Summary of Study ST001933

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 PR001222. The data can be accessed directly via it's Project DOI: 10.21228/M8RH8X 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	ST001933
Study Title	Absolute quantification of plasma cytokines and metabolome reveals the glycylproline regulating antibody-fading in convalescent COVID-19 patients
Study Summary	COVID-19 pandemic has caused tremendous costs worldwide and is still threatening public health in the “new normal”. The association between neutralizing antibody levels and metabolic alterations in convalescent patients with COVID-19 is still poorly understood. In the present work, we conducted absolutely quantitative approach to profile the metabolomes in the plasma of the ordinary convalescent patients with antibody (CA), the convalescents of rapidly faded antibodies (CO) as well as the healthy subjects.
Institute	Hong Kong Baptist University
Last Name	Yang
First Name	Zhu
Address	OEW901, Oen Hall Building West Wing,, Ho Sin Hang Campus, Hong Kong Baptist University, Kowloon Tong, Kowloon, 999077, Hong Kong
Email	yangzhu@gmail.com
Phone	(+852)34115162
Submit Date	2021-09-30
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2022-07-25
Release Version	1

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Project:

Project ID:	PR001222
Project DOI:	doi: 10.21228/M8RH8X
Project Title:	Absolute quantification of plasma cytokines and metabolome reveals the glycylproline regulating antibody-fading in convalescent COVID-19 patients
Project Summary:	COVID-19 pandemic has caused tremendous costs worldwide and is still threatening public health in the “new normal”. The association between neutralizing antibody levels and metabolic alterations in convalescent patients with COVID-19 is still poorly understood. In the present work, we conducted absolutely quantitative approach to profile the metabolomes in the plasma of the ordinary convalescent patients with antibody (CA), the convalescents of rapidly faded antibodies (CO) as well as the healthy subjects.
Institute:	Hong Kong Baptist University
Last Name:	Yang
First Name:	Zhu
Address:	OEW901, Oen Hall Building West Wing,, Ho Sin Hang Campus, Hong Kong Baptist University, Kowloon Tong, Kowloon, 999077, Hong Kong
Email:	yangzhu@gmail.com
Phone:	(+852)34115162

Subject:

Subject ID:	SU002011
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	23-73
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	Group
SA181765	G21	CA
SA181766	G35	CA
SA181767	G37	CA
SA181768	G16	CA
SA181769	G14	CA
SA181770	G2	CA
SA181771	G11	CA
SA181772	G3	CA
SA181773	G4	CA
SA181774	G33	CA
SA181775	G40	CA
SA181776	G30	CA
SA181777	G18	CA
SA181778	G8	CA
SA181779	G15	CA
SA181780	G1	CA
SA181781	G34	CA
SA181782	N23	CO
SA181783	N20	CO
SA181784	N18	CO
SA181785	N27	CO
SA181786	N34	CO
SA181787	N37	CO
SA181788	N36	CO
SA181789	N17	CO
SA181790	N16	CO
SA181791	N5	CO
SA181792	N2	CO
SA181793	N8	CO
SA181794	N12	CO
SA181795	N15	CO
SA181796	N14	CO
SA181797	N38	CO
SA181798	N40	CO
SA181799	N29	CO
SA181800	N28	CO
SA181801	N32	CO
SA181802	N35	CO
SA181803	N39	CO
SA181804	N22	CO
SA181805	N21	CO
SA181806	N3	CO
SA181807	N1	CO
SA181808	N6	CO
SA181809	N7	CO
SA181810	N13	CO
SA181811	N11	CO
SA181812	H2	H
SA181813	H3	H
SA181814	H4	H
SA181815	H30	H
SA181816	H28	H
SA181817	H27	H
SA181818	H31	H
SA181819	H32	H
SA181820	H35	H
SA181821	H34	H
SA181822	H26	H
SA181823	H19	H
SA181824	H7	H
SA181825	H40	H
SA181826	H11	H
SA181827	H14	H
SA181828	H16	H
SA181829	H15	H
SA181830	H39	H
SA181831	H37	H
SA181832	H12	H
SA181833	H13	H
SA181834	H9	H
SA181835	H8	H
SA181836	H5	H
SA181837	H6	H
SA181838	H17	H
SA181839	H18	H
SA181840	H25	H
SA181841	H36	H
SA181842	H24	H
SA181843	H23	H
SA181844	H1	H
SA181845	H21	H
SA181846	H38	H

Showing results 1 to 82 of 82

Showing results 1 to 82 of 82

Collection:

Collection ID:	CO002004
Collection Summary:	All the convalescent patients (both CA and CO groups) were discharged from the hospital after two consecutive negative results from throat swab tests for SARS-CoV-2. All patients were followed up for months after discharging and their plasma samples were collected 60 -100 days after the first onset of the disease symptoms onset. All blood samples were collected with potassium-EDTA blood collection tubes after overnight fasting. We classified the convalescent patients into the CA and CO groups according to the results of the ELISA test of anti-SARS-CoV-2 IgG following the manufacturer’s instructions.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR002023
Treatment Summary:	We classified the convalescent patients into the CA and CO groups according to the results of the ELISA test of anti-SARS-CoV-2 IgG following the manufacturer’s instructions. Briefly, 100 μL of diluted plasma samples (1:100 to 1: 800 dilution) was added to pre-coated plates, and the plates were then incubated at 37°C for 1 h. After washing, 100 μL of horseradish peroxidase (HRP)-conjugated RBD protein of SARS-CoV-2 was added into each well, followed by 30 more min of incubation at 37°C. After washing, the OD value at 450 nm (A450) was determined. The cutoff for negative was calculated by summing 0.090 and the average A450 of negative-control. A sample was determined negative when its A450 was below this cutoff value.

Treatment ID:

TR002023

Treatment Summary:

We classified the convalescent patients into the CA and CO groups according to the results of the ELISA test of anti-SARS-CoV-2 IgG following the manufacturer’s instructions. Briefly, 100 μL of diluted plasma samples (1:100 to 1: 800 dilution) was added to pre-coated plates, and the plates were then incubated at 37°C for 1 h. After washing, 100 μL of horseradish peroxidase (HRP)-conjugated RBD protein of SARS-CoV-2 was added into each well, followed by 30 more min of incubation at 37°C. After washing, the OD value at 450 nm (A450) was determined. The cutoff for negative was calculated by summing 0.090 and the average A450 of negative-control. A sample was determined negative when its A450 was below this cutoff value.

Sample Preparation:

Sampleprep ID:	SP002017
Sampleprep Summary:	Metabolomics of plasma samples were prepared and quantified as according to previously described method with modification. In brief, the standard solutions (5.0 mg/mL) were made by dissolving the accurately weighed chemicals in appropriate solutions including water, methanol, sodium hydroxide solution, or hydrochloric acid solution. Then the stock calibration solutions were mixed from the appropriate amounts of individual stock solutions following the instruction of the manufacturer. After thawing at 4°C, 20-μL aliquots of the samples were added to a 96-well plate. Also were added to the plate the calibration solutions of eight various concentrations, quality control (QC) samples (equally mixed samples), as well as solvent blank. Then 120 μL of standard solution was added to each well. The microporous plate was covered with aluminum film, placed on constant temperature mixer, and vibrated at 10℃, 650rpm for 20min. After centrifugation at 4000g for 20 min, 30μl supernatant from each well was transferred to a new 96-well plate. The derivative reagents of Q300 Kit were added to all wells and the plate was covered and incubated at 1200 rpm at 30℃ to carry out derivatization for 60 min. After derivatization, 330 μL of precooled 50% methanol solution was added to each well and mixed with the samples at 1200 rpm at 10℃ for 5 minutes. Then the plat were centrifuged at 4000g, 4°C for 30 minutes. Finally, the supernatant was further transferred to a new 96-well plate and put into the automatic sampler of UPLC-MS analysis.

Sampleprep ID:

SP002017

Sampleprep Summary:

Metabolomics of plasma samples were prepared and quantified as according to previously described method with modification. In brief, the standard solutions (5.0 mg/mL) were made by dissolving the accurately weighed chemicals in appropriate solutions including water, methanol, sodium hydroxide solution, or hydrochloric acid solution. Then the stock calibration solutions were mixed from the appropriate amounts of individual stock solutions following the instruction of the manufacturer. After thawing at 4°C, 20-μL aliquots of the samples were added to a 96-well plate. Also were added to the plate the calibration solutions of eight various concentrations, quality control (QC) samples (equally mixed samples), as well as solvent blank. Then 120 μL of standard solution was added to each well. The microporous plate was covered with aluminum film, placed on constant temperature mixer, and vibrated at 10℃, 650rpm for 20min. After centrifugation at 4000g for 20 min, 30μl supernatant from each well was transferred to a new 96-well plate. The derivative reagents of Q300 Kit were added to all wells and the plate was covered and incubated at 1200 rpm at 30℃ to carry out derivatization for 60 min. After derivatization, 330 μL of precooled 50% methanol solution was added to each well and mixed with the samples at 1200 rpm at 10℃ for 5 minutes. Then the plat were centrifuged at 4000g, 4°C for 30 minutes. Finally, the supernatant was further transferred to a new 96-well plate and put into the automatic sampler of UPLC-MS analysis.

Combined analysis:

Analysis ID	AN003143
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	The Shim-pack UFLC SHIMADZU CBM A ultrahigh-performance liquid chromatography (UHPLC) system
Column	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	ABI Sciex 6500 QTrap
Ion Mode	UNSPECIFIED
Units	µM

Chromatography:

Chromatography ID:	CH002325
Chromatography Summary:	The Shim-pack UFLC SHIMADZU CBM A ultrahigh-performance liquid chromatography (UHPLC) system (SHIMADZU, Japan) coupled with QTRAP 6500+ triple quadrupole mass spectrometer (Sciex, Washington, USA) was used to analyze the metabolomics. ACQUITY UPLC BEH C18 1.7 µm VanGuard pre-column (2.1mm × 5 mm) and ACQUITY UPLC BEH C18 1.7 µm analytical column (2.1 × 100 mm) (Waters Corporation, Milford, MA, USA) were applied to this system. The mobile phases A and B were 0.1% formic acid solution in water and acetonitrile-IPA mixture (70:30, v/v), respectively. A 5-μL injection of each sample was maintained at 40 °C and the flow rate was 0.40 mL/min. The mobile phase gradient was: 0-1 min (5% B), 1-11min (5-78% B), 11-13.5 min (78-95% B), 13.5-14 min (95-100% B), 14-16 min (100% B), 16-16.1 min (100-5% B), and 16.1-18 min (5% B).
Instrument Name:	The Shim-pack UFLC SHIMADZU CBM A ultrahigh-performance liquid chromatography (UHPLC) system
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	40
Flow Gradient:	0-1 min (5% B), 1-11min (5-78% B), 11-13.5 min (78-95% B), 13.5-14 min (95-100% B), 14-16 min (100% B), 16-16.1 min (100-5% B), and 16.1-18 min (5% B).
Flow Rate:	0.40 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	70% acetonitrile/30% isopropanol
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002923
Analysis ID:	AN003143
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	The Shim-pack UFLC SHIMADZU CBM A ultrahigh-performance liquid chromatography (UHPLC) system (SHIMADZU, Japan) coupled with QTRAP 6500+ triple quadrupole mass spectrometer (Sciex, Washington, USA) was used to analyze the metabolomics. ACQUITY UPLC BEH C18 1.7 µm VanGuard pre-column (2.1mm × 5 mm) and ACQUITY UPLC BEH C18 1.7 µm analytical column (2.1 × 100 mm) (Waters Corporation, Milford, MA, USA) were applied to this system. The mass spectrometer was operated in the both positive and negative modes, with capillary voltages of 1.5 and 2.0 kV, respectively. The source and desolvation temperatures were 150°C and 550 °C, respectively. The flow rate of desolvation gas was 1000 L/Hr.
Ion Mode:	UNSPECIFIED