Summary of study ST001118

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 PR000749. The data can be accessed directly via it's Project DOI: 10.21228/M8VQ31 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.

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Study IDST001118
Study TitleMetabolomics profiles of patients with Wilson disease reveal a distinct metabolic signature
Study SummaryThis study is comparing the plasma metabolomics profile of patients with the genetic disorder, Wilson disease, compared to healthy subjects matched by age, sex, and BMI. Wilson disease is caused by a defect in a copper transporter leading to copper accumulation in the liver and brain leading to liver and/or neuropsychiatric symptoms. Mitochondrial defects are well-documented in Wilson disease. We hypothesize the acylcarnitine and primary metabolite profile will differ between patients with Wilson disease and healthy subjects and that these differences may indicate specific metabolic abnormalities.
Institute
University of California, Davis
Last NameMedici
First NameValentina
Address4150 V St, Sacramento CA 95817
Emailvmedici@ucdavis.edu
PhoneN/A
Submit Date2018-12-21
Num Groups2
Total Subjects110
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2019-09-23
Release Version1
Valentina Medici Valentina Medici
https://dx.doi.org/10.21228/M8VQ31
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000749
Project DOI:doi: 10.21228/M8VQ31
Project Title:Untargeted GC-MS Analysis in human patients with Wilson disease
Project Summary:GC-MS analysis was used to analysis the metabolic profile of human patients with Wilson disease.
Institute:University of California, Davis
Last Name:Fiehn
First Name:Oliver
Address:451 East Health Science Drive
Email:ofiehn@ucdavis.edu
Phone:5307529922

Subject:

Subject ID:SU001164
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 Treatment Group
SA076232K10_042Control
SA076233K2_034Control
SA076234K3_035Control
SA076235K1_033Control
SA076236K4_036Control
SA076237HC126_027Control
SA076238HC123_024Control
SA076239HC124_025Control
SA076240HC125_026Control
SA076241K5_037Control
SA076242K6_038Control
SA076243M4_031Control
SA076244M5_032Control
SA076245HC100_001Control
SA076246M3_030Control
SA076247M2_029Control
SA076248K7_039Control
SA076249K8_040Control
SA076250K9_041Control
SA076251HC122_023Control
SA076252M1_028Control
SA076253HC106_007Control
SA076254HC107_008Control
SA076255HC108_009Control
SA076256HC109_010Control
SA076257HC105_006Control
SA076258HC103_004Control
SA076259HC101_002Control
SA076260HC121_022Control
SA076261HC102_003Control
SA076262HC110_011Control
SA076263HC104_005Control
SA076264HC118_019Control
SA076265HC120_021Control
SA076266HC111_012Control
SA076267HC119_020Control
SA076268HC116_017Control
SA076269HC117_018Control
SA076270HC113_014Control
SA076271HC112_013Control
SA076272HC115_016Control
SA076273HC114_015Control
SA0762742407_092Wilson Disease
SA0762752291_088Wilson Disease
SA0762762301_089Wilson Disease
SA0762772309_090Wilson Disease
SA0762782415_093Wilson Disease
SA0762792275_087Wilson Disease
SA0762802354_091Wilson Disease
SA0762812210_082Wilson Disease
SA0762822123_080Wilson Disease
SA0762832438_094Wilson Disease
SA0762842086_079Wilson Disease
SA0762852124_081Wilson Disease
SA0762862243_083Wilson Disease
SA0762872251_085Wilson Disease
SA0762882245_084Wilson Disease
SA0762892259_086Wilson Disease
SA076290WD101_105Wilson Disease
SA076291WD103_107Wilson Disease
SA076292WD102_106Wilson Disease
SA076293WD100_104Wilson Disease
SA076294WD104_108Wilson Disease
SA076295WD105_109Wilson Disease
SA076296207_044Wilson Disease
SA076297WD106_110Wilson Disease
SA076298972_046Wilson Disease
SA076299970_101Wilson Disease
SA0763002486_097Wilson Disease
SA0763012481_096Wilson Disease
SA0763022506_098Wilson Disease
SA0763032508_099Wilson Disease
SA076304942_045Wilson Disease
SA0763052534_100Wilson Disease
SA0763062452_095Wilson Disease
SA0763071780_059Wilson Disease
SA0763081776_057Wilson Disease
SA0763091749_056Wilson Disease
SA0763101715_055Wilson Disease
SA0763111779_058Wilson Disease
SA0763121783_060Wilson Disease
SA0763131808_062Wilson Disease
SA0763141784_061Wilson Disease
SA0763151658_054Wilson Disease
SA0763161639_053Wilson Disease
SA0763171167_049Wilson Disease
SA0763181149_048Wilson Disease
SA0763191116_047Wilson Disease
SA0763201181_050Wilson Disease
SA0763211317_102Wilson Disease
SA0763221593_052Wilson Disease
SA0763231506_051Wilson Disease
SA0763241816_063Wilson Disease
SA0763251843_064Wilson Disease
SA0763262001_074Wilson Disease
SA0763271998_073Wilson Disease
SA0763281986_072Wilson Disease
SA0763292024_075Wilson Disease
SA076330205_043Wilson Disease
SA0763312055_077Wilson Disease
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Collection:

Collection ID:CO001158
Collection Summary:Plasma samples from patients with WD and healthy subjects were obtained from the Institute of Neurology and Psychiatry in Warsaw. Subjects fasted for 8 hours prior to sampling. Plasma samples were de-identified, shipped to the University of California, Davis and stored at -80°C until further analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001178
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001171
Sampleprep Summary:All samples were removed from -80°C and allowed to thaw on ice. Of the 100-250 uL of plasma shipped to the facility for analysis, 30 µL of plasma was pipetted into a new 1.5 mL Eppendorf tube. 1 mL of 3:3:2 acetonitrile:isopropanol:water was added to each sample. Samples were vortexed for 10 seconds using a MiniVortexer. Samples were then shaken on an Orbital Mixing Chilling/Heating Plate for 5 minutes at 4°C. Samples were centrifuged for 2 minutes at 14,000 rcf used the centrifuge Eppendorf 5415 D. Two 475 µL aliquots were removed from the supernatant. Both samples were dried to complete using Labconco Centrivap cold trap. 500 µL of 50:50 acetonitrile was added to each aliquot of all samples. Samples were vortexed for 10 seconds using the MiniVortexer. Samples were centrifuged for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415 D. 475 µL of supernatant was removed and evaporated to dryness using the Labconco Centrivap cold trap. One sample is submitted to derivitization, the other sample is saved for LC-MS analysis.
Sample Derivatization:To the dried down samples, 10 µL of a prepared methoxyamine solution was added to each sample. Samples were shaken on an Orbital Mixing Chilling/Heating Plate at 30°C for 1.5 hours. 91 µL of a N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) and fatty-acid methyl-esters (FAMES) solution was added to each sample. Samples were shaken on an Orbital Mixing Chilling/Heating Plate at 37°C for 30 minutes. Contents were transferred to individual glass vials with micro-inserts and capped immediately. Submitted to GC-MS analysis.

Combined analysis:

Analysis ID AN001817
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units Peak Height

Chromatography:

Chromatography ID:CH001283
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS001676
Analysis ID:AN001817
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
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