Summary of Study ST003809

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 PR002383. The data can be accessed directly via it's Project DOI: 10.21228/M8M820 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 IDST003809
Study TitleLongitudinal multi-omics analysis of cord blood and childhood serum in Autism Spectrum Disorder (Negative mode)
Study TypeLC MS/MS quantitative analysis
Study SummaryUntargeted Metabolomic analysis was performed on cord blood plasma from 22 children diagnosed with Autism before age 5, and 44 neurotypical controls from the Cork Baseline Birth Cohort.
Institute
University College Cork
DepartmentAnatomy & Neuroscience
LaboratoryDr Jane English Lab
Last NameEnglish
First NameJane
AddressUniversity College Cork
Emailjane.english@ucc.ie
Phone0879915949
Submit Date2025-02-28
Num Groups22 Autism cases vs 44 Neurotypical Controls
Total Subjects66 cord blood plasma samples
Study CommentsAutism case vs control study design
PublicationsA.Noone et al. Molecular Psychiatry 2025
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Waters)
Analysis Type DetailLC-MS
Release Date2025-04-18
Release Version1
Jane English Jane English
https://dx.doi.org/10.21228/M8M820
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002383
Project DOI:doi: 10.21228/M8M820
Project Title:Longitudinal multi-omics analysis of cord blood and childhood serum in Autism Spectrum Disorder
Project Type:Untargeted Metabolomics study
Project Summary:Metabolomic analysis was performed on cord blood plasma from 22 children diagnosed with Autism before age 5, and 44 neurotypical controls from the Cork Baseline Birth Cohort. LC-MS analysis was performed using an ACQUITY ultra performance liquid chromatography (Waters Corp, Milford, MA) coupled with a Synapt G2-S quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometer (Waters Corp, Wilmslow, UK). MSE data were uploaded onto Progenesis QI 2.4 software (Nonlinear Dynamics, Newcastle, U.K.) for peak picking and alignment. Data were normalized to ‘All Compounds’ and the coefficient of variation (CV) was computed for each compound across all QC runs (n=8) to evaluate repeatability of measurement. Compounds with > 20% CV within the QCs were removed. Any compound which had >30% missing values across the entire sample set or >30% in either subgroup (case or control) was removed. Remaining features (429 negative mode, 1353 positive mode) were log2 transformed and normalised on the median values. Mann-Whitney U tests for significant differences between cases and controls were then carried out and corrected for false discovery rate (FDR) using the Benjamini-Hochberg procedure. Altered metabolites (p < 0.05) were uploaded to Metaboanalyst (v6.0) to identify key metabolic pathways implicated. We identified 32 metabolites as significantly altered between cases and controls (see A. Noone et al. 2025, and supplementary data).
Institute:University College Cork
Department:Anatomy & Neuroscience
Laboratory:Dr Jane English Lab
Last Name:English
First Name:Jane
Address:University College Cork
Email:jane.english@ucc.ie
Phone:0879915949
Funding Source:Health Research board Ireland
Publications:A.Noone et al. Molecular Psychiatry 2025
Contributors:Kirsten Dowling and Jane English

Subject:

Subject ID:SU003943
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Birth
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Case_ Control Status
SA417334210315_58Case
SA417335210315_45Case
SA417336210315_47Case
SA417337210315_49Case
SA417338210315_50Case
SA417339210315_29Case
SA417340210315_53Case
SA417341210315_23Case
SA417342210315_22Case
SA417343210315_57Case
SA417344210315_18Case
SA417345210315_20Case
SA417346210315_15Case
SA417347210315_10Case
SA417348210315_03Case
SA417349210315_65Case
SA417350210315_06Case
SA417351210315_64Case
SA417352210315_42Case
SA417353210315_13Case
SA417354210315_62Control
SA417355210315_43Control
SA417356210315_44Control
SA417357210315_60Control
SA417358210315_46Control
SA417359210315_66Control
SA417360210315_48Control
SA417361210315_61Control
SA417362210315_56Control
SA417363210315_51Control
SA417364210315_41Control
SA417365210315_59Control
SA417366210315_63Control
SA417367210315_54Control
SA417368210315_55Control
SA417369210315_52Control
SA417370210315_01Control
SA417371210315_40Control
SA417372210315_25Control
SA417373210315_04Control
SA417374210315_05Control
SA417375210315_08Control
SA417376210315_09Control
SA417377210315_11Control
SA417378210315_12Control
SA417379210315_14Control
SA417380210315_16Control
SA417381210315_17Control
SA417382210315_19Control
SA417383210315_24Control
SA417384210315_26Control
SA417385210315_39Control
SA417386210315_27Control
SA417387210315_28Control
SA417388210315_30Control
SA417389210315_31Control
SA417390210315_32Control
SA417391210315_33Control
SA417392210315_34Control
SA417393210315_02Control
SA417394210315_36Control
SA417395210315_37Control
SA417396210315_38Control
SA417397210315_35Control
Showing results 1 to 64 of 64

Collection:

Collection ID:CO003936
Collection Summary:Cord blood EDTA plasma aliquots were retrieved from the INFANT ISO accredited biobanking facilities and stored at −80 °C until analysed. Blood for the later childhood assessment was collected in BD Vacutainer serum tubes. Following centrifugation, 250µl aliquots (Wilmut) were stored in −80 °C long-term storage. Local standard operating protocols were followed in all handling and storage of human bio-samples.
Collection Protocol Filename:Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003952
Treatment Summary:Case control study

Sample Preparation:

Sampleprep ID:SP003949
Sampleprep Summary:For metabolomics profiling in cord blood, we used 50µl of cord blood plasma, to which 150µl of cold acetonitrile was added, vortexed for 1 min, and chilled for 1 hour at -20˚C. The samples were centrifuged for 15 min at 15,000 rpm; supernatant was transferred to a clean tube and dried in a vacuum centrifuge at 30˚C. The sample was reconstituted in 100µl of 50:50 acetonitrile:water with 0.1% formic acid and transferred to glass autosampler vials for injection onto a Waters ACQUITY-SYNAPT G2-S LC-MS/MS system. LC-MS/MS methodology for metabolomics analysis is described in Morillon et al.
Sampleprep Protocol Filename:Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
Processing Storage Conditions:-20℃

Chromatography:

Chromatography ID:CH004751
Chromatography Summary:LC-MS analysis was performed using an ACQUITY ultra performance liquid chromatography (Waters Corp, Milford, MA) coupled with a Synapt G2-S quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometer (Waters Corp, Wilmslow, UK)
Chromatography Comments:pooled QC injected every tenth injection throughout the analysis.
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um)
Column Temperature:65 °C
Flow Gradient:15min
Flow Rate:0.4 mL/min
Solvent A:0.1% formic acid in water
Solvent B:0.1% formic acid in acetonitrile
Target Sample Temperature:7oC
Randomization Order:yes
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006263
Analysis Type:MS
Analysis Protocol File:Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
Chromatography ID:CH004751
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003809_AN006263_Results.txt
Units:m/z
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