Summary of Study ST003178

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 PR001977. The data can be accessed directly via it's Project DOI: 10.21228/M85Q8Q 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.

Study ID	ST003178
Study Title	Post-Infectious MECFS at the NIH
Study Summary	In 2016, the National Institutes of Health (NIH) launched an initiative to study ME/CFS. The NIH Division of Intramural Research developed an exploratory clinical research program to perform deep phenotyping on a cohort of PI-ME/CFS volunteers and healthy volunteers (HV) as controls. Prior to the SARS-CoV-2 pandemic, this study recruited a cohort of well-characterized PI-ME/CFS patients and applied modern broad and deep scientific measures to describe their biophenotype compared to HVs. The aim was to identify relevant group differences that could generate new hypotheses about the pathogenesis of PI-ME/CFS and provide direction for future research. Over 75 scientists and clinicians across 15 of the 27 institutes that comprise the NIH contributed to this multi-disciplinary work. Importantly, we developed rigorous inclusion criteria which comprised detailed medical and psychological evaluations to minimize diagnostic misattribution. A relatively homogenous population was recruited in whom symptoms were initiated after infection. This study aimed to investigate the underlying pathophysiological mechanisms. The volunteers underwent a multi-dimensional evaluation that included a wide range of physiological measures, physical and cognitive performance testing, and biochemical, microbiological, and immunological assays of blood, cerebrospinal fluid, muscle, and stool. Novel measurement techniques were developed to query issues such as physical capacity, effort preference, and deconditioning that may confound the results. Multi-omic measurements of gene expression, proteins, metabolites, and lipids were performed in parallel on collected samples.
Institute	National Institutes of Health
Last Name	Nath
First Name	Avindra
Address	10 Center Drive, Bethesda, MD 20892
Email	Avindra.nath@nih.gov
Phone	3014961561
Submit Date	2024-01-12
Analysis Type Detail	Other
Release Date	2024-05-14
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001977
Project DOI:	doi: 10.21228/M85Q8Q
Project Title:	Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Project Summary:	Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling disorder that may occur following an infection, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit a cohort of post-infectious ME/CFS (PI-ME/CFS) volunteers (n=17) with matched healthy controls (n=21) to conduct deep clinical and biological phenotyping using an extensive battery of tests. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical deconditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.
Institute:	National Institutes of Health
Department:	NINDS
Laboratory:	National Institute of Neurological Disorders and Stroke
Last Name:	Nath
First Name:	Avindra
Address:	10 Center Drive, Bethesda, MD 20892
Email:	Avindra.nath@nih.gov
Phone:	301.496.1561

Subject:

Subject ID:	SU003297
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	Sample source	MECFS_STATUS	SEX
SA345808	NINR-00428	CSF	Healthy volunteer	F
SA345809	NINR-00429	CSF	Healthy volunteer	F
SA345810	NINR-00433	CSF	Healthy volunteer	F
SA345811	NINR-00432	CSF	Healthy volunteer	F
SA345812	NINR-00431	CSF	Healthy volunteer	F
SA345813	NINR-00424	CSF	Healthy volunteer	F
SA345814	NINR-00437	CSF	Healthy volunteer	F
SA345815	NINR-00423	CSF	Healthy volunteer	F
SA345816	NINR-00420	CSF	Healthy volunteer	F
SA345817	NINR-00418	CSF	Healthy volunteer	F
SA345818	NINR-00421	CSF	Healthy volunteer	F
SA345819	NINR-00434	CSF	Healthy volunteer	M
SA345820	NINR-00417	CSF	Healthy volunteer	M
SA345821	NINR-00435	CSF	Healthy volunteer	M
SA345822	NINR-00436	CSF	Healthy volunteer	M
SA345823	NINR-00422	CSF	Healthy volunteer	M
SA345824	NINR-00430	CSF	Healthy volunteer	M
SA345825	NINR-00425	CSF	Healthy volunteer	M
SA345826	NINR-00419	CSF	Healthy volunteer	M
SA345827	NINR-00426	CSF	Healthy volunteer	M
SA345828	NINR-00427	CSF	Healthy volunteer	M
SA345829	NINR-00448	CSF	MECFS	F
SA345830	NINR-00447	CSF	MECFS	F
SA345831	NINR-00452	CSF	MECFS	F
SA345832	NINR-00446	CSF	MECFS	F
SA345833	NINR-00453	CSF	MECFS	F
SA345834	NINR-00450	CSF	MECFS	F
SA345835	NINR-00444	CSF	MECFS	F
SA345836	NINR-00440	CSF	MECFS	F
SA345837	NINR-00442	CSF	MECFS	F
SA345838	NINR-00438	CSF	MECFS	F
SA345839	NINR-00439	CSF	MECFS	M
SA345840	NINR-00454	CSF	MECFS	M
SA345841	NINR-00441	CSF	MECFS	M
SA345842	NINR-00443	CSF	MECFS	M
SA345843	NINR-00449	CSF	MECFS	M
SA345844	NINR-00445	CSF	MECFS	M
SA345845	NINR-00451	CSF	MECFS	M

Showing results 1 to 38 of 38

Showing results 1 to 38 of 38

Collection:

Collection ID:	CO003290
Collection Summary:	Metabolomics on cerebrospinal fluid samples was performed using Metabolon’s Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS). Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules were bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for two minutes (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.
Sample Type:	Cerebrospinal fluid

Treatment:

Treatment ID:	TR003306
Treatment Summary:	No treatment

Sample Preparation:

Sampleprep ID:	SP003304
Sampleprep Summary:	All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore-mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.1% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however, with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slightly between methods but covered 70-1000 m/z.

Sampleprep ID:

SP003304

Sampleprep Summary:

All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore-mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.1% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however, with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slightly between methods but covered 70-1000 m/z.

Combined analysis:

Analysis ID	AN005217	AN005218	AN005219	AN005220
Analysis type	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	Reversed phase	HILIC
Chromatography system	Waters Acquity	Waters Acquity	Waters Acquity	Waters Acquity
Column	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)	Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	POSITIVE	NEGATIVE	NEGATIVE
Units	Peak area	Peak area	Peak area	Peak area

Chromatography:

Chromatography ID:	CH003945
Chromatography Summary:	Low pH polar (LC/MS Pos early)
Instrument Name:	Waters Acquity
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:	100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:	Reversed phase

Chromatography ID:	CH003946
Chromatography Summary:	Low pH Lipophilic (LC/MS Pos late)
Instrument Name:	Waters Acquity
Column Name:	Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:	0.60 mL/min
Solvent A:	100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:	50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:	Reversed phase

Chromatography ID:	CH003947
Chromatography Summary:	High pH (LC/MS Neg)
Instrument Name:	Waters Acquity
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 6.5 mM ammonium bicarbonate, pH 8
Solvent B:	95% methanol/5% water; 6.5 mM ammonium bicarbonate
Chromatography Type:	Reversed phase

Chromatography ID:	CH003948
Chromatography Summary:	HILIC (LC/MS Polar Neg)
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:	0.50 mL/min
Solvent A:	15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH)
Solvent B:	50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH)
Chromatography Type:	HILIC

MS:

MS ID:	MS004950
Analysis ID:	AN005217
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Metabolon (LC/MS Pos early)
Ion Mode:	POSITIVE

MS ID:	MS004951
Analysis ID:	AN005218
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Metabolon (LC/MS Pos late)
Ion Mode:	POSITIVE

MS ID:	MS004952
Analysis ID:	AN005219
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Metabolon (LC/MS Neg)
Ion Mode:	NEGATIVE

MS ID:	MS004953
Analysis ID:	AN005220
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Metabolon (LC/MS Polar)
Ion Mode:	NEGATIVE