Summary of Study ST002003

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 PR001269. The data can be accessed directly via it's Project DOI: 10.21228/M8PD9N 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 IDST002003
Study TitleA case-control study on plasma metabolomics analysis in Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) (Part 4)
Study SummaryTargeted and untargeted metabolomics analysis consisting of 888 metabolic analytes covering primary metabolites, biogenic amines, complex lipids, and oxylipins in 106 ME/CFS cases and 91 frequency-matched healthy controls
Institute
Columbia University
DepartmentCenter for Infection and Immunity
LaboratoryCenter for Infection and Immunity
Last NameLipkin
First NameW. Ian
Address722 W. 168th St., 17th Floor, New York, NY, 10032
Emailwil2001@cumc.columbia.edu
Phone212-342-9033
Submit Date2021-11-23
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-12-08
Release Version1
W. Ian Lipkin W. Ian Lipkin
https://dx.doi.org/10.21228/M8PD9N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001269
Project DOI:doi: 10.21228/M8PD9N
Project Title:Case-control study on plasma metabolomics analysis in Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)
Project Summary:Targeted and untargeted metabolomics analysis consisting of 888 metabolic analytes covering primary metabolites, biogenic amines, complex lipids, and oxylipins in 106 ME/CFS cases and 91 frequency-matched healthy controls.
Institute:Columbia University
Department:Center for Infection and Immunity
Last Name:Lipkin
First Name:W. Ian
Address:722 W. 168th St., 17th Floor, New York, NY, 10032
Email:wil2001@cumc.columbia.edu
Phone:212-342-9033
Funding Source:This study was funded by National Institutes of Health U54 AI138370 (Center for Solutions for ME/CFS)

Subject:

Subject ID:SU002084
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id treatment
SA187419GH025_157case
SA187420GH024_156case
SA187421CD067_084case
SA187422CD064_082case
SA187423CD065_083case
SA187424CD073_089case
SA187425CD074_090case
SA187426GH019_153case
SA187427GH017_152case
SA187428GH021_154case
SA187429GH022_155case
SA187430CD075_091case
SA187431CD076_092case
SA187432CD063_081case
SA187433CD059_079case
SA187434CD039_064case
SA187435GH053_170case
SA187436GH054_171case
SA187437CD035_061case
SA187438GH058_173case
SA187439CD041_066case
SA187440GH049_168case
SA187441CD055_077case
SA187442GH037_161case
SA187443CD053_076case
SA187444GH040_164case
SA187445GH042_166case
SA187446CD083_097case
SA187447AB003_001case
SA187448EF031_123case
SA187449EF032_124case
SA187450EF029_122case
SA187451EF028_121case
SA187452EF024_118case
SA187453EF026_119case
SA187454EF033_125case
SA187455EF034_126case
SA187456EF043_131case
SA187457GH002-2_142case
SA187458EF041_130case
SA187459GH004_143case
SA187460EF035_127case
SA187461EF023_117case
SA187462EF020_116case
SA187463EF004_105case
SA187464EF005_106case
SA187465EF003_104case
SA187466EF001_102case
SA187467GH060_174case
SA187468GH008_146case
SA187469EF010_110case
SA187470EF017_114case
SA187471EF019_115case
SA187472EF013_113case
SA187473EF012_112case
SA187474EF011_111case
SA187475CD084_098case
SA187476CD043_068case
SA187477IJ043_189case
SA187478AB047_026case
SA187479IJ044_190case
SA187480IJ046_191case
SA187481AB037_020case
SA187482IJ047_192case
SA187483AB049_027case
SA187484AB050_028case
SA187485IJ013_184case
SA187486IJ009_182case
SA187487IJ014_185case
SA187488AB055_031case
SA187489IJ030_187case
SA187490CD030_058case
SA187491AB036_019case
SA187492AB034_018case
SA187493AB010_006case
SA187494AB012_007case
SA187495AB009-2_005case
SA187496AB008_004case
SA187497AB004_002case
SA187498AB006_003case
SA187499AB014_008case
SA187500AB017_009case
SA187501IJ052_194case
SA187502IJ049_193case
SA187503IJ059_195case
SA187504AB023_011case
SA187505AB022_010case
SA187506IJ006_181case
SA187507AB052_030case
SA187508CD016_048case
SA187509CD015_047case
SA187510CD014_046case
SA187511IJ001_178case
SA187512CD001-2_038case
SA187513CD019-2_050case
SA187514CD027_056case
SA187515CD024_053case
SA187516CD022_052case
SA187517CD020_051case
SA187518CD011_044case
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Collection:

Collection ID:CO002077
Collection Summary:Plasma was collected from case and control patients
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002096
Treatment Summary:Case versus control

Sample Preparation:

Sampleprep ID:SP002090
Sampleprep Summary:Extraction is carried out using a bi-phasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more detail, cold methanol (225 µL is added to a 5mg tissue sample aliquot, which is placed into a 1.5 mL Eppendorf tube. Then, 750 µL of cold MTBE is added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase separation is induced by adding 188 µL of mass spec-grade water. After vortexing for 20 s. the sample is centrifuged at 14,000 rpm for 2 min. The upper organic phase is collected in two 300 µL aliquots for lipid analysis polar layer is collected in two 125 µL aliquots for HILIC analysis. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended in acetonitrile.

Combined analysis:

Analysis ID AN003266
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 6600
Column Waters Acquity UPLC BEH amide,(150 x 2.1mm,1.7um)
MS Type ESI
MS instrument type TTOF
MS instrument name Agilent 6560 Ion Mobility
Ion Mode POSITIVE
Units normalized peak height

Chromatography:

Chromatography ID:CH002410
Chromatography Summary:The LC/QTOFMS analyses are performed using an Agilent 1290 Infinity LC system (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat) coupled to a SCIEX Triple TOF mass spectrometer. Polar compounds are separated on an Acquity UPLC BEH Amide Column, 130Å, 1.7 µm, 2.1 mm X 150 mm maintained at 45°C at a flow-rate of 0.4 mL/min. Solvent pre-heating (Agilent G1316) was used. The mobile phases consist of: Water, 10 mM Ammonium Formate, 0.125% Formic Acid (A) and Acetonitrile: Water (95/5, v/v), 10 mM Ammonium Formate, 0.125% Formic Acid (B)
Instrument Name:Agilent 6600
Column Name:Waters Acquity UPLC BEH amide,(150 x 2.1mm,1.7um)
Column Temperature:45
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS003038
Analysis ID:AN003266
Instrument Name:Agilent 6560 Ion Mobility
Instrument Type:TTOF
MS Type:ESI
MS Comments:SCIEX Triple TOF 6600mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 50–1200. Number of cycles in MS1 is 1667 with cycle time of 500ms and accumulation time 475ms. Mass spectrometer parameters are as follows (positive mode) Gas Temp 300°C, gas pressures in psi units with : GS1 and GS2 50 psi, CUR: 35. ISVF is 4500V and DP and CE are 10V and 100 V.
Ion Mode:POSITIVE
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