#METABOLOMICS WORKBENCH KGDowling_20250228_021722 DATATRACK_ID:5686 STUDY_ID:ST003809 ANALYSIS_ID:AN006263 PROJECT_ID:PR002383
VERSION             	1
CREATED_ON             	March 25, 2025, 10:28 am
#PROJECT
PR:PROJECT_TITLE                 	Longitudinal multi-omics analysis of cord blood and childhood serum in Autism
PR:PROJECT_TITLE                 	Spectrum Disorder
PR:PROJECT_TYPE                  	Untargeted Metabolomics study
PR:PROJECT_SUMMARY               	Metabolomic analysis was performed on cord blood plasma from 22 children
PR:PROJECT_SUMMARY               	diagnosed with Autism before age 5, and 44 neurotypical controls from the Cork
PR:PROJECT_SUMMARY               	Baseline Birth Cohort. LC-MS analysis was performed using an ACQUITY ultra
PR:PROJECT_SUMMARY               	performance liquid chromatography (Waters Corp, Milford, MA) coupled with a
PR:PROJECT_SUMMARY               	Synapt G2-S quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometer (Waters
PR:PROJECT_SUMMARY               	Corp, Wilmslow, UK). MSE data were uploaded onto Progenesis QI 2.4 software
PR:PROJECT_SUMMARY               	(Nonlinear Dynamics, Newcastle, U.K.) for peak picking and alignment. Data were
PR:PROJECT_SUMMARY               	normalized to ‘All Compounds’ and the coefficient of variation (CV) was
PR:PROJECT_SUMMARY               	computed for each compound across all QC runs (n=8) to evaluate repeatability of
PR:PROJECT_SUMMARY               	measurement. Compounds with > 20% CV within the QCs were removed. Any compound
PR:PROJECT_SUMMARY               	which had >30% missing values across the entire sample set or >30% in either
PR:PROJECT_SUMMARY               	subgroup (case or control) was removed. Remaining features (429 negative mode,
PR:PROJECT_SUMMARY               	1353 positive mode) were log2 transformed and normalised on the median values.
PR:PROJECT_SUMMARY               	Mann-Whitney U tests for significant differences between cases and controls were
PR:PROJECT_SUMMARY               	then carried out and corrected for false discovery rate (FDR) using the
PR:PROJECT_SUMMARY               	Benjamini-Hochberg procedure. Altered metabolites (p < 0.05) were uploaded to
PR:PROJECT_SUMMARY               	Metaboanalyst (v6.0) to identify key metabolic pathways implicated. We
PR:PROJECT_SUMMARY               	identified 32 metabolites as significantly altered between cases and controls
PR:PROJECT_SUMMARY               	(see A. Noone et al. 2025, and supplementary data).
PR:INSTITUTE                     	University College Cork
PR:DEPARTMENT                    	Anatomy & Neuroscience
PR:LABORATORY                    	Dr Jane English Lab
PR:LAST_NAME                     	English
PR:FIRST_NAME                    	Jane
PR:ADDRESS                       	University College Cork
PR:EMAIL                         	jane.english@ucc.ie
PR:PHONE                         	0879915949
PR:FUNDING_SOURCE                	Health Research board Ireland
PR:PUBLICATIONS                  	A.Noone et al. Molecular Psychiatry 2025
PR:CONTRIBUTORS                  	Kirsten Dowling and Jane English
#STUDY
ST:STUDY_TITLE                   	Longitudinal multi-omics analysis of cord blood and childhood serum in Autism
ST:STUDY_TITLE                   	Spectrum Disorder (Negative mode)
ST:STUDY_TYPE                    	LC MS/MS quantitative analysis
ST:STUDY_SUMMARY                 	Untargeted Metabolomic analysis was performed on cord blood plasma from 22
ST:STUDY_SUMMARY                 	children diagnosed with Autism before age 5, and 44 neurotypical controls from
ST:STUDY_SUMMARY                 	the Cork Baseline Birth Cohort.
ST:INSTITUTE                     	University College Cork
ST:DEPARTMENT                    	Anatomy & Neuroscience
ST:LABORATORY                    	Dr Jane English Lab
ST:LAST_NAME                     	English
ST:FIRST_NAME                    	Jane
ST:ADDRESS                       	University College Cork
ST:EMAIL                         	jane.english@ucc.ie
ST:PHONE                         	0879915949
ST:NUM_GROUPS                    	22 Autism cases vs 44 Neurotypical Controls
ST:TOTAL_SUBJECTS                	66 cord blood plasma samples
ST:STUDY_COMMENTS                	Autism case vs control study design
ST:PUBLICATIONS                  	A.Noone et al. Molecular Psychiatry 2025
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:AGE_OR_AGE_RANGE              	Birth
SU:GENDER                        	Male and female
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	210315_01	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_01
SUBJECT_SAMPLE_FACTORS           	-	210315_02	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_02
SUBJECT_SAMPLE_FACTORS           	-	210315_03	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_03
SUBJECT_SAMPLE_FACTORS           	-	210315_04	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_04
SUBJECT_SAMPLE_FACTORS           	-	210315_05	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_05
SUBJECT_SAMPLE_FACTORS           	-	210315_06	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_06
SUBJECT_SAMPLE_FACTORS           	-	210315_08	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_08
SUBJECT_SAMPLE_FACTORS           	-	210315_09	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_09
SUBJECT_SAMPLE_FACTORS           	-	210315_10	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_10
SUBJECT_SAMPLE_FACTORS           	-	210315_11	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_11
SUBJECT_SAMPLE_FACTORS           	-	210315_12	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_12
SUBJECT_SAMPLE_FACTORS           	-	210315_13	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_13
SUBJECT_SAMPLE_FACTORS           	-	210315_14	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_14
SUBJECT_SAMPLE_FACTORS           	-	210315_15	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_15
SUBJECT_SAMPLE_FACTORS           	-	210315_16	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_16
SUBJECT_SAMPLE_FACTORS           	-	210315_17	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_17
SUBJECT_SAMPLE_FACTORS           	-	210315_18	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_18
SUBJECT_SAMPLE_FACTORS           	-	210315_19	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_19
SUBJECT_SAMPLE_FACTORS           	-	210315_20	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_20
SUBJECT_SAMPLE_FACTORS           	-	210315_22	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_22
SUBJECT_SAMPLE_FACTORS           	-	210315_23	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_23
SUBJECT_SAMPLE_FACTORS           	-	210315_24	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_24
SUBJECT_SAMPLE_FACTORS           	-	210315_25	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_25
SUBJECT_SAMPLE_FACTORS           	-	210315_26	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_26
SUBJECT_SAMPLE_FACTORS           	-	210315_27	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_27
SUBJECT_SAMPLE_FACTORS           	-	210315_28	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_28
SUBJECT_SAMPLE_FACTORS           	-	210315_29	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_29
SUBJECT_SAMPLE_FACTORS           	-	210315_30	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_30
SUBJECT_SAMPLE_FACTORS           	-	210315_31	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_31
SUBJECT_SAMPLE_FACTORS           	-	210315_32	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_32
SUBJECT_SAMPLE_FACTORS           	-	210315_33	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_33
SUBJECT_SAMPLE_FACTORS           	-	210315_34	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_34
SUBJECT_SAMPLE_FACTORS           	-	210315_35	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_35
SUBJECT_SAMPLE_FACTORS           	-	210315_36	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_36
SUBJECT_SAMPLE_FACTORS           	-	210315_37	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_37
SUBJECT_SAMPLE_FACTORS           	-	210315_38	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_38
SUBJECT_SAMPLE_FACTORS           	-	210315_39	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_39
SUBJECT_SAMPLE_FACTORS           	-	210315_40	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_40
SUBJECT_SAMPLE_FACTORS           	-	210315_41	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_41
SUBJECT_SAMPLE_FACTORS           	-	210315_42	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_42
SUBJECT_SAMPLE_FACTORS           	-	210315_43	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_43
SUBJECT_SAMPLE_FACTORS           	-	210315_44	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_44
SUBJECT_SAMPLE_FACTORS           	-	210315_45	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_45
SUBJECT_SAMPLE_FACTORS           	-	210315_46	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_46
SUBJECT_SAMPLE_FACTORS           	-	210315_47	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_47
SUBJECT_SAMPLE_FACTORS           	-	210315_48	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_48
SUBJECT_SAMPLE_FACTORS           	-	210315_49	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_49
SUBJECT_SAMPLE_FACTORS           	-	210315_50	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_50
SUBJECT_SAMPLE_FACTORS           	-	210315_51	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_51
SUBJECT_SAMPLE_FACTORS           	-	210315_52	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_52
SUBJECT_SAMPLE_FACTORS           	-	210315_53	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_53
SUBJECT_SAMPLE_FACTORS           	-	210315_54	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_54
SUBJECT_SAMPLE_FACTORS           	-	210315_55	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_55
SUBJECT_SAMPLE_FACTORS           	-	210315_56	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_56
SUBJECT_SAMPLE_FACTORS           	-	210315_57	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_57
SUBJECT_SAMPLE_FACTORS           	-	210315_58	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_58
SUBJECT_SAMPLE_FACTORS           	-	210315_59	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_59
SUBJECT_SAMPLE_FACTORS           	-	210315_60	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_60
SUBJECT_SAMPLE_FACTORS           	-	210315_61	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_61
SUBJECT_SAMPLE_FACTORS           	-	210315_62	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_62
SUBJECT_SAMPLE_FACTORS           	-	210315_63	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_63
SUBJECT_SAMPLE_FACTORS           	-	210315_64	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_64
SUBJECT_SAMPLE_FACTORS           	-	210315_65	Case_ Control Status:Case | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_65
SUBJECT_SAMPLE_FACTORS           	-	210315_66	Case_ Control Status:Control | Sample source:Cord blood_plasma	RAW_FILE_NAME(Raw_File_name)=210315_66
#COLLECTION
CO:COLLECTION_SUMMARY            	Cord blood EDTA plasma aliquots were retrieved from the INFANT ISO accredited
CO:COLLECTION_SUMMARY            	biobanking facilities and stored at −80 °C until analysed. Blood for the
CO:COLLECTION_SUMMARY            	later childhood assessment was collected in BD Vacutainer serum tubes. Following
CO:COLLECTION_SUMMARY            	centrifugation, 250µl aliquots (Wilmut) were stored in −80 °C long-term
CO:COLLECTION_SUMMARY            	storage. Local standard operating protocols were followed in all handling and
CO:COLLECTION_SUMMARY            	storage of human bio-samples.
CO:COLLECTION_PROTOCOL_FILENAME  	Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
CO:SAMPLE_TYPE                   	Blood (plasma)
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	Case control study
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	For metabolomics profiling in cord blood, we used 50µl of cord blood plasma, to
SP:SAMPLEPREP_SUMMARY            	which 150µl of cold acetonitrile was added, vortexed for 1 min, and chilled for
SP:SAMPLEPREP_SUMMARY            	1 hour at -20˚C. The samples were centrifuged for 15 min at 15,000 rpm;
SP:SAMPLEPREP_SUMMARY            	supernatant was transferred to a clean tube and dried in a vacuum centrifuge at
SP:SAMPLEPREP_SUMMARY            	30˚C. The sample was reconstituted in 100µl of 50:50 acetonitrile:water with
SP:SAMPLEPREP_SUMMARY            	0.1% formic acid and transferred to glass autosampler vials for injection onto a
SP:SAMPLEPREP_SUMMARY            	Waters ACQUITY-SYNAPT G2-S LC-MS/MS system. LC-MS/MS methodology for
SP:SAMPLEPREP_SUMMARY            	metabolomics analysis is described in Morillon et al.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
SP:PROCESSING_STORAGE_CONDITIONS 	-20℃
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	LC-MS analysis was performed using an ACQUITY ultra performance liquid
CH:CHROMATOGRAPHY_SUMMARY        	chromatography (Waters Corp, Milford, MA) coupled with a Synapt G2-S quadrupole
CH:CHROMATOGRAPHY_SUMMARY        	time-of-flight (UPLC-Q-TOF) mass spectrometer (Waters Corp, Wilmslow, UK)
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um)
CH:SOLVENT_A                     	0.1% formic acid in water
CH:SOLVENT_B                     	0.1% formic acid in acetonitrile
CH:FLOW_GRADIENT                 	15min
CH:FLOW_RATE                     	0.4 mL/min
CH:COLUMN_TEMPERATURE            	65 °C
CH:TARGET_SAMPLE_TEMPERATURE     	7oC
CH:RANDOMIZATION_ORDER           	yes
CH:CHROMATOGRAPHY_COMMENTS       	pooled QC injected every tenth injection throughout the analysis.
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:ANALYSIS_PROTOCOL_FILE        	Noone_et_al_Cord_Blood_Metabolomics_Protocol.pdf
#MS
MS:INSTRUMENT_NAME               	Waters Synapt G2 S QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	MSE data were uploaded onto Progenesis QI 2.4 software (Nonlinear Dynamics,
MS:MS_COMMENTS                   	Newcastle, U.K.) for peak picking and alignment. Data were normalized to ‘All
MS:MS_COMMENTS                   	Compounds’ and the coefficient of variation (CV) was computed for each
MS:MS_COMMENTS                   	compound across all QC runs (n=8) to evaluate repeatability of measurement.
MS:MS_COMMENTS                   	Compounds with > 20% CV within the QCs were removed. Any compound which had >30%
MS:MS_COMMENTS                   	missing values across the entire sample set or >30% in either subgroup (case or
MS:MS_COMMENTS                   	control) was removed. Remaining features (429 negative mode, 1353 positive mode)
MS:MS_COMMENTS                   	were log2 transformed and normalised on the median values. Mann-Whitney U tests
MS:MS_COMMENTS                   	for significant differences between cases and controls were then carried out and
MS:MS_COMMENTS                   	corrected for false discovery rate (FDR) using the Benjamini-Hochberg procedure.
MS:MS_COMMENTS                   	Altered metabolites (p < 0.05) were uploaded to Metaboanalyst (v6.0) to identify
MS:MS_COMMENTS                   	key metabolic pathways implicated. Lastly, Spearman’s correlation coefficient
MS:MS_COMMENTS                   	was employed to assess for correlation between steroid metabolites.
MS:MS_RESULTS_FILE               	ST003809_AN006263_Results.txt	UNITS:m/z	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END