Summary of Study ST000801

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 PR000576. The data can be accessed directly via it's Project DOI: 10.21228/M86X1F This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000801
Study TitleInsights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part II)
Study TypeObservational
Study SummaryThe pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls.
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 Date2017-07-19
Study CommentsKey: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
PublicationsInsights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics. Scientific Reports volume 8, Article number: 10056 (2018). Dorottya Nagy-Szakal, Dinesh K. Barupal, Bohyun Lee, Xiaoyu Che, Brent L. Williams, Ellie J. R. Kahn, Joy E. Ukaigwe, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, Jose G. Montoya, Daniel L. Peterson, Bruce Levin, Mady Hornig, Oliver Fiehn & W. Ian Lipkin.
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2018-08-16
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M86X1F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000576
Project DOI:doi: 10.21228/M86X1F
Project Title:Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
Project Summary:The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls.
Institute:Columbia University
Department:Center for Infection and Immunity, Mailman School of Public Health
Last Name:Lipkin
First Name:Ian
Address:722 West 168th Street, Room 1703a, New York, NY USA 10032
Email:wil2001@columbia.edu
Phone:212-342-9044
Publications:Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics. Scientific Reports volume 8, Article number: 10056 (2018). Dorottya Nagy-Szakal, Dinesh K. Barupal, Bohyun Lee, Xiaoyu Che, Brent L. Williams, Ellie J. R. Kahn, Joy E. Ukaigwe, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, Jose G. Montoya, Daniel L. Peterson, Bruce Levin, Mady Hornig, Oliver Fiehn & W. Ian Lipkin.

Subject:

Subject ID:SU000826
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id CaseStatus MECFS IBS
SA044010ESP-0423Case 1 -
SA044011ESP-0462Case 1 -
SA044012ESP-0514Case 1 -
SA044013ESP-1164Case 1 -
SA044014ESP-0592Case 1 -
SA044015ESP-0306Case 1 -
SA044016ESP-0332Case 1 -
SA044017ESP-0904Case 1 -
SA044018ESP-1138Case 1 -
SA044019ESP-0956Case 1 -
SA044020ESP-0800Case 1 -
SA044021ESP-0813Case 1 -
SA044022ESP-0865Case 1 -
SA044023ESP-0891Case 1 -
SA044024ESP-0280Case 1 -
SA044025ESP-0761Case 1 -
SA044026ESP-0644Case 1 -
SA044027ESP-0657Case 1 -
SA044028ESP-0982Case 1 -
SA044029ESP-0605Case 1 -
SA044030ESP-1151Case 1 -
SA044031ESP-0189Case 1 -
SA044032ESP-0046Case 1 -
SA044033ESP-0137Case 1 -
SA044034ESP-0072Case 1 -
SA044035ESP-0124Case 1 -
SA044036ESP-0033Case 1 -
SA044037ESP-1203Case 1 -
SA044038ESP-1255Case 1 -
SA044039ESP-1047Case 1 1
SA044040ESP-1034Case 1 1
SA044041ESP-0566Case 1 1
SA044042ESP-0085Case 1 1
SA044043ESP-0696Case 1 1
SA044044ESP-0709Case 1 1
SA044045ESP-0683Case 1 1
SA044046ESP-0995Case 1 1
SA044047ESP-0748Case 1 1
SA044048ESP-0943Case 1 1
SA044049ESP-0501Case 1 1
SA044050ESP-0241Case 1 1
SA044051ESP-0228Case 1 1
SA044052ESP-0345Case 1 1
SA044053ESP-0878Case 1 1
SA044054ESP-0007Case 1 1
SA044055ESP-0215Case 1 1
SA044056ESP-1125Case 1 1
SA044057ESP-0826Case 1 1
SA044058ESP-0488Case 1 1
SA044059ESP-0020Case 1 1
SA044060ESP-0930Control - -
SA044061ESP-0917Control - -
SA044062ESP-0969Control - -
SA044063ESP-1307Control - -
SA044064ESP-1281Control - -
SA044065ESP-1229Control - -
SA044066ESP-1099Control - -
SA044067ESP-1112Control - -
SA044068ESP-1216Control - -
SA044069ESP-1177Control - -
SA044070ESP-1086Control - -
SA044071ESP-1073Control - -
SA044072ESP-1021Control - -
SA044073ESP-1008Control - -
SA044074ESP-1190Control - -
SA044075ESP-1268Control - -
SA044076ESP-1060Control - -
SA044077ESP-1294Control - -
SA044078ESP-0579Control - -
SA044079ESP-0293Control - -
SA044080ESP-0267Control - -
SA044081ESP-0319Control - -
SA044082ESP-0358Control - -
SA044083ESP-0384Control - -
SA044084ESP-0371Control - -
SA044085ESP-0254Control - -
SA044086ESP-0202Control - -
SA044087ESP-0098Control - -
SA044088ESP-0059Control - -
SA044089ESP-0111Control - -
SA044090ESP-0150Control - -
SA044091ESP-0176Control - -
SA044092ESP-0163Control - -
SA044093ESP-0397Control - -
SA044094ESP-0410Control - -
SA044095ESP-0722Control - -
SA044096ESP-0670Control - -
SA044097ESP-0735Control - -
SA044098ESP-0774Control - -
SA044099ESP-0839Control - -
SA044100ESP-0787Control - -
SA044101ESP-0631Control - -
SA044102ESP-0618Control - -
SA044103ESP-0449Control - -
SA044104ESP-0436Control - -
SA044105ESP-0475Control - -
SA044106ESP-0527Control - -
SA044107ESP-0553Control - -
SA044108ESP-0540Control - -
SA044109ESP-0852Control - -
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Collection:

Collection ID:CO000820
Collection Summary:Subjects included 50 cases and 50 controls from the Chronic Fatigue Initiative (CFI) Cohort (28) recruited at 4 sites across the US who met the 1994 CDC Fukuda and/or Canadian consensus criteria for ME/CFS.
Sample Type:Blood
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000840
Treatment Summary:Subjects included 50 cases and 50 controls from the Chronic Fatigue Initiative (CFI) Cohort (28) recruited at 4 sites across the US who met the 1994 CDC Fukuda and/or Canadian consensus criteria for ME/CFS

Sample Preparation:

Sampleprep ID:SP000833
Sampleprep Summary:1.Thaw each 20 μL plasma aliquot at room temperature (see Aliquoting TEDDY samples SOP). Once thawed (~10min) place liquid plasma samples on ice. 2. Add 225 μL cold “MeOH with QC mix” (see SOP “QC mix for LC-MS lipid analysis”). Keep MeOH on ice during extraction 3. Vortex each sample for 10s, keeping the rest on ice during all the extraction. 4. Add 750 μL of cold MTBE with 22:1 CE, keep MTBE on ice during extraction 5. Vortex for 10s 6. Shake for 6min at 4°C in the orbital mixer. 7. Add 188 μL room temperature LC/MS grade water. 8. Vortex for 20 s 9. Centrifuge for 2 min @ 14,000 rcf (12300 rpm) 10. Remove supernatant, splitting into two aliquots of 350 μL, keeping one at –20°C for backup 11. Dry samples to complete dryness in the speed vacuum concentration system
Sampleprep Protocol Filename:SP_SOP_Extraction_of_plasma.pdf

Combined analysis:

Analysis ID AN001273
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 6530
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530 QTOF
Ion Mode POSITIVE
Units Counts

Chromatography:

Chromatography ID:CH000889
Instrument Name:Agilent 6530
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Pressure:200-700 bar
Column Temperature:40 C
Flow Gradient:0 min 100% (B), 0-2 min 100% (B), 2-7 min 70% (B), 7.7-9 min 40% (B), 9.5-10.25 min 30% (B), 10.25- 12.75 min 100% (B), 16.75 min 100% (B)
Flow Rate:0.4 mL/min
Injection Temperature:4 C
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:3 μL
Analytical Time:14 min
Capillary Voltage:4500 eV
Time Program:16.75 min
Weak Wash Solvent Name:1:1 ACN:H2O
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:HILIC

MS:

MS ID:MS001166
Analysis ID:AN001273
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500 eV
Collision Energy:45 eV
Collision Gas:Nitrogen
Dry Gas Flow:8L/min
Dry Gas Temp:325 C
Fragment Voltage:120 eV
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325 C
Ion Spray Voltage:1000
Ionization:Pos
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
Resolution Setting:Extended Dyamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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