Summary of Study ST003039

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 PR001891. The data can be accessed directly via it's Project DOI: 10.21228/M88X46 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	ST003039
Study Title	A Non-Targeted Metabolomics Comparative Study on Plasma of Pfizer and Sinopharm COVID- 19 Vaccinated individuals, Assessed by (TIMS-QTOF) Mass Spectrometry.
Study Summary	COVID-19 is a contagious globally threatening infectious disease that accounted for an ongoing pandemic that manifested in multi-organs diseases and failures. The current study aimed to investigate the effectiveness of the Pfizer and Sinopharm vaccines in relation to metabolomic alterations and their association with immune pathways. The study employed a cross-sectional design and utilized an untargeted metabolomics-based approach. Plasma samples were collected from three groups: non- vaccinated participants, Sinopharm vaccinated participants, and Pfizer vaccinated participants. Comparative metabolomic analysis was performed using TIMS-QTOF, and a one-way ANOVA test was conducted using MetaboAnalyst Software. Out of the 105 detected metabolites, 72 showed statistically significant alterations (p<0.05) among the different groups. Several metabolites, including neopterin, pyridoxal, and syringic acid, were highly altered in individuals vaccinated with Pfizer. On the other hand, sphinganine, neopterin, and sphingosine were impacted in individuals vaccinated with Sinopharm. These metabolites could potentially serve as biomarkers for vaccine efficacy. Furthermore, both Pfizer and Sinopharm vaccinations were found to affect sphingolipid metabolism pathways and histidine metabolism pathways when compared to the control group. The Sinopharm group exhibited altered lysine degradation compared to the control group. When comparing the enriched pathways of the Pfizer and Sinopharm groups, purine metabolism was found to be affected. Additionally, perturbations in tryptophan metabolism and vitamin B6 metabolism were observed when comparing the Pfizer group with both the control and Sinopharm groups. These findings highlight the importance of metabolomics in assessing vaccine effectiveness and identifying potential biomarkers.
Institute	Sharjah Institute for Medical Research
Last Name	Facility
First Name	Core
Address	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email	tims-tof@sharjah.ac.ae
Phone	+971 6 5057656
Submit Date	2024-01-02
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2024-01-31
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001891
Project DOI:	doi: 10.21228/M88X46
Project Title:	A Non-Targeted Metabolomics Comparative Study on Plasma of Pfizer and Sinopharm COVID- 19 Vaccinated individuals, Assessed by (TIMS-QTOF) Mass Spectrometry.
Project Summary:	COVID-19 is a contagious globally threatening infectious disease that accounted for an ongoing pandemic that manifested in multi-organs diseases and failures. The current study aimed to investigate the effectiveness of the Pfizer and Sinopharm vaccines in relation to metabolomic alterations and their association with immune pathways. The study employed a cross-sectional design and utilized an untargeted metabolomics-based approach. Plasma samples were collected from three groups: non- vaccinated participants, Sinopharm vaccinated participants, and Pfizer vaccinated participants. Comparative metabolomic analysis was performed using TIMS-QTOF, and a one-way ANOVA test was conducted using MetaboAnalyst Software. Out of the 105 detected metabolites, 72 showed statistically significant alterations (p<0.05) among the different groups. Several metabolites, including neopterin, pyridoxal, and syringic acid, were highly altered in individuals vaccinated with Pfizer. On the other hand, sphinganine, neopterin, and sphingosine were impacted in individuals vaccinated with Sinopharm. These metabolites could potentially serve as biomarkers for vaccine efficacy. Furthermore, both Pfizer and Sinopharm vaccinations were found to affect sphingolipid metabolism pathways and histidine metabolism pathways when compared to the control group. The Sinopharm group exhibited altered lysine degradation compared to the control group. When comparing the enriched pathways of the Pfizer and Sinopharm groups, purine metabolism was found to be affected. Additionally, perturbations in tryptophan metabolism and vitamin B6 metabolism were observed when comparing the Pfizer group with both the control and Sinopharm groups. These findings highlight the importance of metabolomics in assessing vaccine effectiveness and identifying potential biomarkers.
Institute:	Sharjah Institute for Medical Research
Last Name:	Facility
First Name:	Core
Address:	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email:	tims-tof@sharjah.ac.ae
Phone:	+971 6 5057656

Subject:

Subject ID:	SU003153
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male

Factors:

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

mb_sample_id	local_sample_id	Treatment
SA329877	Dual 123-8783	Dual
SA329878	Dual 372-8784	Dual
SA329879	Dual 573-8787	Dual
SA329880	Dual 59-8782	Dual
SA329881	Dual 414-8785	Dual
SA329882	Dual 517-8786	Dual
SA329883	Pfizer-50-8429	Pfizer
SA329884	Pfizer-455-8538	Pfizer
SA329885	Pfizer-500-8539	Pfizer
SA329886	Pfizer-452-8537	Pfizer
SA329887	Pfizer-441-8532	Pfizer
SA329888	Pfizer-505-8540	Pfizer
SA329889	Pfizer-445-8533	Pfizer
SA329890	Pfizer-450-8535	Pfizer
SA329891	Pfizer-451-8536	Pfizer
SA329892	Pfizer-515-8544	Pfizer
SA329893	Pfizer-520-8546	Pfizer
SA329894	Pfizer-522-8547	Pfizer
SA329895	Pfizer-524-8548	Pfizer
SA329896	Pfizer-516-8545	Pfizer
SA329897	Pfizer-438-8531	Pfizer
SA329898	Pfizer-51-8430	Pfizer
SA329899	Pfizer-512-8542	Pfizer
SA329900	Pfizer-513-8543	Pfizer
SA329901	Pfizer-509-8541	Pfizer
SA329902	Pfizer-426-8525	Pfizer
SA329903	Pfizer-381-8517	Pfizer
SA329904	Pfizer-393-8518	Pfizer
SA329905	Pfizer-397-8519	Pfizer
SA329906	Pfizer-378-8516	Pfizer
SA329907	Pfizer-377-8515	Pfizer
SA329908	Pfizer-364-8512	Pfizer
SA329909	Pfizer-371-8513	Pfizer
SA329910	Pfizer-374-8514	Pfizer
SA329911	Pfizer-400-8520	Pfizer
SA329912	Pfizer-411-8521	Pfizer
SA329913	Pfizer-429-8526	Pfizer
SA329914	Pfizer-432-8528	Pfizer
SA329915	Pfizer-436-8529	Pfizer
SA329916	Pfizer-525-8549	Pfizer
SA329917	Pfizer-424-8582	Pfizer
SA329918	Pfizer-412-8522	Pfizer
SA329919	Pfizer-415-8523	Pfizer
SA329920	Pfizer-421-8524	Pfizer
SA329921	Pfizer-437-8530	Pfizer
SA329922	Pfizer-531-8552	Pfizer
SA329923	Pfizer-568-8574	Pfizer
SA329924	Pfizer-569-8575	Pfizer
SA329925	Pfizer-571-8576	Pfizer
SA329926	Pfizer-567-8573	Pfizer
SA329927	Pfizer-566-8572	Pfizer
SA329928	Pfizer-563-8569	Pfizer
SA329929	Pfizer-564-8570	Pfizer
SA329930	Pfizer-565-8571	Pfizer
SA329931	Pfizer-572-8577	Pfizer
SA329932	Pfizer-575-8578	Pfizer
SA329933	Pfizer-65-8436	Pfizer
SA329934	Pfizer-67-8437	Pfizer
SA329935	Pfizer-72-8438	Pfizer
SA329936	Pfizer-64-8435	Pfizer
SA329937	Pfizer-58-8434	Pfizer
SA329938	Pfizer-577-8579	Pfizer
SA329939	Pfizer-578-8580	Pfizer
SA329940	Pfizer-579-8581	Pfizer
SA329941	Pfizer-562-8568	Pfizer
SA329942	Pfizer-561-8567	Pfizer
SA329943	Pfizer-542-8555	Pfizer
SA329944	Pfizer-544-8556	Pfizer
SA329945	Pfizer-545-8557	Pfizer
SA329946	Pfizer-536-8554	Pfizer
SA329947	Pfizer-534-8553	Pfizer
SA329948	Pfizer-527-8551	Pfizer
SA329949	Pfizer-53-8431	Pfizer
SA329950	Pfizer-361-8511	Pfizer
SA329951	Pfizer-546-8559	Pfizer
SA329952	Pfizer-547-8560	Pfizer
SA329953	Pfizer-555-8564	Pfizer
SA329954	Pfizer-556-8565	Pfizer
SA329955	Pfizer-560-8566	Pfizer
SA329956	Pfizer-554-8563	Pfizer
SA329957	Pfizer-55-8433	Pfizer
SA329958	Pfizer-548-8561	Pfizer
SA329959	Pfizer-549-8562	Pfizer
SA329960	Pfizer-526-8550	Pfizer
SA329961	Pfizer-446-8534	Pfizer
SA329962	Pfizer-201-8457	Pfizer
SA329963	Pfizer-202-8458	Pfizer
SA329964	Pfizer-203-8459	Pfizer
SA329965	Pfizer-205-8460	Pfizer
SA329966	Pfizer-200-8456	Pfizer
SA329967	Pfizer-20-8424	Pfizer
SA329968	Pfizer-154-8454	Pfizer
SA329969	Pfizer-155-8455	Pfizer
SA329970	Pfizer-18-8423	Pfizer
SA329971	Pfizer-209-8461	Pfizer
SA329972	Pfizer-211-8462	Pfizer
SA329973	Pfizer-220-8468	Pfizer
SA329974	Pfizer-221-8469	Pfizer
SA329975	Pfizer-222-8470	Pfizer
SA329976	Pfizer-22-8425	Pfizer

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Collection:

Collection ID:	CO003146
Collection Summary:	A total of 340 subjects (aged between 10-85 years) were enrolled from Al-Quds Medical Labs (AL-Zarqa, Jordan). Blood samples were collected from 77 healthy individuals (had not received any of the COVID- 19 vaccines), 107 individuals who received the Sinopharm vaccine, and 156 individuals who received the Pfizer vaccine. The samples were collected using heparinized tubes and were then subjected to centrifugation for five minutes to obtain plasma. The study received ethical approval from The Institutional Review Board at The University of Jordan (UHS-HERC-094-21032022), and all participants signed an informed consent before collecting the blood samples. Individuals who tested positive for COVID-19, had received booster doses, had received a third dose of COVID-19 vaccine, or had received a single dose of either Pfizer or Sinopharm vaccines were excluded from the study
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003162
Treatment Summary:	Blood samples were collected from 77 healthy individuals (had not received any of the COVID- 19 vaccines), 107 individuals who received the Sinopharm vaccine, and 156 individuals who received the Pfizer vaccine

Sample Preparation:

Sampleprep ID:	SP003159
Sampleprep Summary:	we used chloroform/methanol extraction protocol to increase the coverage of the extracted metabolites. At first, the samples (cells and buffer) were transferred into Eppendorf tubes then centrifuged at 14000 rpm for 5 min. Afterward, the buffer was discarded, and the cells were preserved. To each sample, 400 µL of the mixture containing one protease inhibitor tablet and 10 mL of lysis buffer was added. Following rest for 10 minutes, samples were transferred to 10 mL tubes, vortexed for 2–4 minutes, and sonicated with a COPLEY probe-sonicator (QSONICA SONICATOR, USA) for 30 seconds while utilizing a 30 % amplifier in an ice bath. The samples were then transferred to Eppendorf tubes and centrifuged for 5 minutes at 14000 rpm. The supernatant was then transferred to another Eppendorf, and 400 µL of methanol and 300 µL of chloroform were added. Following that, the samples were vortexed for 30 seconds and centrifuged for 5 minutes at 14000 rpm. After that, two metabolite-containing layers are obtained, after transferring the upper layer of each sample to glass vials, 400 µl of methanol was added, followed by vertexing and centrifugation. The remaining supernatant was transferred to the same glass vials used before for the drying step, with the remaining protein pellets being air-dried for proteomics. A dried metabolomics sample was resuspended in 200 µL (0.1% formic acid in water) and injected into HPLC to be analysed by Q-TOF MS.In summary, After dividing the samples into 100 µL portions in Eppendorf tubes, 300 µL of methanol from Wunstorfer Strasse, Seelze, Germany, was introduced. The tubes were subsequently vortexed and placed in an incubator at -20°C for two hours. Following incubation, the samples underwent another round of vortexing and were centrifuged for 15 minutes at 14000 rpm. The resulting supernatant was evaporated at 35 to 40 °C through speed vacuum evaporation. To assess the analysis's repeatability, a quality control (QC) sample was created by pooling the same volume of each sample (10µl). The extracted samples were then resuspended in 100 µL of Honeywell's LC-MS CHROMASOLV's 0.1% formic acid in Deionized Water (Wunstorfer Strasse, Seelze, Germany). Following that, 100 µL of the prepared sample was collected in an insert inside LC glass vials after filtration through a 0.45µm hydrophilic nylon syringe filter for LC-MS/MS analysis.

Sampleprep ID:

SP003159

Sampleprep Summary:

we used chloroform/methanol extraction protocol to increase the coverage of the extracted metabolites. At first, the samples (cells and buffer) were transferred into Eppendorf tubes then centrifuged at 14000 rpm for 5 min. Afterward, the buffer was discarded, and the cells were preserved. To each sample, 400 µL of the mixture containing one protease inhibitor tablet and 10 mL of lysis buffer was added. Following rest for 10 minutes, samples were transferred to 10 mL tubes, vortexed for 2–4 minutes, and sonicated with a COPLEY probe-sonicator (QSONICA SONICATOR, USA) for 30 seconds while utilizing a 30 % amplifier in an ice bath. The samples were then transferred to Eppendorf tubes and centrifuged for 5 minutes at 14000 rpm. The supernatant was then transferred to another Eppendorf, and 400 µL of methanol and 300 µL of chloroform were added. Following that, the samples were vortexed for 30 seconds and centrifuged for 5 minutes at 14000 rpm. After that, two metabolite-containing layers are obtained, after transferring the upper layer of each sample to glass vials, 400 µl of methanol was added, followed by vertexing and centrifugation. The remaining supernatant was transferred to the same glass vials used before for the drying step, with the remaining protein pellets being air-dried for proteomics. A dried metabolomics sample was resuspended in 200 µL (0.1% formic acid in water) and injected into HPLC to be analysed by Q-TOF MS.In summary, After dividing the samples into 100 µL portions in Eppendorf tubes, 300 µL of methanol from Wunstorfer Strasse, Seelze, Germany, was introduced. The tubes were subsequently vortexed and placed in an incubator at -20°C for two hours. Following incubation, the samples underwent another round of vortexing and were centrifuged for 15 minutes at 14000 rpm. The resulting supernatant was evaporated at 35 to 40 °C through speed vacuum evaporation. To assess the analysis's repeatability, a quality control (QC) sample was created by pooling the same volume of each sample (10µl). The extracted samples were then resuspended in 100 µL of Honeywell's LC-MS CHROMASOLV's 0.1% formic acid in Deionized Water (Wunstorfer Strasse, Seelze, Germany). Following that, 100 µL of the prepared sample was collected in an insert inside LC glass vials after filtration through a 0.45µm hydrophilic nylon syringe filter for LC-MS/MS analysis.

Combined analysis:

Analysis ID	AN004986
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Bruker Elute
Column	Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8 um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Bruker timsTOF
Ion Mode	POSITIVE
Units	AU

Chromatography:

Chromatography ID:	CH003766
Chromatography Summary:	Samples were chromatographically separated by inline reversed-phase chromatography using the Elute HPG 1300 pumps and Elute Autosampler (Bruker, Darmstadt, Germany) with solvent A 0.1% FA in HPLC grade water and solvent B 0.1% FA in ACN. A Hamilton Intensity Solo 2 C18 column (100 mm x 2.1 mm, 1.8µm beads) was maintained at 35C. For metabolomics, 10 µL was injected twice for each sample and eluted using a 30-minute gradient as follows: 1% ACN was held for 2 minutes, ramping to 99% ACN over 15 minutes, held at 99% ACN for 3 minutes before re-equilibrating to 1% ACN for 10 minutes. Flow rates were 250 µL/min for elution and 350 µL/min for re-equilibration.
Instrument Name:	Bruker Elute
Column Name:	Hamilton Intensity Solo 2 C18 (100 x 2.1 mm, 1.8 um)
Column Temperature:	35
Flow Gradient:	1%B to 99%B in 15 min
Flow Rate:	250 uL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004726
Analysis ID:	AN004986
Instrument Name:	Bruker timsTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The MS analysis was performed using a TimsTOF (Bruker, Darmstadt, Germany) with Apollo II electrospray ionization (ESI) source. The drying gas was set to flow at 10 L/min and the drying temperature to 220C and the nebulizer pressure to 2.2 bar. The capillary voltage was 4500 V and the end plate offset 500V. For metabolomics the scan range was 20-1300 m/z. The collision energy was set to 20 eV, the cycle time to 0.5 seconds with a relative minimum intensity threshold of 400 counts per thousand and target intensity of 20,000. Sodium formate was injected as an external calibrant in the first 0.3 minutes of each LC-MS/MS run. MetaboScape 4.0 software was used for metabolite processing and statistical analysis (Bruker Daltonics). The following parameters for molecular feature identification and "bucketing" were set in the T-ReX 2D/3D workflow: For peak detection, a minimum intensity threshold of 1,000 counts is required, as well as a minimum peak duration of 7 spectra, with feature quantification determine using peak area. The file masses were recalibrated based on the external calibrant injected between 0-0.3 min.
Ion Mode:	POSITIVE