Summary of Study ST003049

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 PR001899. The data can be accessed directly via it's Project DOI: 10.21228/M88147 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	ST003049
Study Title	Plasma instead of serum avoids critical confounding of clinical metabolomics studies by platelets (Part 2/3 - Eicosadomics of isolated platelets)
Study Summary	Metabolomics is an emerging and powerful molecular profiling method supporting clinical investigations. Serum and plasma are commonly used without rational prioritization. Serum is collected after blood coagulation, a complex biochemical process involving active platelet metabolism. This may affect the metabolome and increase the variance as platelet counts and function may vary substantially in individuals. A multi-omics approach systematically investigating the suitability of serum and plasma for clinical studies demonstrated that metabolites correlated well (n=461, R2=0.991), whereas lipid mediators (n=104, R2=0.906) and proteins (n=322, R2=0.860) differed substantially between specimen. Independently, analysis of platelet releasates identified most biomolecules significantly enriched in serum when compared to plasma. A prospective, randomized, controlled parallel group metabolomics trial with acetylsalicylic acid administered for 7 days demonstrated that the apparent drug effects significantly differ depending on analyzed specimen. Only serum analyses of healthy individuals suggested a significant downregulation of TXB2 and 12-HETE, which were specifically formed during coagulation in vitro. Plasma analyses reliably identified acetylsalicylic acid effects on metabolites and lipids occurring in vivo such as a decrease in polyunsaturated fatty acids. The present data suggests that plasma should be preferred above serum for clinical metabolomics studies as the serum metabolome may be substantially confounded by platelets.
Institute	University of Vienna
Department	Department of Analytical Chemistry
Laboratory	Gerner lab
Last Name	Hagn
First Name	Gerhard
Address	Währingerstraße 38, 1090 Vienna, Austria
Email	gerhard.hagn@univie.ac.at
Phone	+43 1 4277 52375
Submit Date	2024-01-22
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-04-12
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP003170
Sampleprep Summary:	PLATELETS: The supernatant was transferred into new tubes and protein precipitation was performed by adding ice cold ethanol (LC-MS grade) in a ratio of 1:5. Additionally, 5 μL of an internal standard mixture of 12S‐HETE‐d8, 15S‐HETE‐d8, 5‐Oxo‐eicosatetraenoic acid (ETE)‐d7, 11,12‐dihydroxy-5Z,8Z,14Z-eicosatrienoic acid (DiHETrE)‐d11, PGE2‐d4 and 20‐HETE‐d6 (concentration per sample can be found above) were added to each sample. Samples were then stored at -20°C. After overnight precipitation, samples were centrifuged for 30 min at 4536 g at +4°C. The supernatant was then transferred into new 15 mL FalconTM tubes. EtOH was evaporated via vacuum centrifugation at 37°C until the original sample volume was restored. For solid phase extraction (SPE) samples were loaded onto preconditioned StrataX SPE columns (30 mg mL-1; Phenomenex, Torrance, CA, USA) using Pasteur pipettes. After sample loading, the SPE columns were washed with 5 mL of MS grade water and eluted with ice-cold MeOH (500 µL; MeOH abs.; VWR International, Vienna, Austria) containing 2% formic acid (FA; Sigma-Aldrich). MeOH was evaporated using a gentle nitrogen stream at room temperature and the dried samples were reconstituted in 150 µL reconstitution buffer (H2O:ACN:MeOH + 0.2% FA–vol% 65:31.5:3.5). The samples were then transferred into an autosampler held at stored at 4°C and subsequently measured via LC-MS/MS. 12S-HETE-d8: 6.67 pg/µL 15S-HETE-d8: 6.67 pg/µL 5-Oxo-ETE-d7: 20 pg/µL 11,12-DiHETrE-d11: 6.67 pg/µL PGE2-d4: 13.33 pg/µL 20-HETE-d6: 6.67 pg/µL

Sampleprep ID:

SP003170

Sampleprep Summary:

PLATELETS: The supernatant was transferred into new tubes and protein precipitation was performed by adding ice cold ethanol (LC-MS grade) in a ratio of 1:5. Additionally, 5 μL of an internal standard mixture of 12S‐HETE‐d8, 15S‐HETE‐d8, 5‐Oxo‐eicosatetraenoic acid (ETE)‐d7, 11,12‐dihydroxy-5Z,8Z,14Z-eicosatrienoic acid (DiHETrE)‐d11, PGE2‐d4 and 20‐HETE‐d6 (concentration per sample can be found above) were added to each sample. Samples were then stored at -20°C. After overnight precipitation, samples were centrifuged for 30 min at 4536 g at +4°C. The supernatant was then transferred into new 15 mL FalconTM tubes. EtOH was evaporated via vacuum centrifugation at 37°C until the original sample volume was restored. For solid phase extraction (SPE) samples were loaded onto preconditioned StrataX SPE columns (30 mg mL-1; Phenomenex, Torrance, CA, USA) using Pasteur pipettes. After sample loading, the SPE columns were washed with 5 mL of MS grade water and eluted with ice-cold MeOH (500 µL; MeOH abs.; VWR International, Vienna, Austria) containing 2% formic acid (FA; Sigma-Aldrich). MeOH was evaporated using a gentle nitrogen stream at room temperature and the dried samples were reconstituted in 150 µL reconstitution buffer (H2O:ACN:MeOH + 0.2% FA–vol% 65:31.5:3.5). The samples were then transferred into an autosampler held at stored at 4°C and subsequently measured via LC-MS/MS. 12S-HETE-d8: 6.67 pg/µL 15S-HETE-d8: 6.67 pg/µL 5-Oxo-ETE-d7: 20 pg/µL 11,12-DiHETrE-d11: 6.67 pg/µL PGE2-d4: 13.33 pg/µL 20-HETE-d6: 6.67 pg/µL