Summary of Study ST001993

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 PR001266. The data can be accessed directly via it's Project DOI: 10.21228/M82M5M 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 IDST001993
Study TitleCE-MS based metabolomics to study plasma samples that reveal new pathways implicated in SARS-CoV-2 pathogenesis
Study SummaryCE-MS based metabolomics was used in this study to analize COVID-19 disease and the susceptibility to SARS-CoV-2. In total, 63 plasma samples were analyzed and different comparisons were performed. To our knowledge, CE-MS has never been used to study COVID-19 and it is considered in this study an appropriate approach to extend the polar metabolome beyond what has been obtained by LC-MS and GC-MS
Institute
Universidad CEU San Pablo
DepartmentPharmacy
LaboratoryCentro de Metabolomica y Bioanálisis (CEMBIO)
Last NameBarbas
First NameCoral
AddressCEU Universities, Urbanización Montepríncipe
Emailcbarbas@ceu.es
Phone+34 913724700
Submit Date2021-11-16
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2021-12-05
Release Version1
Coral Barbas Coral Barbas
https://dx.doi.org/10.21228/M82M5M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001266
Project DOI:doi: 10.21228/M82M5M
Project Title:Metabolic snapshot of plasma samples to study SARS-CoV-2 pathogenesis
Project Summary:MS based metabolomics was used in this study to analyze COVID-19 disease and the susceptibility to SARS-CoV-2. In total, 63 plasma samples were analyzed and different comparisons were performed.
Institute:Universidad CEU San Pablo
Department:Pharmacy
Laboratory:Centro de Metabolomica y Bioanálisis (CEMBIO)
Last Name:Barbas
First Name:Coral
Address:CEU Universities, Urbanización Montepríncipe
Email:cbarbas@ceu.es
Phone:+34 913724700

Subject:

Subject ID:SU002074
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 Label
SA18666222Healthy
SA18666323Healthy
SA18666429Healthy
SA18666531Healthy
SA1866662Healthy
SA18666759Healthy
SA18666811_0Mild_d0
SA18666917_0Mild_d0
SA18667019_0Mild_d0
SA18667130_0Mild_d0
SA18667234_0Mild_d0
SA18667342_0Mild_d0
SA1866748Mild_d0
SA1866757Mild_d0
SA1866769Mild_d0
SA18667767_0Mild_d0
SA18667848_0Mild_d0
SA18667934_8Mild_d8
SA18668011_8Mild_d8
SA18668117_8Mild_d8
SA18668248_8Mild_d8
SA18668342_8Mild_d8
SA1866847_8Mild_d8
SA18668530_8Mild_d8
SA18668619_8Mild_d8
SA18668726_0Moderate_d0
SA18668868_0Moderate_d0
SA18668940_0Moderate_d0
SA1866903_0Moderate_d0
SA1866915_0Moderate_d0
SA1866924_0Moderate_d0
SA18669333_0Moderate_d0
SA18669432_0Moderate_d0
SA18669510_0Moderate_d0
SA18669674_0Moderate_d0
SA18669712Moderate_d0
SA1866983_8Moderate_d8
SA18669926_8Moderate_d8
SA18670032_8Moderate_d8
SA18670112_8Moderate_d8
SA18670233_8Moderate_d8
SA1867034_8Moderate_d8
SA18670440_8Moderate_d8
SA18670574_8Moderate_d8
SA1867065_8Moderate_d8
SA18670710_8Moderate_d8
SA186708QC_10QC
SA186709QC_8QC
SA186710QC_9QC
SA186711QC_1QC
SA186712QC_11QC
SA186713QC_14QC
SA186714QC_13QC
SA186715QC_12QC
SA186716QC_2QC
SA186717QC_7QC
SA186718QC_6QC
SA186719QC_3QC
SA186720QC_15QC
SA186721QC_4QC
SA186722QC_5QC
SA18672314Resistant
SA18672418Resistant
SA18672569BResistant
SA18672624Resistant
SA18672721Resistant
SA18672815Resistant
SA18672925Resistant
SA18673043Resistant
SA18673165Resistant
SA18673264Resistant
SA18673366Resistant
SA18673470Resistant
SA18673572Resistant
SA18673671Resistant
SA18673763Resistant
SA18673862Resistant
SA18673957Resistant
SA18674056Resistant
SA18674158Resistant
SA18674254Resistant
SA18674360Resistant
SA18674452Resistant
SA18674553Resistant
SA18674646Resistant
SA18674755Resistant
SA18674845Resistant
SA18674947Resistant
SA18675050Resistant
SA18675144Resistant
SA18675251Resistant
SA18675341_0Severe_d0
SA18675437Severe_d0
SA18675535_0Severe_d0
SA18675620_0Severe_d0
SA1867571_0Severe_d0
SA1867581_8Severe_d8
SA18675941_8Severe_d8
SA18676020_8Severe_d8
SA18676135_8Severe_d8
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Collection:

Collection ID:CO002067
Collection Summary:Blood samples were collected in EDTA tubes and then plasma was obtained.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002086
Treatment Summary:Cryopreserved plasma was processed for virus inactivation by adding 1500 µL of cold methanol:ethanol (MeOH:EtOH) in a 1:1 (v/v) proportion to 500 µL of plasma. Then, samples were vortex-mixed for 1 min, incubated on ice for 5 min and centrifuged at 16,000 x g for 20 min at 4 °C to precipitate and remove proteins. The clean upper layer or supernatant, which contained the metabolites of interest, was transferred to Eppendorf tubes and stored at -80 °C until analysis.

Sample Preparation:

Sampleprep ID:SP002080
Sampleprep Summary:Two hundred microliters of frozen supernatant were thawed on ice and evaporated to dryness using a SpeedVac Concentrator System (Thermo Fisher Scientific, Waltham, MA). Then, it was resuspended in 100 µL of 0.2 mM methionine sulfone (MetS) in 0.1 M formic acid. Samples were vortex-mixed for 1 min, transferred to a Millipore filter (30 kDa protein cutoff) and centrifuged for 40 min at 2000 xg at 4 °C. Finally, the ultrafiltrate was transferred to a CE-MS vial for analysis. Quality control samples (QC) were prepared by pooling equal volumes of plasma supernatant from each sample and were treated as previously described. Finally, blank solutions were also prepared with MeOH:EtOH (1:1, v/v).

Combined analysis:

Analysis ID AN003250
Analysis type MS
Chromatography type Unspecified
Chromatography system 7100 capillary electrophoresis (CE)
Column fused-silica capillary from Agilent Technologies (total length,100 cm; inner diameter,50um)
MS Type ESI
MS instrument type TOF
MS instrument name Agilent 6230 TOF
Ion Mode POSITIVE
Units Peak Area

Chromatography:

Chromatography ID:CH002395
Chromatography Summary:Metabolite separation was carried out using a previously developed method in a fused-silica capillary from Agilent Technologies (total length, 100 cm; inner diameter, 50 µm) 1. Before each analysis, the capillary was flushed with background electrolyte (BGE) (1 M formic acid in 10% MeOH) for 5 min at 950 mbar. Samples were injected over 50 s at 50 mbar, and to improve the analysis reproducibility, BGE was injected for 10 s at 100 mbar after each sample injection. The separation was performed with an internal pressure of 25 mbar and 30 kV voltage, and the current observed under these conditions was 30 µA. The total analytical run time was 35 min.
Instrument Name:7100 capillary electrophoresis (CE)
Column Name:fused-silica capillary from Agilent Technologies (total length,100 cm; inner diameter,50um)
Chromatography Type:Unspecified

MS:

MS ID:MS003023
Analysis ID:AN003250
Instrument Name:Agilent 6230 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:The mass spectra data were acquired in positive polarity with a full scan range from 70 - 1000 m/z at a rate of 1.36 scan/s. The other MS parameters were as follows: fragmentor set to 125 V, skimmer to 65 V, OCT RF Vpp to 750 V, drying gas temperature to 200 °C, flow rate to 10 L/min, nebulizer to 10 psig, and capillary voltage to 3500 V. The sheath liquid contained two reference masses (5 µL of purine with m/z 121.0509 and 5 µL of HP-0921 with m/z 922.0098) in MeOH:H2O (1/1, v/v) with 1 mM formic acid, and the flow rate was 0.6 mL/min (1:100 split). The MS data were acquired using the Agilent MassHunter Workstation (version B.09.00, Agilent Technologies), and the raw data were inspected with the MassHunter Qualitative software (version B.08.00, Agilent Technologies) before data processing. CE-MS raw data were checked using MassHunter Qualitative software (version 10.0) to determine the data quality, the system mass accuracy and the reproducibility of QC injection and MetS area. Then, raw data were processed with MassHunter Profinder software (version 10.0 SP1) applying molecular feature extraction (MFE) to clean the data background and unrelated ions. MFE was also applied to find coeluting adducts (+H+ and +Na+ in positive ionization and neutral loss of water). Afterwards, the batch recursive feature extraction (RFE) algorithm, also included in the software, was used to align all the features across the samples by using the mass and retention time (RT). RFE re-extracts the batch files and improves the final compound group list, as it uses the previous results (mass and RT) obtained by the MFE algorithm to perform a more targeted extraction.
Ion Mode:POSITIVE
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