and Fukuda criteria.
Institute
University of California, San Diego
DepartmentThe Mitochondrial and Metabolic Disease Center
Last NameNaviaux
First NameRobert
Address214 Dikinson Street, CTF-C102, San Diego, CA, 92103
Emailmaviaux@ucsd.edu
Phone619-993-2904
Submit Date2016-08-11
Num Groups2 groups for men (control and CFS) and 2 groups for women (control and CFS)
Total Subjects84
Release Date2016-12-22
Release Version1
Robert Naviaux Robert Naviaux
https://dx.doi.org/10.21228/M82K58
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000348
Project DOI:doi: 10.21228/M82K58
Project Title:Metabolic features of chronic fatigue
Project Type:Human plasma
Project Summary:More than 2 million people in the United States have myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). We performed targeted, broad-spectrum metabolomics to gain insights into the biology of CFS. We studied a total of 84 subjects using these methods. Forty-five subjects (n = 22 men and 23 women) met diagnostic criteria for ME/CFS by Institute of Medicine, Canadian, and Fukuda criteria. We targeted 612 metabolites in plasma from 63 biochemical pathways by hydrophilic interaction liquid chromatography, electrospray ionization, and tandem mass spectrometry in a single-injection method. Our data show that despite the heterogeneity of factors leading to CFS, the cellular metabolic response in patients was homogeneous, statistically robust, and chemically similar to the evolutionarily conserved persistence response to environmental stress known as dauer.
Institute:University of California, San Diego
Department:The Mitochondrial and Metabolic Disease Center
Last Name:Naviaux
First Name:Robert
Address:214 Dikinson Street, CTF-C102, San Diego, CA, 92103
Email:maviaux@ucsd.edu
Phone:(619) 993-2904
Funding Source:UCSD Christini Fund,The Wright Family Foundation,The Lennox Foundation, The It Takes Guts Foundation, The UCSD Mitochondrial Disease Research Fund
Publications:PNAS publication

Subject:

Subject ID:SU000471
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Males with CFS were 53 (±2.8) y old (mean±SEM; range, 21–67 y). Females were 52 (±2.5) y old (range, 20–67 y).
Gender:23 females and 22 males with CFS and 18 male and 21 female controls.
Human Ethnicity:White/non-Hispanic
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Disease gender
SA022784101CFS Female
SA022785117CFS Female
SA022786121CFS Female
SA022787105CFS Female
SA022788118CFS Female
SA022789108CFS Female
SA022790116CFS Female
SA022791115CFS Female
SA022792112CFS Female
SA022793122CFS Female
SA022794107CFS Female
SA022795119CFS Female
SA022796133CFS Female
SA022797132CFS Female
SA022798123CFS Female
SA022799135CFS Female
SA022800136CFS Female
SA022801131CFS Female
SA022802134CFS Female
SA022803130CFS Female
SA022804126CFS Female
SA022805127CFS Female
SA022806129CFS Female
SA022807210CFS Male
SA022808221CFS Male
SA022809228CFS Male
SA022810219CFS Male
SA022811206CFS Male
SA022812214CFS Male
SA022813202CFS Male
SA022814208CFS Male
SA022815209CFS Male
SA022816215CFS Male
SA022817205CFS Male
SA022818207CFS Male
SA022819203CFS Male
SA022820225CFS Male
SA022821223CFS Male
SA022822220CFS Male
SA022823231CFS Male
SA022824218CFS Male
SA022825211CFS Male
SA022826224CFS Male
SA022827213CFS Male
SA022828201CFS Male
SA022829fctrl_008Normal Female
SA022830fctrl_021Normal Female
SA022831fctrl_019Normal Female
SA022832fctrl_020Normal Female
SA022833fctrl_014Normal Female
SA022834fctrl_026Normal Female
SA022835fctrl_023Normal Female
SA022836fctrl_018Normal Female
SA022837fctrl_002Normal Female
SA022838fctrl_012Normal Female
SA022839fctrl_013Normal Female
SA022840fctrl_015Normal Female
SA022841fctrl_024Normal Female
SA022842fctrl_027Normal Female
SA022843fctrl_016Normal Female
SA022844fctrl_022Normal Female
SA022845fctrl_028Normal Female
SA022846fctrl_011Normal Female
SA022847fctrl_025Normal Female
SA022848fctrl_005Normal Female
SA022849fctrl_017Normal Female
SA022850mctrl_004Normal Male
SA022851mctrl_003Normal Male
SA022852mctrl_031Normal Male
SA022853mctrl_009Normal Male
SA022854mctrl_001Normal Male
SA022855mctrl_007Normal Male
SA022856mctrl_040Normal Male
SA022857mctrl_034Normal Male
SA022858mctrl_010Normal Male
SA022859mctrl_033Normal Male
SA022860mctrl_039Normal Male
SA022861mctrl_037Normal Male
SA022862mctrl_036Normal Male
SA022863mctrl_030Normal Male
SA022864mctrl_032Normal Male
SA022865mctrl_041Normal Male
SA022866mctrl_029Normal Male
SA022867mctrl_035Normal Male

Collection:

Collection ID:CO000465
Collection Summary:None
Sample Type:Blood
Collection Method:Lithium-heparin vacutainer tubes
Storage Conditions:-80C
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000485
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000478
Sampleprep Summary:None
Extraction Method:Typically, 90 μl of plasma was thawed on ice and mixed with 5 μl of isotope standards and incubated for 10 min at 20°C to permit small molecules and vitamins in the internal standards to associate with plasma binding proteins. Macromolecules (protein, DNA, RNA, glycans, etc.) were precipitated by extraction with 4 volumes (400 μl) of cold (-20°C), acetonitrile:methanol (50:50) and incubated on crushed ice for 10 min, then removed by centrifugation at 16,000g x 10 min at 4°C. The supernatants containing the extracted metabolites and internal standards were transferred to labeled cryotubes and stored at -80°C for LCMS/MS analysis.
Extract Storage:-80°C
Sample Derivatization:No
Sample Spiking:25-35 commercial stable isotope internal standards, and 57 stable isotope internal standards that were custom-synthesized in E. coli and S. cerevisiae by metabolic labeling with 13C-glucose and 13C bicarbonate

Combined analysis:

Analysis ID AN000705 AN000706
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Shimadzu 20AD Shimadzu 20AD
Column Shodex NH2P-40 2E (250 mm × 2.0 mm) Shodex NH2P-40 2E (250 mm × 2.0 mm)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode POSITIVE NEGATIVE
Units AUC AUC

Chromatography:

Chromatography ID:CH000510
Chromatography Summary:HILIC
Instrument Name:Shimadzu 20AD
Column Name:Shodex NH2P-40 2E (250 mm × 2.0 mm)
Column Pressure:920~2600 psi
Column Temperature:25C
Flow Gradient:0-3.5 min: 95%B, 3.6-8 min: 85% B, 8.1-13 min: 75% B, 13.5–35 min: 0% B, 36–46 min: 95% B, 46.1 min: end.
Flow Rate:0.2 ml/min
Solvent A:95% water with 20 mM (NH4)2CO3, 5% acetonitrile, and 38 mM NH4OH, final pH 9.75
Solvent B:100% acetonitrile
Analytical Time:46.1 min
Oven Temperature:25C
Sample Loop Size:10 ul
Sample Syringe Size:100 ul
Chromatography Type:HILIC

MS:

MS ID:MS000627
Analysis ID:AN000705
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
Collision Energy:Compound-specific
Collision Gas:High
Ion Source Temperature:500C
Ion Spray Voltage:5500V
Ionization:ESI
Mass Accuracy:0.1Da
  
MS ID:MS000628
Analysis ID:AN000706
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
Collision Energy:Compound-specific
Collision Gas:High
Ion Source Temperature:500C
Ion Spray Voltage:-4500V
Ionization:ESI
Mass Accuracy:0.1Da