Summary of Study ST002477

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 PR001600. The data can be accessed directly via it's Project DOI: 10.21228/M8W70C 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	ST002477
Study Title	Neutrophil metabolomics in COVID-19
Study Summary	Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in COVID-19 patients or how metabolic changes may contribute to immune dysfunction. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19, or healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism.
Institute	UT Southwestern Medical Center
Last Name	Li
First Name	Yafeng
Address	5323 Harry Hines Blvd, Children's Research Institute, Dallas, TX, 75309, USA
Email	yafeng.li@utsouthwestern.edu
Phone	4047696693
Submit Date	2023-02-14
Raw Data Available	Yes
Raw Data File Type(s)	mzXML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-02-26
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001600
Project DOI:	doi: 10.21228/M8W70C
Project Title:	Human neutrophil metabolomics
Project Type:	MS qualitative analysis
Project Summary:	Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in COVID-19 patients or how metabolic changes may contribute to immune dysfunction. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19, or healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism.
Institute:	UT Southwestern Medical Center
Department:	Children's Research Institute
Last Name:	Li
First Name:	Yafeng
Address:	5323 Harry Hines Blvd, Children's Research Institute, Dallas, TX, 75309, USA
Email:	yafeng.li@utsouthwestern.edu
Phone:	4047696693

Subject:

Subject ID:	SU002567
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	Experimental Factors
SA247968	Blank_03	Blank
SA247969	Blank_01	Blank
SA247970	Blank_02	Blank
SA247971	PMN_89	Control
SA247972	PMN_88	Control
SA247973	PMN_87	Control
SA247974	PMN_90	Control
SA247975	PMN_91	Control
SA247976	PMN_86	Control
SA247977	PMN_92	Control
SA247978	PMN_79	Control
SA247979	PMN_85	Control
SA247980	PMN_75	Control
SA247981	PMN_76	Control
SA247982	PMN_77	Control
SA247983	PMN_78	Control
SA247984	PMN_80	Control
SA247985	PMN_74	Control
SA247986	PMN_84	Control
SA247987	PMN_82	Control
SA247988	PMN_83	Control
SA247989	PMN_81	Control
SA247990	PMN_41	Mild
SA247991	PMN_42	Mild
SA247992	PMN_40	Mild
SA247993	PMN_46	Mild
SA247994	PMN_43	Mild
SA247995	PMN_38	Mild
SA247996	PMN_27	Mild
SA247997	PMN_28	Mild
SA247998	PMN_13	Mild
SA247999	PMN_12	Mild
SA248000	PMN_25	Mild
SA248001	PMN_22	Mild
SA248002	PMN_15	Mild
SA248003	PMN_16	Mild
SA248004	PMN_19	Mild
SA248005	PMN_21	Mild
SA248006	PMN_10	Mild
SA248007	PMN_08	Mild
SA248008	PMN_32	Mild
SA248009	PMN_29	Mild
SA248010	PMN_34	Mild
SA248011	PMN_35	Mild
SA248012	PMN_36	Mild
SA248013	PMN_02	Mild
SA248014	PMN_03	Mild
SA248015	PMN_07	Mild
SA248016	PMN_06	Mild
SA248017	PMN_05	Mild
SA248018	PMN_04	Mild
SA248019	PMN_14	Mild
SA248020	QC_pool_01	QC
SA248021	QC_pool_08	QC
SA248022	QC_pool_09	QC
SA248023	QC_pool_10	QC
SA248024	QC_pool_11	QC
SA248025	QC_pool_07	QC
SA248026	QC_pool_06	QC
SA248027	QC_pool_03	QC
SA248028	QC_pool_04	QC
SA248029	QC_pool_05	QC
SA248030	QC_pool_02	QC
SA248031	PMN_59	Severe
SA248032	PMN_55	Severe
SA248033	PMN_54	Severe
SA248034	PMN_56	Severe
SA248035	PMN_57	Severe
SA248036	PMN_58	Severe
SA248037	PMN_53	Severe
SA248038	PMN_52	Severe
SA248039	PMN_48	Severe
SA248040	PMN_49	Severe
SA248041	PMN_50	Severe
SA248042	PMN_51	Severe
SA248043	PMN_60	Severe
SA248044	PMN_61	Severe
SA248045	PMN_69	Severe
SA248046	PMN_68	Severe
SA248047	PMN_70	Severe
SA248048	PMN_71	Severe
SA248049	PMN_72	Severe
SA248050	PMN_67	Severe
SA248051	PMN_66	Severe
SA248052	PMN_62	Severe
SA248053	PMN_63	Severe
SA248054	PMN_64	Severe
SA248055	PMN_65	Severe
SA248056	PMN_73	Severe

Showing results 1 to 89 of 89

Showing results 1 to 89 of 89

Collection:

Collection ID:	CO002560
Collection Summary:	COVID-19 patient samples were obtained through the University of Texas Southwestern Medical Center biorepository. Sample collection from COVID-19 patients or healthy controls was performed according to procedures approved by the Institutional Review Board of the University of Texas Southwestern Medical Center (STU-2020-0375 for SARS-CoV2 Biorepository and STU 012014-040 to J. Moreland) and the UT Southwestern Biorepository. Neutrophils were isolated using Ficoll-paque density gradient centrifugation, dextran sedimentation and erythrocyte hypotonic lysis following standard procedures as previously described (Hook et al., 2021). The number of neutrophils in each sample was counted using a microscope before freezing. Samples were stored at -800 C until metabolite extraction.
Sample Type:	Neutrophils

Treatment:

Treatment ID:	TR002579
Treatment Summary:	No treatment were done

Sample Preparation:

Sampleprep ID:	SP002573
Sampleprep Summary:	Metabolites from pellets containing 2 million neutrophils were extracted with 100 μl of chilled solvent of 40:40:20 methanol:acetonitrile:water (v:v:v) per million cells. The cell pellet was resuspended in the extraction solvent, vortexed for 30’’, and freeze-thawed 3 times. Then the samples were centrifuged at 21,000 g for 15 minutes at 4 °C and the supernatant transferred to LC-MS autosampler vials.

Sampleprep ID:

SP002573

Sampleprep Summary:

Metabolites from pellets containing 2 million neutrophils were extracted with 100 μl of chilled solvent of 40:40:20 methanol:acetonitrile:water (v:v:v) per million cells. The cell pellet was resuspended in the extraction solvent, vortexed for 30’’, and freeze-thawed 3 times. Then the samples were centrifuged at 21,000 g for 15 minutes at 4 °C and the supernatant transferred to LC-MS autosampler vials.

Combined analysis:

Analysis ID	AN004046
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Scientific QExactive HF-X hybrid quadrupole orbitrap high-resolution mass spectrometer (HRMS)
Column	Millipore ZIC-pHILIC column (5 mm, 2.1×150 mm)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF-X Orbitrap
Ion Mode	UNSPECIFIED
Units	MS reading

Chromatography:

Chromatography ID:	CH002993
Chromatography Summary:	Liquid chromatography was performed using a Millipore ZIC-pHILIC column (5 mm, 2.1×150 mm) with a binary solvent system of 10 mM ammonium acetate in water, pH 9.8 (solvent A) and acetonitrile (solvent B) with a constant ﬂow rate of 0.25 mL/min. The column was equilibrated with 90% solvent B. The liquid chromatography gradient was: 0–15 minutes linear ramp from 90% B to 30% B; 15–18 minutes isocratic ﬂow of 30% B; 18–19 minutes linear ramp from 30% B to 90% B; 19–27 column regeneration with isocratic ﬂow of 90% B.
Instrument Name:	Thermo Scientific QExactive HF-X hybrid quadrupole orbitrap high-resolution mass spectrometer (HRMS)
Column Name:	Millipore ZIC-pHILIC column (5 mm, 2.1×150 mm)
Column Temperature:	40
Flow Gradient:	0–15 minutes linear ramp from 90% B to 30% B; 15–18 minutes isocratic ﬂow of 30% B; 18–19 minutes linear ramp from 30% B to 90% B; 19–27 column regeneration with isocratic ﬂow of 90% B.
Flow Rate:	0.25 mL/min
Solvent A:	100% water; 10 mM ammonium acetate, pH 9.8
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS003793
Analysis ID:	AN004046
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Polarity switching was used to detect both positive and negative ions. A pooled quality control (QC) sample was used through the LC-MS run interspersed with the neutrophil samples to monitor the quality and consistency of detection. All samples were randomized to avoid artifactual changes caused by systematic drift. For data acquired with the QExactive, chromatogram peak areas were integrated using Tracefinder (Thermo Scientific) for targeted analysis using an in-house database.
Ion Mode:	UNSPECIFIED