Summary of Study ST001485

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001003. The data can be accessed directly via it's Project DOI: 10.21228/M8210V This work is supported by NIH grant, U2C- DK119886.


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Study IDST001485
Study TitleMetabolomics of Ndufs4 KO brain regions (part - V)
Study SummaryTargeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT mouse cerebellum (CB)
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
Phone+27 18 299 4074
Submit Date2020-09-11
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2021-09-10
Release Version1
Roan Louw Roan Louw application/zip

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Project ID:PR001003
Project DOI:doi: 10.21228/M8210V
Project Title:Ndufs4 KO mouse model metabolomics studies
Project Type:Multi-platform metabolomics analysis
Project Summary:Multi-platform metabolomics analysis of tissues and biofluids from the Ndufs4 knockout (Ndufs4-/-) mouse model of human Leigh syndrome
Institute:North-West University
Last Name:Louw
First Name:Roan
Address:Hofman Street
Phone:+27 18 299 4074


Subject ID:SU001559
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Ndufs4, n/02705 8
Age Or Age Range:45-50 days
Animal Animal Supplier:Jackson Laboratory (ME, USA)
Animal Light Cycle:12:12 h
Animal Feed:Rodent Breeder, Cat. #RM1845, LabChef, Nutritionhub
Animal Water:ad libitum


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA125239CB1 15 (15)KO
SA125240CB1 16 (16)KO
SA125241CB1 21 (21)KO
SA125242CB1 12 (14)KO
SA125243CB1 19 (19)KO
SA125244CB1 5 (E5)KO
SA125245CB1 1 (E1)KO
SA125246CB1 2 (E2)KO
SA125247CB1 4 (E4)KO
SA125248CB1 24 (24)KO
SA125249CB1 9 (10)KO
SA125250CB2 29 (29)KO
SA125251CB2 38 (38)KO
SA125252CB2 40 (41)KO
SA125253CB2 41 (42)KO
SA125254CB2 45 (3)KO
SA125255CB2 37 (36)KO
SA125256CB2 35 (35)KO
SA125257CB2 31 (34)KO
SA125258CB2 27 (27)KO
SA125259CB2 32 (32)KO
SA125260CB2 33 (33)KO
SA125261CB2 47 (5)WT
SA125262CB2 46 (4)WT
SA125263CB1 14 (13)WT
SA125264CB1 17 (17)WT
SA125265CB1 18 (18)WT
SA125266CB1 20 (20)WT
SA125267CB1 13 (12)WT
SA125268CB1 11 (11)WT
SA125269CB1 6 (E6)WT
SA125270CB1 7 (7)WT
SA125271CB1 8 (8)WT
SA125272CB1 10 (9)WT
SA125273CB1 22 (22)WT
SA125274CB1 23 (23)WT
SA125275CB2 39 (39)WT
SA125276CB2 42 (40)WT
SA125277CB2 43 (1)WT
SA125278CB2 44 (2)WT
SA125279CB2 36 (37)WT
SA125280CB2 34 (31)WT
SA125281CB2 25 (25)WT
SA125282CB2 26 (26)WT
SA125283CB2 28 (28)WT
SA125284CB2 30 (30)WT
SA125285CB1 3 (E3)WT
Showing results 1 to 47 of 47


Collection ID:CO001554
Collection Summary:Mice were euthanized between postnatal day (P) 45-50 via cervical dislocation at the same time of day (8:00-9:00 AM) after overnight (12-h) fasting. The brain was removed and rinsed with saline solution (SABAX PBS; 0.9% NaCl (w/v), #7634, Adcock Ingram) to remove surrounding blood. The brain regions of interest, namely the anterior cortex (AC), brainstem (BS), cerebellum (CB) and olfactory bulbs (OB), were then dissected, snap-frozen in liquid nitrogen (within 15 minutes postmortem) and stored at − 80°C until used.
Sample Type:Brain


Treatment ID:TR001574
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001567
Sampleprep Summary:Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a biphasic Bligh–Dyer extraction method (methanol/water/chloroform, 2:1.8:2). The polar phases of biphasic extracts were used for LC-MS/MS analysis
Sampleprep Protocol Filename:GC_sample_prep_protocol.pdf

Combined analysis:

Analysis ID AN002462
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1200
Column Agilent C18 Zorbax SB-AQ (150 x 2.1mm, 3.5um)
MS instrument type Triple quadrupole
MS instrument name Agilent 6410 QQQ
Units Area


Chromatography ID:CH001804
Instrument Name:Agilent 1200
Column Name:Agilent C18 Zorbax SB-AQ (150 x 2.1mm, 3.5um)
Chromatography Type:Reversed phase


MS ID:MS002282
Analysis ID:AN002462
Instrument Name:Agilent 6410 QQQ
Instrument Type:Triple quadrupole
MS Comments:The Agilent© MassHunter Workstation (v B02.01) and MassHunter Optimiser (v B02.01) software were used for data acquisition in the multiple reaction monitoring (MRM) configuration setting with parameters set for target amino acids, -derivatives, acylcarnitines, and isotopes. Data extraction was done using the Agilent© MassHunter Workstation software (v B06.00; Qualitative Analysis and Quantitative Analysis)