Summary of Study ST001479

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 IDST001479
Study TitleMetabolomics of Ndufs4 KO brain regions (part - I)
Study SummaryTargeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT mouse anterior cortex (AC)
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
Phone+27 18 299 4074
Submit Date2020-09-09
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:SU001553
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Ndufs4
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
SA124960AC1 15 (15)KO
SA124961AC1 16 (16)KO
SA124962AC1 19 (19)KO
SA124963AC1 12 (14)KO
SA124964AC1 5 (E5)KO
SA124965AC1 1 (E1)KO
SA124966AC1 2 (E2)KO
SA124967AC1 21 (21)KO
SA124968AC1 9 (10)KO
SA124969AC1 24 (24)KO
SA124970AC2 38 (38)KO
SA124971AC2 40 (41)KO
SA124972AC2 41 (42)KO
SA124973AC2 35 (35) RKO
SA124974AC2 37 (36)KO
SA124975AC2 27 (27)KO
SA124976AC2 29 (29)KO
SA124977AC2 32 (32)KO
SA124978AC2 43 (3)WT
SA124979AC2 44 (4)WT
SA124980AC2 42 (40)WT
SA124981AC2 39 (39)WT
SA124982AC1 13 (12)WT
SA124983AC1 14 (13)WT
SA124984AC1 17 (17)WT
SA124985AC1 18 (18)WT
SA124986AC1 11 (11)WT
SA124987AC1 10 (9)WT
SA124988AC1 4 (5)WT
SA124989AC1 6 (E6)WT
SA124990AC1 7 (7)WT
SA124991AC1 8 (8)WT
SA124992AC1 20 (20)WT
SA124993AC1 22 (22)WT
SA124994AC2 31 (31)WT
SA124995AC2 33 (1)WT
SA124996AC2 34 (2)WT
SA124997AC2 36 (37) rWT
SA124998AC2 30 (30)WT
SA124999AC2 28 (28)WT
SA125000AC1 23 (23)WT
SA125001AC2 25 (25)WT
SA125002AC2 26 (26)WT
SA125003AC1 3 (E3)WT
Showing results 1 to 44 of 44


Collection ID:CO001548
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. Mice strain:
Sample Type:Brain


Treatment ID:TR001568
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001561
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

Combined analysis:

Analysis ID AN002455
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:CH001798
Instrument Name:Agilent 1200
Column Name:Agilent C18 Zorbax SB-AQ (150 x 2.1mm, 3.5um)
Chromatography Type:Reversed phase


MS ID:MS002275
Analysis ID:AN002455
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)