Summary of Study ST003069

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	ST003069
Study Title	Plasma instead of serum avoids critical confounding of clinical metabolomics studies by platelets (Part 3/3 - Plasma and serum metabolomics)
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	Meier-Menches
First Name	Samuel
Address	Währingerstraße 38, 1090 Vienna, Austria
Email	samuel.meier-menches@univie.ac.at
Phone	+43-1-4277-52373
Submit Date	2024-01-22
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2024-04-12
Release Version	1

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Project:

Project ID:	PR001899
Project DOI:	doi: 10.21228/M88147
Project Title:	Plasma instead of serum avoids critical confounding of clinical metabolomics studies by platelets
Project 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
Publications:	https://doi.org/10.1021/acs.jproteome.3c00761

Subject:

Subject ID:	SU003184
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	Sample material	Treatment	Sex
SA332108	MXP500L-0-5711_1036867631_89_1_1_1_00_1036867083_6_R24V3	Plasma	after_Aspirin	F
SA332109	MXP500L-0-5711_1036867631_71_1_1_1_00_1036867050_3_R22V3	Plasma	after_Aspirin	F
SA332110	MXP500L-0-5711_1036867631_10_1_1_1_00_1036866394_12_R28V3	Plasma	after_Aspirin	F
SA332111	MXP500L-0-5711_1036867631_19_1_1_1_00_1036866439_16_R30V3	Plasma	after_Aspirin	F
SA332112	MXP500L-0-5711_1036867631_89_0_1_1_00_1036867083_6_R24V3	Plasma	after_Aspirin	F
SA332113	MXP500L-0-5711_1036867631_71_0_1_1_00_1036867050_3_R22V3	Plasma	after_Aspirin	F
SA332114	MXP500L-0-5711_1036867631_10_0_1_1_00_1036866394_12_R28V3	Plasma	after_Aspirin	F
SA332115	MXP500L-0-5711_1036867631_19_0_1_1_00_1036866439_16_R30V3	Plasma	after_Aspirin	F
SA332116	MXP500L-0-5711_1036867631_40_1_1_1_00_1036867113_9_R26V3	Plasma	after_Aspirin	M
SA332117	MXP500L-0-5711_1036867631_40_0_1_1_00_1036867113_9_R26V3	Plasma	after_Aspirin	M
SA332118	MXP500L-0-5711_1036867631_60_0_1_1_00_1036866410_14_R29V3	Plasma	after_Aspirin	M
SA332119	MXP500L-0-5711_1036867631_60_1_1_1_00_1036866410_14_R29V3	Plasma	after_Aspirin	M
SA332120	MXP500L-0-5711_1036867631_72_1_1_1_00_1036866380_11_R28V2	Plasma	before_Aspirin	F
SA332121	MXP500L-0-5711_1036867631_66_0_1_1_00_1036867045_2_R22V2	Plasma	before_Aspirin	F
SA332122	MXP500L-0-5711_1036867631_52_1_1_1_00_1036866424_15_R30V2	Plasma	before_Aspirin	F
SA332123	MXP500L-0-5711_1036867631_42_1_1_1_00_1036867079_5_R24V2	Plasma	before_Aspirin	F
SA332124	MXP500L-0-5711_1036867631_66_1_1_1_00_1036867045_2_R22V2	Plasma	before_Aspirin	F
SA332125	MXP500L-0-5711_1036867631_72_0_1_1_00_1036866380_11_R28V2	Plasma	before_Aspirin	F
SA332126	MXP500L-0-5711_1036867631_42_0_1_1_00_1036867079_5_R24V2	Plasma	before_Aspirin	F
SA332127	MXP500L-0-5711_1036867631_52_0_1_1_00_1036866424_15_R30V2	Plasma	before_Aspirin	F
SA332128	MXP500L-0-5711_1036867631_46_1_1_1_00_1036866405_13_R29V2	Plasma	before_Aspirin	M
SA332129	MXP500L-0-5711_1036867631_46_0_1_1_00_1036866405_13_R29V2	Plasma	before_Aspirin	M
SA332130	MXP500L-0-5711_1036867631_94_0_1_1_00_1036867109_8_R26V2	Plasma	before_Aspirin	M
SA332131	MXP500L-0-5711_1036867631_94_1_1_1_00_1036867109_8_R26V2	Plasma	before_Aspirin	M
SA332096	MXP500L-0-5711_1036867631_66_0_1_1_00_1036867045_2_D1	Plasma	Plasma	F
SA332097	MXP500L-0-5711_1036867631_42_1_1_1_00_1036867079_5_D2	Plasma	Plasma	F
SA332098	MXP500L-0-5711_1036867631_66_1_1_1_00_1036867045_2_D1	Plasma	Plasma	F
SA332099	MXP500L-0-5711_1036867631_72_1_1_1_00_1036866380_11_D4	Plasma	Plasma	F
SA332100	MXP500L-0-5711_1036867631_52_0_1_1_00_1036866424_15_D6	Plasma	Plasma	F
SA332101	MXP500L-0-5711_1036867631_42_0_1_1_00_1036867079_5_D2	Plasma	Plasma	F
SA332102	MXP500L-0-5711_1036867631_52_1_1_1_00_1036866424_15_D6	Plasma	Plasma	F
SA332103	MXP500L-0-5711_1036867631_72_0_1_1_00_1036866380_11_D4	Plasma	Plasma	F
SA332104	MXP500L-0-5711_1036867631_46_0_1_1_00_1036866405_13_D5	Plasma	Plasma	M
SA332105	MXP500L-0-5711_1036867631_67_1_1_1_00_1036867128_10_D3	Plasma	Plasma	M
SA332106	MXP500L-0-5711_1036867631_46_1_1_1_00_1036866405_13_D5	Plasma	Plasma	M
SA332107	MXP500L-0-5711_1036867631_67_0_1_1_00_1036867128_10_D3	Plasma	Plasma	M
SA332144	MXP500L-0-5711_1036867631_17_1_1_1_00_1036865856_34_R30V3	Serum	after_Aspirin	F
SA332145	MXP500L-0-5711_1036867631_30_0_1_1_00_1036866481_21_R22V3	Serum	after_Aspirin	F
SA332146	MXP500L-0-5711_1036867631_45_1_1_1_00_1036865818_30_R28V3	Serum	after_Aspirin	F
SA332147	MXP500L-0-5711_1036867631_58_1_1_1_00_1036866511_24_R24V3	Serum	after_Aspirin	F
SA332148	MXP500L-0-5711_1036867631_45_0_1_1_00_1036865818_30_R28V3	Serum	after_Aspirin	F
SA332149	MXP500L-0-5711_1036867631_30_1_1_1_00_1036866481_21_R22V3	Serum	after_Aspirin	F
SA332150	MXP500L-0-5711_1036867631_17_0_1_1_00_1036865856_34_R30V3	Serum	after_Aspirin	F
SA332151	MXP500L-0-5711_1036867631_58_0_1_1_00_1036866511_24_R24V3	Serum	after_Aspirin	F
SA332152	MXP500L-0-5711_1036867631_06_1_1_1_00_1036866545_27_R26V3	Serum	after_Aspirin	M
SA332153	MXP500L-0-5711_1036867631_06_0_1_1_00_1036866545_27_R26V3	Serum	after_Aspirin	M
SA332154	MXP500L-0-5711_1036867631_33_1_1_1_00_1036865837_32_R29V3	Serum	after_Aspirin	M
SA332155	MXP500L-0-5711_1036867631_33_0_1_1_00_1036865837_32_R29V3	Serum	after_Aspirin	M
SA332156	MXP500L-0-5711_1036867631_05_0_1_1_00_1036865841_33_R30V2	Serum	before_Aspirin	F
SA332157	MXP500L-0-5711_1036867631_93_0_1_1_00_1036866564_29_R28V2	Serum	before_Aspirin	F
SA332158	MXP500L-0-5711_1036867631_82_1_1_1_00_1036866477_20_R22V2	Serum	before_Aspirin	F
SA332159	MXP500L-0-5711_1036867631_48_0_1_1_00_1036866507_23_R24V2	Serum	before_Aspirin	F
SA332160	MXP500L-0-5711_1036867631_93_1_1_1_00_1036866564_29_R28V2	Serum	before_Aspirin	F
SA332161	MXP500L-0-5711_1036867631_48_1_1_1_00_1036866507_23_R24V2	Serum	before_Aspirin	F
SA332162	MXP500L-0-5711_1036867631_05_1_1_1_00_1036865841_33_R30V2	Serum	before_Aspirin	F
SA332163	MXP500L-0-5711_1036867631_82_0_1_1_00_1036866477_20_R22V2	Serum	before_Aspirin	F
SA332164	MXP500L-0-5711_1036867631_95_0_1_1_00_1036866531_26_R26V2	Serum	before_Aspirin	M
SA332165	MXP500L-0-5711_1036867631_95_1_1_1_00_1036866531_26_R26V2	Serum	before_Aspirin	M
SA332166	MXP500L-0-5711_1036867631_24_1_1_1_00_1036865822_31_R29V2	Serum	before_Aspirin	M
SA332167	MXP500L-0-5711_1036867631_24_0_1_1_00_1036865822_31_R29V2	Serum	before_Aspirin	M
SA332132	MXP500L-0-5711_1036867631_05_1_1_1_00_1036865841_33_D6	Serum	Serum	F
SA332133	MXP500L-0-5711_1036867631_93_0_1_1_00_1036866564_29_D4	Serum	Serum	F
SA332134	MXP500L-0-5711_1036867631_48_0_1_1_00_1036866507_23_D2	Serum	Serum	F
SA332135	MXP500L-0-5711_1036867631_82_0_1_1_00_1036866477_20_D1	Serum	Serum	F
SA332136	MXP500L-0-5711_1036867631_82_1_1_1_00_1036866477_20_D1	Serum	Serum	F
SA332137	MXP500L-0-5711_1036867631_05_0_1_1_00_1036865841_33_D6	Serum	Serum	F
SA332138	MXP500L-0-5711_1036867631_48_1_1_1_00_1036866507_23_D2	Serum	Serum	F
SA332139	MXP500L-0-5711_1036867631_93_1_1_1_00_1036866564_29_D4	Serum	Serum	F
SA332140	MXP500L-0-5711_1036867631_24_1_1_1_00_1036865822_31_D5	Serum	Serum	M
SA332141	MXP500L-0-5711_1036867631_07_0_1_1_00_1036866550_28_D3	Serum	Serum	M
SA332142	MXP500L-0-5711_1036867631_07_1_1_1_00_1036866550_28_D3	Serum	Serum	M
SA332143	MXP500L-0-5711_1036867631_24_0_1_1_00_1036865822_31_D5	Serum	Serum	M

Showing results 1 to 72 of 72

Showing results 1 to 72 of 72

Collection:

Collection ID:	CO003177
Collection Summary:	SERUM/PLASMA: Blood samples were obtained at baseline and after 7 days intake of the study medication. On both study days two blood samples using 6 mL K3EDTA and serum collection tubes (both Vacuette, Greiner Bio-One GmbH, Kremsmünster, Austria) were obtained from each subject. EDTA-anticoagulated tubes were carefully inverted two times after blood draw and centrifuged immediately at room temperature at 2000 g for 10 min. In contrast, filled serum tubes were carefully inverted after blood draw and placed to sit upright for 15 to 30 minutes to allow clot formation. Then, tubes were centrifuged at room temperature at 2000 g for 10 min. Directly after centrifugation, 500 µL of plasma or serum, respectively, were transferred into pre-labelled Eppendorf safe-lock tubes and stored at -80°C until analysis.
Sample Type:	Blood (serum) and blood (plasma)

Treatment:

Treatment ID:	TR003193
Treatment Summary:	Subjects received acetylsalicylic acid for 7 days. The study cohort was instructed to take 500 mg acetylsalicylic acid (Aspirin® 500 mg acetylsalicylic acid, Cellulose powder, maize starche) per day in the evening.

Sample Preparation:

Sampleprep ID:	SP003190
Sampleprep Summary:	Targeted metabolomics experiments were conducted by applying the MxP® Quant 500 Kit (Biocrates Life Sciences AG, Innsbruck, Austria). Therefore, 10 µL of sample was used and the kit was performed according to the manufacturer’s instructions. Phenyl isothiocyanate (Sigma-Aldrich, St. Louis, USA) was purchased separately and was used for derivatization of amino acids and biogenic amines according to the kit manual.

Sampleprep ID:

SP003190

Sampleprep Summary:

Targeted metabolomics experiments were conducted by applying the MxP® Quant 500 Kit (Biocrates Life Sciences AG, Innsbruck, Austria). Therefore, 10 µL of sample was used and the kit was performed according to the manufacturer’s instructions. Phenyl isothiocyanate (Sigma-Aldrich, St. Louis, USA) was purchased separately and was used for derivatization of amino acids and biogenic amines according to the kit manual.

Combined analysis:

Analysis ID	AN005026	AN005027
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA)	ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA)
Column	MxP Quant 500 Column System (Biocrates Part No: 21117)	MxP Quant 500 Column System (Biocrates Part No: 21117)
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	ABI Sciex 6500+ QTrap	ABI Sciex 6500+ QTrap
Ion Mode	NEGATIVE	POSITIVE
Units	µM	µM

Chromatography:

Chromatography ID:	CH003798
Chromatography Summary:	Measurements were carried out using LC-MS/MS and flow injection (FIA)-MS/MS analyses on a Sciex 6500+ series mass spectrometer coupled to an ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA), utilizing the Analyst 1.7.1 software with hotfix 1 (also AB SCIEX). All required standards, quality controls and eluents were included in the kit, as well as the chromatographic column for the LC-MS/MS analysis part. LC1_pos: The UHPLC autosampler and column oven are held at 10 °C and 50 °C, respectively. The injection volume was 5 µL. Eluent A is water (0.2% formic acid) and eluent B is acetonitrile (0.2% formic acid). Gradient run time of 5.8 mins. Remain at 0% B for 0.25 min, linear gradient to 12% B at 1.5 min and 17.5% B at 2.7 min. Further linear increase to 50% B at 4 mins and 100% B at 4.5 min, where it remains until 5 min. Reduction to 0% at 5.1 min and remaining at 0% until 5.8 min. Flow rate of 0.8 mL/min until 4.5 min, then increase to 1 mL/min until 4.7 min and remaining until 5.1 min. Finally, reduction to 0.8 mL/min until 5.8 min.
Instrument Name:	ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA)
Column Name:	MxP Quant 500 Column System (Biocrates Part No: 21117)
Column Temperature:	50°C
Flow Gradient:	Gradient run time of 5.8 mins. Remain at 0% B for 0.25 min, linear gradient to 12% B at 1.5 min and 17.5% B at 2.7 min. Further linear increase to 50% B at 4 mins and 100% B at 4.5 min, where it remains until 5 min. Reduction to 0% at 5.1 min and remaining at 0% until 5.8 min. Flow rate of 0.8 mL/min until 4.5 min, then increase to 1 mL/min until 4.7 min and remaining until 5.1 min. Finally, reduction to 0.8 mL/min until 5.8 min.
Flow Rate:	0.8 mL/min
Solvent A:	100% Water; 0.2% FA
Solvent B:	100% ACN; 0.2% FA
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004765
Analysis ID:	AN005026
Instrument Name:	ABI Sciex 6500+ QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Measurements were carried out using LC-MS/MS and flow injection (FIA)-MS/MS analyses on a Sciex 6500+ series mass spectrometer coupled to an ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA), utilizing the Analyst 1.7.1 software with hotfix 1 (also AB SCIEX). All required standards, quality controls and eluents were included in the kit, as well as the chromatographic column for the LC-MS/MS analysis part. Preparation of the measurement worklist as well as data validation and evaluation were performed with the software supplied with the kit (MetIDQ-Oxygen-DB110-3005, Biocrates Life Sciences). MS(LC2_neg): Scheduled MRM experiment in negative polarity. Detection window of 30 s, target scan time of 0.15 s and 3 ms pause between mass ranges. Q1 and Q3 were held at unit resolution. Source parameters were as follows: CUR 35, CAD 8, voltage –4.5 kV, temperature 650 °C, ion source gas at 40 and 40.
Ion Mode:	NEGATIVE

MS ID:	MS004766
Analysis ID:	AN005027
Instrument Name:	ABI Sciex 6500+ QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Measurements were carried out using LC-MS/MS and flow injection (FIA)-MS/MS analyses on a Sciex 6500+ series mass spectrometer coupled to an ExionLC AD chromatography system (AB Sciex, Framingham, MA, USA), utilizing the Analyst 1.7.1 software with hotfix 1 (also AB SCIEX). All required standards, quality controls and eluents were included in the kit, as well as the chromatographic column for the LC-MS/MS analysis part. Preparation of the measurement worklist as well as data validation and evaluation were performed with the software supplied with the kit (MetIDQ-Oxygen-DB110-3005, Biocrates Life Sciences). MS(LC1_pos): Scheduled MRM experiment in positive polarity. Detection window of 30 s, target scan time of 0.15 s and 3 ms pause between mass ranges. Q1 and Q3 were held at unit resolution. Source parameters were as follows: CUR 45, CAD 9, voltage 5.5 kV, temperature 500 °C, ion source gas at 60 and 70.
Ion Mode:	POSITIVE