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MB Sample ID: SA248044

Local Sample ID:PMN_61
Subject ID:SU002567
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

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Subject:

Subject ID:SU002567
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
PMN_61SA248044FL031177SevereExperimental Factors

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.

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
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