Summary of Study ST003414

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 PR002113. The data can be accessed directly via it's Project DOI: 10.21228/M8GV5R This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003414
Study TitleMetabolic analysis of Anterior Cingulate Cortex in two Autism Spectrum Disorder mouse models
Study SummaryIn this project, we performed metabolomic analysis of anterior cingulate cortex (ACC) of two autism mouse models (Shank3b-/- and FMR1-/- mice), in comparison with their corresponding wild type controls. The results showed abnormal metabolism of amino acids, especially sulfur containing amino acid, in both Shank3b-/- and FMR1-/- ACC.
Institute
Fourth Military Medical University
Last NameWang
First NameYazhou
Address169 Chang Le Xi Road, Xi'an, Shaanxi, 710032, China
Emailyazhouw@fmmu.edu.cn
Phone+86-29-84774562
Submit Date2024-08-16
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-06-22
Release Version1
Yazhou Wang Yazhou Wang
https://dx.doi.org/10.21228/M8GV5R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002113
Project DOI:doi: 10.21228/M8GV5R
Project Title:Metabolic analysis of Anterior Cingulate Cortex in two Autism Spectrum Disorder mouse models
Project Summary:In this project, we performed metabolomic analysis of anterior cingulate cortex (ACC) of two autism mouse models (Shank3b-/- and FMR1-/- mice), in comparison with their corresponding wild type controls. The results showed abnormal metabolism of amino acids, especially sulfur containing amino acid, in both Shank3b-/- and FMR1-/- ACC.
Institute:Fourth Military Medical University
Last Name:Wang
First Name:Yazhou
Address:169 Chang Le Xi Road, Xi'an, Shaanxi, 710032, China
Email:yazhouw@fmmu.edu.cn
Phone:+86-29-84774562

Subject:

Subject ID:SU003540
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Treatment Genotype
SA376460FMR1MKO FMR1-KO
SA376461FMR4MKO FMR1-KO
SA376462FMR3MKO FMR1-KO
SA376463FMR2MKO FMR1-KO
SA376464shank1MKO Shank3b-KO
SA376465shank2MKO Shank3b-KO
SA376466shank3MKO Shank3b-KO
SA376467shank4MKO Shank3b-KO
SA376468c57-1MWT C57
SA376469c57-2MWT C57
SA376470c57-4MWT C57
SA376471c57-3MWT C57
SA376472FVB3MWT FVB129
SA376473FVB4MWT FVB129
SA376474FVB2MWT FVB129
SA376475FVB1MWT FVB129
Showing results 1 to 16 of 16

Collection:

Collection ID:CO003533
Collection Summary:Tissues were quickly isolated and individually grounded with liquid nitrogen.
Sample Type:Brain cortex

Treatment:

Treatment ID:TR003549
Treatment Summary:WT and KO mice were used.

Sample Preparation:

Sampleprep ID:SP003547
Sampleprep Summary:Tissues were individually grounded with liquid nitrogen and the homogenate was resuspended with 500μL prechilled 80% methanol by well vortex. The samples were incubated on ice for 5 min and then were centrifuged at 15,000 g, 4°C for 20 min. Some of supernatant was diluted to final concentration containing 53% methanol by LC-MS grade water. The samples were subsequently transferred to a fresh Eppendorf tube and then were centrifuged at 15000 g, 4°C for 20 min.

Combined analysis:

Analysis ID AN005608 AN005609
Chromatography ID CH004260 CH004260
MS ID MS005333 MS005334
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Vanquish UHPLC Vanquish UHPLC
Column Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um) Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH004260
Instrument Name:Vanquish UHPLC
Column Name:Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
Column Temperature:40° C
Flow Gradient:0 min, 1% B; 1 min, 1% B; 8 min, 99% B; 10 min, 99% B; 10.1 min, 1% B; 12 min, 1% B.
Flow Rate:0.5 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS005333
Analysis ID:AN005608
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The acquisition software (Xcalibur 4.0.27, Thermo) was used to evaluates the full scan survey MS data.ESI source conditions were set as follows: sheath gas flow rate was 45 Arb, aux gas flow rate was 15 Arb, capillary temperature was 320° C, full MS resolution was 70,000, MS/MS resolution was 17,500, collision energy was 20/40/60 eV in the NCE model, spray voltage was 3.8 kV (positive) or −3.1 kV (negative), respectively. The peak identification was performed as follows: The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, Thermo Fisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2minutes actual mass tolerance, 5ppm signal intensity tolerance, 30% signal/noise ratio, 3 and minimum intensity, 100,000. After that, peak intensities were normalized to the total spectral intensity. The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud(https://www.mzcloud.org/)， mz Vaultand Mass Listdatabase to obtain the accurate qualitative and relative quantitative results. Statistical analyses were performed using the statistical software R (R version R-3.4.3), Python (Python 2.7.6 version) and CentOS (CentOS release 6.6)
Ion Mode:POSITIVE
  
MS ID:MS005334
Analysis ID:AN005609
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The acquisition software (Xcalibur 4.0.27, Thermo) was used to evaluates the full scan survey MS data.ESI source conditions were set as follows: sheath gas flow rate was 45 Arb, aux gas flow rate was 15 Arb, capillary temperature was 320° C, full MS resolution was 70,000, MS/MS resolution was 17,500, collision energy was 20/40/60 eV in the NCE model, spray voltage was 3.8 kV (positive) or −3.1 kV (negative), respectively. The peak identification was performed as follows: The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, Thermo Fisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2minutes actual mass tolerance, 5ppm signal intensity tolerance, 30% signal/noise ratio, 3 and minimum intensity, 100,000. After that, peak intensities were normalized to the total spectral intensity. The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud(https://www.mzcloud.org/)， mz Vaultand Mass Listdatabase to obtain the accurate qualitative and relative quantitative results. Statistical analyses were performed using the statistical software R (R version R-3.4.3), Python (Python 2.7.6 version) and CentOS (CentOS release 6.6)
Ion Mode:NEGATIVE
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