Summary of Study ST002002

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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002002
Study TitleA case-control study on plasma metabolomics analysis in Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) (Part 3)
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)d
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:SU002083
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
SA187222GH025_157case
SA187223GH024_156case
SA187224CD067_084case
SA187225CD064_082case
SA187226CD065_083case
SA187227CD073_089case
SA187228CD074_090case
SA187229GH019_153case
SA187230GH017_152case
SA187231GH021_154case
SA187232GH022_155case
SA187233CD075_091case
SA187234CD076_092case
SA187235CD063_081case
SA187236CD059_079case
SA187237CD039_064case
SA187238GH053_170case
SA187239GH054_171case
SA187240CD035_061case
SA187241GH058_173case
SA187242CD041_066case
SA187243GH049_168case
SA187244CD055_077case
SA187245GH037_161case
SA187246CD053_076case
SA187247GH040_164case
SA187248GH042_166case
SA187249CD083_097case
SA187250AB003_001case
SA187251EF031_123case
SA187252EF032_124case
SA187253EF029_122case
SA187254EF028_121case
SA187255EF024_118case
SA187256EF026_119case
SA187257EF033_125case
SA187258EF034_126case
SA187259EF043_131case
SA187260GH002-2_142case
SA187261EF041_130case
SA187262GH004_143case
SA187263EF035_127case
SA187264EF023_117case
SA187265EF020_116case
SA187266EF004_105case
SA187267EF005_106case
SA187268EF003_104case
SA187269EF001_102case
SA187270GH060_174case
SA187271GH008_146case
SA187272EF010_110case
SA187273EF017_114case
SA187274EF019_115case
SA187275EF013_113case
SA187276EF012_112case
SA187277EF011_111case
SA187278CD084_098case
SA187279CD043_068case
SA187280IJ043_189case
SA187281AB047_026case
SA187282IJ044_190case
SA187283IJ046_191case
SA187284AB037_020case
SA187285IJ047_192case
SA187286AB049_027case
SA187287AB050_028case
SA187288IJ013_184case
SA187289IJ009_182case
SA187290IJ014_185case
SA187291AB055_031case
SA187292IJ030_187case
SA187293CD030_058case
SA187294AB036_019case
SA187295AB034_018case
SA187296AB010_006case
SA187297AB012_007case
SA187298AB009-2_005case
SA187299AB008_004case
SA187300AB004_002case
SA187301AB006_003case
SA187302AB014_008case
SA187303AB017_009case
SA187304IJ052_194case
SA187305IJ049_193case
SA187306IJ059_195case
SA187307AB023_011case
SA187308AB022_010case
SA187309IJ006_181case
SA187310AB052_030case
SA187311CD016_048case
SA187312CD015_047case
SA187313CD014_046case
SA187314IJ001_178case
SA187315CD001-2_038case
SA187316CD019-2_050case
SA187317CD027_056case
SA187318CD024_053case
SA187319CD022_052case
SA187320CD020_051case
SA187321CD011_044case
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 197

Collection:

Collection ID:CO002076
Collection Summary:Plasma was collected from case and control patients.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002095
Treatment Summary:Case versus control

Sample Preparation:

Sampleprep ID:SP002089
Sampleprep Summary:Extraction of plasma lipids is based on the “Maytash'' method [1] which was subsequently modified. 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) containing a mixture of odd chain and deuterated lipid internal standards [lysoPE(17:1), lysoPC(17:0), PC(12:0/13:0), PE(17:0/17:0), PG(17:0/17:0), sphingosine (d17:1), d7-cholesterol, SM(17:0), C17 ceramide, d3-palmitic acid, MG(17:0/0:0/0:0), DG(18:1/2:0/0:0), DG(12:0/12:0/0:0), and d5-TG(17:0/17:1/17:0)] is added to a 20 µL sample aliquot, which is placed into a 1.5 mL Eppendorf tube, and the tube is vortexed for 10 s. Then, 750 µL of cold MTBE containing CE(22:1) (internal standard) are 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. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended using a mixture of methanol/toluene (9:1, v/v) (60 µL) containing an internal standard [12-​[[(cyclohexylamino)carbonyl]amino]-​dodecanoic acid (CUDA)] used as a quality control.

Combined analysis:

Analysis ID AN003265
Analysis type MS
Chromatography type Unspecified
Chromatography system Agilent 6530 B
Column Waters CSH
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530 QTOF
Ion Mode UNSPECIFIED
Units normalized peak height

Chromatography:

Chromatography ID:CH002409
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 either an Agilent 6530 (positive ion mode) or an Agilent 6550 mass spectrometer equipped with an ion funnel (iFunnel) (negative ion mode). Lipids are separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) maintained at 65°C at a flow-rate of 0.6 mL/min. Solvent pre-heating (Agilent G1316) was used. The mobile phases consist of 60:40 acetonitrile:water with 10 mM ammonium formate and 0.1% formic acid (A) and 90:10 propan-2-ol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid. The gradient is as follows: 0 min 85% (A); 0–2 min 70% (A); 2–2.5 min 52% (A); 2.5–11 min 18% (A); 11–11.5 min 1% (A); 11.5–12 min 1% (A); 12–12.1 min 85% (A); 12.1–15 min 85% (A). A sample volume of 3 µL is used for the injection. Sample temperature is maintained at 4°C in the autosampler. The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and negative (Agilent 6550, equipped with a dual JetStream Source) modes producing both unique and complementary spectra. Instrument parameters are as follows (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 l/min, Fragmentor 175V, with the other parameters identical to positive ion mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and these are used for continuous mass correction. For the 6550, the reference solution is introduced via a dual spray ESI, with the same ions and continuous mass correction. Samples are injected (1.7 μl in positive mode and 5 μl in negative ion mode) with a needle wash for 20 seconds (wash solvent is isopropanol). The valve is switched back and forth during the run for washing; this has been shown to be essential for reducing carryover of less polar lipids.
Instrument Name:Agilent 6530 B
Column Name:Waters CSH
Chromatography Type:Unspecified

MS:

MS ID:MS003037
Analysis ID:AN003265
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and negative (Agilent 6550, equipped with a dual JetStream Source) modes producing both unique and complementary spectra. Instrument parameters are as follows (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 l/min, Fragmentor 175V, with the other parameters identical to positive ion mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and these are used for continuous mass correction. For the 6550, the reference solution is introduced via a dual spray ESI, with the same ions and continuous mass correction.
Ion Mode:UNSPECIFIED
  logo