Summary of Study ST001814

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 PR001147. The data can be accessed directly via it's Project DOI: 10.21228/M8FH7R 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	ST001814
Study Title	Searching for prognostic biomarkers of Parkinson´s Disease development in the Spanish EPIC cohort through a multiplatform metabolomics approach
Study Summary	The lack of knowledge about the onset and progression of Parkinson’s disease (PD) hampers its early diagnosis and treatment. We used a multiplatform untargeted metabolomics-based approach to uncover the biochemical remodeling induced by PD in a really early and pre-symptomatic stage and unveiling early potential diagnostic biomarkers. Baseline pre-clinical plasma samples (Pre-PD n=39; control group n=39) were obtained from the European Prospective Study on Nutrition and Cancer (EPIC) cohort, which healthy volunteers were followed for around 15 years to ascertain incident PD. Our finding revealed alterations in fatty acids metabolism, mitochondrial dysfunction, oxidative stress, and gut-brain axis dysregulation. This study is of inestimable value since this is the first study conducted with samples collected many years before the disease development.
Institute	Universidad CEU San Pablo
Last Name	Gonzalez-Riano
First Name	Carolina
Address	km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501, 28925 Alcorcón
Email	carolina.gonzalezriano@ceu.es
Phone	646251045
Submit Date	2021-06-01
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	GC-MS/LC-MS
Release Date	2021-06-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001147
Project DOI:	doi: 10.21228/M8FH7R
Project Title:	Searching for prognostic biomarkers of Parkinson´s Disease development in the Spanish EPIC cohort through a multiplatform metabolomics approach
Project Summary:	The lack of knowledge about the onset and progression of Parkinson’s disease (PD) hampers its early diagnosis and treatment. We used a multiplatform untargeted metabolomics-based approach to uncover the biochemical remodeling induced by PD in a really early and pre-symptomatic stage and unveiling early potential diagnostic biomarkers. Baseline pre-clinical plasma samples (Pre-PD n=39; control group n=39) were obtained from the European Prospective Study on Nutrition and Cancer (EPIC) cohort, which healthy volunteers were followed for around 15 years to ascertain incident PD. Our finding revealed alterations in fatty acids metabolism, mitochondrial dysfunction, oxidative stress, and gut-brain axis dysregulation. This study is of inestimable value since this is the first study conducted with samples collected many years before the disease development.
Institute:	Universidad CEU San Pablo
Department:	Center of Metabolomics and Bioanalysis
Last Name:	Gonzalez-Riano
First Name:	Carolina
Address:	Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Boadilla del Monte, Madrid, 28668, Spain
Email:	carolina.gonzalezriano@ceu.es
Phone:	00 34 91 3724753

Subject:

Subject ID:	SU001891
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Factor1
SA168835	49	CASE
SA168836	50	CASE
SA168837	53	CASE
SA168838	48	CASE
SA168839	46	CASE
SA168840	43	CASE
SA168841	44	CASE
SA168842	54	CASE
SA168843	47	CASE
SA168844	57	CASE
SA168845	67	CASE
SA168846	68	CASE
SA168847	70	CASE
SA168848	65	CASE
SA168849	64	CASE
SA168850	42	CASE
SA168851	60	CASE
SA168852	62	CASE
SA168853	56	CASE
SA168854	71	CASE
SA168855	19	CASE
SA168856	21	CASE
SA168857	23	CASE
SA168858	15	CASE
SA168859	12	CASE
SA168860	40	CASE
SA168861	5	CASE
SA168862	8	CASE
SA168863	25	CASE
SA168864	2	CASE
SA168865	35	CASE
SA168866	36	CASE
SA168867	39	CASE
SA168868	27	CASE
SA168869	34	CASE
SA168870	33	CASE
SA168871	30	CASE
SA168872	28	CASE
SA168873	32	CASE
SA168913	Sample name	Classification
SA168874	C54A	CONTROL
SA168875	C57A	CONTROL
SA168876	C56B	CONTROL
SA168877	C47A	CONTROL
SA168878	C5A	CONTROL
SA168879	C48A	CONTROL
SA168880	C49A	CONTROL
SA168881	C50B	CONTROL
SA168882	C53A	CONTROL
SA168883	C67B	CONTROL
SA168884	C71B	CONTROL
SA168885	C8A	CONTROL
SA168886	C46B	CONTROL
SA168887	C70A	CONTROL
SA168888	C68A	CONTROL
SA168889	C62B	CONTROL
SA168890	C64B	CONTROL
SA168891	C65A	CONTROL
SA168892	C60A	CONTROL
SA168893	C32B	CONTROL
SA168894	C25B	CONTROL
SA168895	C27A	CONTROL
SA168896	C28A	CONTROL
SA168897	C23A	CONTROL
SA168898	C21B	CONTROL
SA168899	C12A	CONTROL
SA168900	C15B	CONTROL
SA168901	C19B	CONTROL
SA168902	C2A	CONTROL
SA168903	C30B	CONTROL
SA168904	C40B	CONTROL
SA168905	C42A	CONTROL
SA168906	C43A	CONTROL
SA168907	C39A	CONTROL
SA168908	C36A	CONTROL
SA168909	C33A	CONTROL
SA168910	C44B	CONTROL
SA168911	C34B	CONTROL
SA168912	C35B	CONTROL

Showing results 1 to 79 of 79

Showing results 1 to 79 of 79

Collection:

Collection ID:	CO001884
Collection Summary:	On the day of the interview subjects were appointed for blood sample analysis within the next week at the primary care centre, where the interview took place, and a 30 ml blood sample were obtained at baseline. Fasting venous blood samples were drawn and immediately processed and were divided into 0.5 ml aliquots of plasma, serum, concentrated red blood cells and buffy coat, and stored in liquid nitrogen tanks at –190ºC until analysis.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001904
Treatment Summary:	Briefly, for GC-MS analysis, protein precipitation was achieved by mixing 1 volume of plasma with 3 volumes of cold (-20°C) acetonitrile, followed by methoximation with O-methoxyamine hydrochloride (15 mg/mL) in pyridine, and silylation with BSTFA:TMSC (99:1). Finally, 20 ppm of tricosane in heptane was added as internal standard (IS). For CE-MS analysis, 100 µL of plasma was mixed with 100 µL of 0.2 M formic acid containing 5% acetonitrile and 0.4 mM methionine sulfone as IS. The sample was transferred to a centrifree ultracentrifugation device (Millipore Ireland Ltd.,Carrigtohill, Ireland) with a 30 kDa protein cutoff for deproteinization through centrifugation (2000 g, 4 °C, 70 min). For LC-MS analysis, 100 µL of plasma was mixed with 300 µL of a cold mixture (-20°C) of methanol:ethanol (1:1, v/v) for deproteinization. Samples were centrifuged (13,000 g, 4°C, 20 min). After centrifugation, 100 µL of the supernatant was directly injected into the system.

Treatment ID:

TR001904

Treatment Summary:

Briefly, for GC-MS analysis, protein precipitation was achieved by mixing 1 volume of plasma with 3 volumes of cold (-20°C) acetonitrile, followed by methoximation with O-methoxyamine hydrochloride (15 mg/mL) in pyridine, and silylation with BSTFA:TMSC (99:1). Finally, 20 ppm of tricosane in heptane was added as internal standard (IS). For CE-MS analysis, 100 µL of plasma was mixed with 100 µL of 0.2 M formic acid containing 5% acetonitrile and 0.4 mM methionine sulfone as IS. The sample was transferred to a centrifree ultracentrifugation device (Millipore Ireland Ltd.,Carrigtohill, Ireland) with a 30 kDa protein cutoff for deproteinization through centrifugation (2000 g, 4 °C, 70 min). For LC-MS analysis, 100 µL of plasma was mixed with 300 µL of a cold mixture (-20°C) of methanol:ethanol (1:1, v/v) for deproteinization. Samples were centrifuged (13,000 g, 4°C, 20 min). After centrifugation, 100 µL of the supernatant was directly injected into the system.

Sample Preparation:

Sampleprep ID:	SP001897
Sampleprep Summary:	for GC-MS analysis, protein precipitation was achieved by mixing 1 volume of plasma with 3 volumes of cold (-20°C) acetonitrile, followed by methoximation with O-methoxyamine hydrochloride (15 mg/mL) in pyridine, and silylation with BSTFA:TMSC (99:1). Finally, 20 ppm of tricosane in heptane was added as internal standard (IS). For CE-MS analysis, 100 µL of plasma was mixed with 100 µL of 0.2 M formic acid containing 5% acetonitrile and 0.4 mM methionine sulfone as IS. The sample was transferred to a centrifree ultracentrifugation device (Millipore Ireland Ltd.,Carrigtohill, Ireland) with a 30 kDa protein cutoff for deproteinization through centrifugation (2000 g, 4 °C, 70 min). For LC-MS analysis, 100 µL of plasma was mixed with 300 µL of a cold mixture (-20°C) of methanol:ethanol (1:1, v/v) for deproteinization. Samples were centrifuged (13,000 g, 4°C, 20 min). After centrifugation, 100 µL of the supernatant was directly injected into the system.

Sampleprep ID:

SP001897

Sampleprep Summary:

for GC-MS analysis, protein precipitation was achieved by mixing 1 volume of plasma with 3 volumes of cold (-20°C) acetonitrile, followed by methoximation with O-methoxyamine hydrochloride (15 mg/mL) in pyridine, and silylation with BSTFA:TMSC (99:1). Finally, 20 ppm of tricosane in heptane was added as internal standard (IS). For CE-MS analysis, 100 µL of plasma was mixed with 100 µL of 0.2 M formic acid containing 5% acetonitrile and 0.4 mM methionine sulfone as IS. The sample was transferred to a centrifree ultracentrifugation device (Millipore Ireland Ltd.,Carrigtohill, Ireland) with a 30 kDa protein cutoff for deproteinization through centrifugation (2000 g, 4 °C, 70 min). For LC-MS analysis, 100 µL of plasma was mixed with 300 µL of a cold mixture (-20°C) of methanol:ethanol (1:1, v/v) for deproteinization. Samples were centrifuged (13,000 g, 4°C, 20 min). After centrifugation, 100 µL of the supernatant was directly injected into the system.

Combined analysis:

Analysis ID	AN002940	AN002941	AN002942	AN002943
Analysis type	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	GC	Normal phase
Chromatography system	Agilent 1200	Agilent 1200	Agilent 7890A	Agilent 7100 CE
Column	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)	Agilent DB5-MS (30m x 0.25mm, 0.25um)	Agilent Technologies fused silica capillary 96cm x 50μm
MS Type	ESI	ESI	EI	ESI
MS instrument type	QTOF	QTOF	Single quadrupole	TOF
MS instrument name	Agilent 6520 QTOF	Agilent 6520 QTOF	Agilent 5975C	Agilent 6224 TOF
Ion Mode	POSITIVE	NEGATIVE	UNSPECIFIED	POSITIVE
Units	AREA	AREA		AREA

Chromatography:

Chromatography ID:	CH002177
Chromatography Summary:	The analysis of the samples was accomplished using an UHPLC system (1200 Infinity system, Agilent Technologies, Waldbronn, Germany), coupled to a 6520 QTOF MS (Agilent Technologies) with an ESI ion source. The sample injection volume was set up to 10 μL. The separation was achieved using a Discovery® HS C18 15cm x 2.1 mm, 3 µm (Supelco analytical) reverse phase column at thermostated 40 °C.
Instrument Name:	Agilent 1200
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH002178
Chromatography Summary:	An Agilent GC system (7890A) coupled to a- 5975C mass spectrometer (Agilent Technologies) was used to perform metabolite fingerprinting of plasma samples. Briefly, 2 μL of derivatized samples were automatically injected in split mode (ratio 1:10) through a split liner of ultra-inert deactivated glass wool from Agilent. The separation of the compounds was achieved using a pre-column (10 m J&W integrated with Agilent 122‐5532G) combined with a GC DB5-MS column (length, 30 m; internal diameter, 0.25 mm; and 0.25 μm film of 95% of dimethyl/5% diphenylpolysiloxane).
Instrument Name:	Agilent 7890A
Column Name:	Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:	GC

Chromatography ID:	CH002179
Chromatography Summary:	The analysis was performed using a 7100 capillary electrophoresis (Agilent Technologies) coupled to a TOF MS 6224 mass spectrometer (Agilent Technologies), equipped with an ESI ion source. For the separation of metabolites, an Agilent Technologies fused silica capillary (total length, 96 cm; internal diameter, 50 μm) was used, working in normal polarity. Before each analysis, the capillary was washed for 5 min (950 mbar) with background electrolyte (BGE) (0.8 M formic acid solution in 10% methanol (v/v)). The sample injection was performed during 50 s at 50 mbar and, in order to improve the reproducibility of the analysis, the BGE was injected for 20 s at 100 mbar after the injection of each sample.
Instrument Name:	Agilent 7100 CE
Column Name:	Agilent Technologies fused silica capillary 96cm x 50μm
Chromatography Type:	Normal phase

MS:

MS ID:	MS002730
Analysis ID:	AN002940
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	Agilent Technologies MassHunter WorkStation Data Acquisition B.08.00 software; Agilent Technologies MassHunter Profinder B.08.00 SP1 software (Waldbronn, Germany)
Ion Mode:	POSITIVE

MS ID:	MS002731
Analysis ID:	AN002941
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	Agilent Technologies MassHunter WorkStation Data Acquisition B.08.00 software; Agilent Technologies MassHunter Profinder B.08.00 SP1 software (Waldbronn, Germany)
Ion Mode:	NEGATIVE

MS ID:	MS002732
Analysis ID:	AN002942
Instrument Name:	Agilent 5975C
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	Agilent MSD ChemStation software (Agilent Technologies); Agilent MassHunter Qualitative B.08.00; Agilent MassHunter Unknowns Analysis Tool 9.0.
Ion Mode:	UNSPECIFIED

MS ID:	MS002733
Analysis ID:	AN002943
Instrument Name:	Agilent 6224 TOF
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	Agilent Technologies MassHunter WorkStation Data Acquisition B.08.00 software; Agilent Technologies MassHunter Profinder B.08.00 SP1 software (Waldbronn, Germany)
Ion Mode:	POSITIVE