Summary of Study ST001518

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 PR001023. The data can be accessed directly via it's Project DOI: 10.21228/M8G410 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	ST001518
Study Title	Metabolome analysis in the diagnosis of childhood cerebellar ataxia
Study Summary	Metabolome studies to aid in the diagnosis and molecular elucidation of a child presenting chronic progressive cerebellar ataxia and an undiagnosed condition.
Institute	CEMBIO
Last Name	Sáiz
First Name	Jorge
Address	km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501, 28925 Alcorcón
Email	jorge.saizgalindo@ceu.es
Phone	913 72 47 11
Submit Date	2020-10-20
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	GC-MS/LC-MS
Release Date	2021-10-20
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001023
Project DOI:	doi: 10.21228/M8G410
Project Title:	Metabolome analysis in the diagnosis of childhood cerebellar ataxia
Project Summary:	Metabolome studies to aid in the diagnosis and molecular elucidation of a child presenting chronic progressive cerebellar ataxia and an undiagnosed condition.
Institute:	CEMBIO
Last Name:	Sáiz
First Name:	Jorge
Address:	km 0, Universidad CEU-San Pablo Urbanización Montepríncipe, M-501, 28925 Alcorcón
Email:	jorge.saizgalindo@ceu.es
Phone:	0034913 72 47 11

Subject:

Subject ID:	SU001592
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Subject
SA127689	Case_Plasma_CE	Case
SA127690	Case_Plasma_GC	Case
SA127691	Case_Urine_LC_POS	Case
SA127692	Case_Urine_LC_NEG	Case
SA127693	Case_Urine_CE	Case
SA127694	Case_Plasma_LC_NEG	Case
SA127695	Case_Plasma_LC_POS	Case
SA127696	Control_Plasma_GC	Control
SA127697	Control_Plasma_LC_NEG	Control
SA127698	Control_Plasma_CE	Control
SA127699	Control_Urine_LC_POS	Control
SA127700	Control_Urine_CE	Control
SA127701	Control_Urine_LC_NEG	Control
SA127702	Control_Plasma_LC_POS	Control

Showing results 1 to 14 of 14

Showing results 1 to 14 of 14

Collection:

Collection ID:	CO001587
Collection Summary:	Metabolite extraction was performed in plasma and urine samples from the patient and a healthy control, matched for age, sex and weight, according to standard protocols with some modifications.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001607
Treatment Summary:	Metabolite extraction was performed in plasma and urine samples from the patient and a healthy control, matched for age, sex and weight, according to standard protocols with some modifications.

Sample Preparation:

Sampleprep ID:	SP001600
Sampleprep Summary:	Plasma sample preparation for liquid chromatography–mass spectrometry (LC–MS) entailed the following steps: (1) thaw sample on ice, vortex for 2 min and transfer 100 µL of plasma into an Eppendorf tube; (2) for protein precipitation, add 300 µL of cold (-18˚C) methanol/ethanol (1:1 v/v), vortex for 1 min, incubate on ice for 5 min and vortex again briefly; (3) centrifuge at 13000 rpm, 4˚C, for 20 min; and (4) transfer the supernatant into the LC–MS system. Plasma sample preparation for gas chromatography–mass spectrometry (GC–MS) entailed the following steps: (1) thaw sample on ice, vortex for 2 min and transfer 40 µL of plasma into an Eppendorf tube; (2) for protein precipitation, add 120 µL of cold acetonitrile, vortex for 2 min and incubate on ice for 5 min; (3) centrifuge at 15400 rpm, 4˚C, for 10 min; and (4) transfer the supernatant into a GC vial with insert; (5) evaporate in a Speedvac at 30°C until dry; (6) add 10 µL of O-methoxyamine hydrochloride (15 mg/mL) in pyridine and vortex for 5 min; (7) sonicate for 2 min and vortex for 2 min (repeat step a total of three times); (8) incubate at room temperature for 16 h in darkness for the reaction of the methoxymation; (9) add 10 µL of N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1 % trimethylchlorosilane (TMCS) and incubate 1 h at 70 ˚C for the silylation; (10) add 100 µL of 10 ppm C18:0 methyl ester in n-heptane as internal standard, vortex for 2 min and centrifuge at 2500 rpm, 20˚C, for 15 min; and (11) transfer into the GC–MS system. Plasma sample preparation for capillary electrophoresis–mass spectrometry (CE–MS) entailed the following steps: (1) thaw sample on ice, vortex for 1 min and transfer 100 µL of plasma into an Eppendorf tube already filled with 100 µL of 0.2 M formic acid with 5 % acetonitrile and 0.4 mM methionine sulfone as internal standard; (2) vortex for 2 min and transfer to a Millipore filter (30 kDa protein cutoff); (3) centrifuge at 2000 rpm, 4˚C, for 70 min; and (4) transfer the filtrate into a CE vial where the volume is directly injected into the CE–MS system. Urine samples for LC–MS were thawed on ice and vortexed prior injection into the LC-MS system (without pre-treatment). For CE–MS, sample procedure entailed: (1) thaw on ice and vortex for 1 min and transfer 200 µL into an Eppendorf tube; (2) centrifuge at 13200 rpm, 4˚C, for 20 min; (3) transfer 100 µL of the supernatant into an Eppendorf tube already filled with 400 µL of 0.125 M formic acid with 0.25 mM methionine sulfone as internal standard; (4) vortex for 1 min and centrifuge at 13200 rpm, 4˚C, for 10 min; and (5) transfer 200 µL of the supernatant into a CE vial where the volume is directly injected into the CE–MS system. Quality control (QC) samples were independently prepared for each technique and followed the same procedure as applied for experimental samples. QC samples were always injected at the beginning of each analytical run, followed by samples randomized independently. A QC sample was rerun after each block of 5 samples.

Sampleprep ID:

SP001600

Sampleprep Summary:

Plasma sample preparation for liquid chromatography–mass spectrometry (LC–MS) entailed the following steps: (1) thaw sample on ice, vortex for 2 min and transfer 100 µL of plasma into an Eppendorf tube; (2) for protein precipitation, add 300 µL of cold (-18˚C) methanol/ethanol (1:1 v/v), vortex for 1 min, incubate on ice for 5 min and vortex again briefly; (3) centrifuge at 13000 rpm, 4˚C, for 20 min; and (4) transfer the supernatant into the LC–MS system. Plasma sample preparation for gas chromatography–mass spectrometry (GC–MS) entailed the following steps: (1) thaw sample on ice, vortex for 2 min and transfer 40 µL of plasma into an Eppendorf tube; (2) for protein precipitation, add 120 µL of cold acetonitrile, vortex for 2 min and incubate on ice for 5 min; (3) centrifuge at 15400 rpm, 4˚C, for 10 min; and (4) transfer the supernatant into a GC vial with insert; (5) evaporate in a Speedvac at 30°C until dry; (6) add 10 µL of O-methoxyamine hydrochloride (15 mg/mL) in pyridine and vortex for 5 min; (7) sonicate for 2 min and vortex for 2 min (repeat step a total of three times); (8) incubate at room temperature for 16 h in darkness for the reaction of the methoxymation; (9) add 10 µL of N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1 % trimethylchlorosilane (TMCS) and incubate 1 h at 70 ˚C for the silylation; (10) add 100 µL of 10 ppm C18:0 methyl ester in n-heptane as internal standard, vortex for 2 min and centrifuge at 2500 rpm, 20˚C, for 15 min; and (11) transfer into the GC–MS system. Plasma sample preparation for capillary electrophoresis–mass spectrometry (CE–MS) entailed the following steps: (1) thaw sample on ice, vortex for 1 min and transfer 100 µL of plasma into an Eppendorf tube already filled with 100 µL of 0.2 M formic acid with 5 % acetonitrile and 0.4 mM methionine sulfone as internal standard; (2) vortex for 2 min and transfer to a Millipore filter (30 kDa protein cutoff); (3) centrifuge at 2000 rpm, 4˚C, for 70 min; and (4) transfer the filtrate into a CE vial where the volume is directly injected into the CE–MS system. Urine samples for LC–MS were thawed on ice and vortexed prior injection into the LC-MS system (without pre-treatment). For CE–MS, sample procedure entailed: (1) thaw on ice and vortex for 1 min and transfer 200 µL into an Eppendorf tube; (2) centrifuge at 13200 rpm, 4˚C, for 20 min; (3) transfer 100 µL of the supernatant into an Eppendorf tube already filled with 400 µL of 0.125 M formic acid with 0.25 mM methionine sulfone as internal standard; (4) vortex for 1 min and centrifuge at 13200 rpm, 4˚C, for 10 min; and (5) transfer 200 µL of the supernatant into a CE vial where the volume is directly injected into the CE–MS system. Quality control (QC) samples were independently prepared for each technique and followed the same procedure as applied for experimental samples. QC samples were always injected at the beginning of each analytical run, followed by samples randomized independently. A QC sample was rerun after each block of 5 samples.

Combined analysis:

Analysis ID	AN002521	AN002522	AN002523	AN002524
Analysis type	MS	MS	MS	MS
Chromatography type	GC	Reversed phase	Reversed phase	CE
Chromatography system	Agilent 7890A	Agilent 1290 Infinity	Agilent 1290	Agilent 7100 CE
Column	Agilent DB5-MS (30m x 0.25mm, 0.25um)	Discovery HS C18 (15cm x 2.1 mm,3um)	Discovery HS C18 (15cm x 2.1 mm,3um)	capillary with an inner diameter of 50um and a total length of 100 cm
MS Type	EI	ESI	ESI	ESI
MS instrument type	Single quadrupole	QTOF	QTOF	Other
MS instrument name	Agilent 5975C	Agilent 6520 QTOF	Agilent 6520 QTOF	Agilent 6224 TOF
Ion Mode	POSITIVE	POSITIVE	NEGATIVE	POSITIVE
Units		area	area	area

Chromatography:

Chromatography ID:	CH001841
Instrument Name:	Agilent 7890A
Column Name:	Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:	GC

Chromatography ID:	CH001842
Chromatography Summary:	Positive ionization
Instrument Name:	Agilent 1290 Infinity
Column Name:	Discovery HS C18 (15cm x 2.1 mm,3um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH001843
Chromatography Summary:	Negative ionization
Instrument Name:	Agilent 1290
Column Name:	Discovery HS C18 (15cm x 2.1 mm,3um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH001844
Instrument Name:	Agilent 7100 CE
Column Name:	capillary with an inner diameter of 50um and a total length of 100 cm
Chromatography Type:	CE

MS:

MS ID:	MS002339
Analysis ID:	AN002521
Instrument Name:	Agilent 5975C
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	None
Ion Mode:	POSITIVE

MS ID:	MS002340
Analysis ID:	AN002522
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	None
Ion Mode:	POSITIVE

MS ID:	MS002341
Analysis ID:	AN002523
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	None
Ion Mode:	NEGATIVE

MS ID:	MS002342
Analysis ID:	AN002524
Instrument Name:	Agilent 6224 TOF
Instrument Type:	Other
MS Type:	ESI
MS Comments:	None
Ion Mode:	POSITIVE