Summary of study ST000617

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 PR000451. The data can be accessed directly via it's Project DOI: 10.21228/M8RP6W This work is supported by NIH grant, U2C- DK119886.

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Study IDST000617
Study TitleValidation of the application of targeted metabolomic appraoch in the diagnosis of CFS
Study TypePlasma metabolomic profiling
Study SummaryThis study was to validate the utility of the developed targeted metabolomic method in the diagnosis of chronic fatigue syndrome (CFS). Clinical validation consisted of a cohort of 20 male CFS (53 ± 2.8 years old, mean ± SEM, range 21-67 y) and 18 male controls (53 ± 3.5 years old, mean ± SEM, range 23-69 y), who were enrolled in a previous study (Naviaux et al. 2016). These plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
Institute
University of California, San Diego
DepartmentDepartment of Medicine
LaboratoryThe Mitochondrial and Metabolic Disease Center
Last NameNaviaux
First NameRobert
Address214 Dikinson Street, CTF-C102, San Diego, CA, 92103
Emailrnaviaux@ucsd.edu
Phone619-993-2904
Submit Date2017-05-17
Num Groups2
Total Subjects38
Num Males38
Study CommentsThese plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
Analysis Type DetailLC-MS
Release Date2017-06-17
Release Version1
Robert Naviaux Robert Naviaux
https://dx.doi.org/10.21228/M8RP6W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000451
Project DOI:doi: 10.21228/M8RP6W
Project Title:Clinical validation for the utility of targeted metabolomic method in chronic fatigue syndrome
Project Type:Plasma samples
Project Summary:Chronic fatigue syndrome (CFS) is a complex, multisystem disease that has affected more than 2 million people in the United States. No biochemical diagnostic lab test is currently available.As a practical test of the reproducibility of our new metabolomic method, we reanalyzed 40 samples from an earlier CFS study
Institute:University of California, San Diego
Department:Department of Medicine
Last Name:Naviaux
First Name:Robert
Address:214 Dickinson St., Bldg CTF, Rm C102, San Diego, CA, 92103, USA
Email:naviaux@ucsd.edu
Phone:619-543-2904

Subject:

Subject ID:SU000640
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:53 ± 3.5 (23-69 yr)
Gender:Male
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 Treatment
SA034196211_CFSCFS
SA034197213_CFSCFS
SA034198214_CFSCFS
SA034199210_CFSCFS
SA034200202_CFSCFS
SA034201206_CFSCFS
SA034202201_CFSCFS
SA034203215_CFSCFS
SA034204207_CFSCFS
SA034205218_CFSCFS
SA034206231_CFSCFS
SA034207228_CFSCFS
SA034208208_CFSCFS
SA034209224_CFSCFS
SA034210225_CFSCFS
SA034211221_CFSCFS
SA034212223_CFSCFS
SA034213205_CFSCFS
SA034214219_CFSCFS
SA034215209_CFSCFS
SA034216M46MP_010Control
SA034217M23CV_036Control
SA034218M26JC_040Control
SA034219M37AF_034Control
SA034220M54MD_004Control
SA034221M66CC_039Control
SA034222M65WA_030Control
SA034223M47WA_009Control
SA034224M27RW_001Control
SA034225M58JG_031Control
SA034226M64EG_032Control
SA034227M67NN_033Control
SA034228M69JB_037Control
SA034229M63RD_029Control
SA034230M62JR_041Control
SA034231M58RN_007Control
SA034232M59JM_035Control
SA034233M56MF_003Control
Showing results 1 to 38 of 38

Collection:

Collection ID:CO000634
Collection Summary:Blood samples from 18 male subjects with chronic fatigue syndrome and 20 age and sex matched controls were collected. Plasma was prepared according to the standard protocol. The metabolites were extracted from
Sample Type:Blood
Collection Method:Lithium-heparin vacutainer tubes
Storage Conditions:-80 C
Collection Vials:Lithium-heparin vacutainer tubes
Collection Tube Temp:-80 C
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000654
Treatment Summary:No treatment. There are only two groups: control and disease group (Chronic fatigue syndrome)

Sample Preparation:

Sampleprep ID:SP000647
Sampleprep Summary:Metabolites from plasma were extracted using pre-chilled methanol/acetonitrile (50:50)
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
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 AN000946 AN000947
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 NEGATIVE POSITIVE
Units AUC AUC

Chromatography:

Chromatography ID:CH000674
Chromatography Summary:hydrophilic interaction chromatography (HILIC) on shodex column
Instrument Name:Shimadzu 20AD
Column Name:Shodex NH2P-40 2E (250 mm × 2.0 mm)
Column Pressure:900~2800 psi
Column Temperature:25 C
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
Injection Temperature:room temperature
Solvent A:95% water with 20 mM (NH4)2CO3, 5% acetonitrile, and 38 mM NH4OH, final pH 9.8
Solvent B:100% acetonitrile
Analytical Time:46.1 min
Oven Temperature:25 C
Sample Loop Size:10 ul
Sample Syringe Size:100 ul
Chromatography Type:HILIC

MS:

MS ID:MS000842
Analysis ID:AN000946
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:500 C
Ion Spray Voltage:-4500
Ionization:ESI
Mass Accuracy:0.1 Da
Scanning:MRM
  
MS ID:MS000843
Analysis ID:AN000947
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:500 C
Ion Spray Voltage:5500
Mass Accuracy:0.1 Da
Scanning:MRM
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