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

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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.