#METABOLOMICS WORKBENCH OihaneAlboniga001_20200716_005253 DATATRACK_ID:2099 STUDY_ID:ST001427 ANALYSIS_ID:AN002386
VERSION                          	1
CREATED_ON                       	02-08-2024
#PROJECT
PR:PROJECT_TITLE                 	LC-MS based metabolomics to study paediatric population using animal model
PR:PROJECT_SUMMARY               	A deep knowledge about the biological development of children is essential for
PR:PROJECT_SUMMARY               	an appropriate drug administration and dosage in paediatrics. Even though the
PR:PROJECT_SUMMARY               	advances made in developmental biology the information available about organ
PR:PROJECT_SUMMARY               	maturation in the early stages of life is limited. This fact, together with the
PR:PROJECT_SUMMARY               	scarcity of clinical trials in children, sometimes leads to the use of off-label
PR:PROJECT_SUMMARY               	drugs. The best approximation to study organ maturation is analysing tissue
PR:PROJECT_SUMMARY               	samples but their collection requires a very invasive method. For this reason, a
PR:PROJECT_SUMMARY               	surrogate matrix such as plasma, which represents a snapshot of global
PR:PROJECT_SUMMARY               	organ/tissue metabolism, may be a suitable alternative.
PR:INSTITUTE                     	University of the Basque Country
PR:LAST_NAME                     	Alboniga
PR:FIRST_NAME                    	Oihane E.
PR:ADDRESS                       	Barrio Sarriena s/n
PR:EMAIL                         	oihaneelena.alboniga@ehu.eus
PR:PHONE                         	0034 946 012 686
PR:DOI                           	http://dx.doi.org/10.21228/M84X3K
#STUDY
ST:STUDY_TITLE                   	HPLC-(Q)-TOF-MS based study of plasma metabolic profiles differences associated
ST:STUDY_TITLE                   	with age in paediatric population using animal model
ST:STUDY_SUMMARY                 	A deep knowledge about the biological development of children is essential for
ST:STUDY_SUMMARY                 	an appropriate drug administration and dosage in paediatrics. Even though the
ST:STUDY_SUMMARY                 	advances made in developmental biology the information available about organ
ST:STUDY_SUMMARY                 	maturation in the early stages of life is limited. This fact, together with the
ST:STUDY_SUMMARY                 	scarcity of clinical trials in children, sometimes leads to the use of off-label
ST:STUDY_SUMMARY                 	drugs. The best approximation to study organ maturation is analysing tissue
ST:STUDY_SUMMARY                 	samples but their collection requires a very invasive method. For this reason, a
ST:STUDY_SUMMARY                 	surrogate matrix such as plasma, which represents a snapshot of global
ST:STUDY_SUMMARY                 	organ/tissue metabolism, may be a suitable alternative. To test this hypothesis,
ST:STUDY_SUMMARY                 	plasma metabolic profiles from piglets of different ages (newborns, infants, and
ST:STUDY_SUMMARY                 	children) obtained by HPLC-(Q)-TOF-MS at positive and negative ionization modes
ST:STUDY_SUMMARY                 	were here studied. The multiblock principal component analysis used in this work
ST:STUDY_SUMMARY                 	proved to be a useful tool to improve the clustering within groups compared to
ST:STUDY_SUMMARY                 	classical principal component analysis. Furthermore, the separation observed
ST:STUDY_SUMMARY                 	among groups was better resolved by using partial least squares-discriminant
ST:STUDY_SUMMARY                 	analysis, which was validated by bootstrapping and permutation testing. Finally,
ST:STUDY_SUMMARY                 	27 relevant features in positive and 74 features in negative ionization mode
ST:STUDY_SUMMARY                 	were selected by univariate analysis. Among the significant metabolies, an
ST:STUDY_SUMMARY                 	acylcarnitine and eight glycerophospholipids were annotated. The findings
ST:STUDY_SUMMARY                 	indicate that changes with age in the lipid metabolism, where
ST:STUDY_SUMMARY                 	lysophosphatidylcholine and lysophoshatidylethanolamine are included, might be
ST:STUDY_SUMMARY                 	related with the organ maturation state.
ST:INSTITUTE                     	University of the Basque Country
ST:LAST_NAME                     	Alboniga
ST:FIRST_NAME                    	Oihane E.
ST:ADDRESS                       	Barrio Sarriena s/n
ST:EMAIL                         	oihaneelena.alboniga@ehu.eus
ST:PHONE                         	0034 946 012 686
ST:SUBMIT_DATE                   	2020-07-16
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Sus scrofa
SU:TAXONOMY_ID                   	9823
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	C1	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071954.d 17072655.d
SUBJECT_SAMPLE_FACTORS           	-	C10	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071942.d 17072642.d
SUBJECT_SAMPLE_FACTORS           	-	C11	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071935.d 17072635.d
SUBJECT_SAMPLE_FACTORS           	-	C12	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071973.d 17072723.d
SUBJECT_SAMPLE_FACTORS           	-	C2	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071941.d 17072641.d
SUBJECT_SAMPLE_FACTORS           	-	C3	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071938.d 17072638.d
SUBJECT_SAMPLE_FACTORS           	-	C4	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071959.d 17072705.d
SUBJECT_SAMPLE_FACTORS           	-	C5	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071971.d 17072721.d
SUBJECT_SAMPLE_FACTORS           	-	C6	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071955.d 17072656.d
SUBJECT_SAMPLE_FACTORS           	-	C7	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071966.d 17072716.d
SUBJECT_SAMPLE_FACTORS           	-	C8	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071919.d 17072619.d
SUBJECT_SAMPLE_FACTORS           	-	C9	Paediatric Group:child	Group Name=C; Age in days=30; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071957.d 17072703.d
SUBJECT_SAMPLE_FACTORS           	-	B1	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071939.d 17072639.d
SUBJECT_SAMPLE_FACTORS           	-	B10	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071940.d 17072640.d
SUBJECT_SAMPLE_FACTORS           	-	B11	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071965.d 17072715.d
SUBJECT_SAMPLE_FACTORS           	-	B12	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071921.d 17072621.d
SUBJECT_SAMPLE_FACTORS           	-	B2	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071927.d 17072627.d
SUBJECT_SAMPLE_FACTORS           	-	B3	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071961.d 17072707.d
SUBJECT_SAMPLE_FACTORS           	-	B4	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071928.d 17072628.d
SUBJECT_SAMPLE_FACTORS           	-	B5	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071950.d 17072651.d
SUBJECT_SAMPLE_FACTORS           	-	B6	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071931.d 17072631.d
SUBJECT_SAMPLE_FACTORS           	-	B7	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071972.d 17072722.d
SUBJECT_SAMPLE_FACTORS           	-	B8	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071962.d 17072708.d
SUBJECT_SAMPLE_FACTORS           	-	B9	Paediatric Group:infant	Group Name=B; Age in days=15; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071964.d 17072710.d
SUBJECT_SAMPLE_FACTORS           	-	A1	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071951.d 17072652.d
SUBJECT_SAMPLE_FACTORS           	-	A10	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071960.d 17072706.d
SUBJECT_SAMPLE_FACTORS           	-	A11	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071937.d 17072637.d
SUBJECT_SAMPLE_FACTORS           	-	A12	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071953.d 17072654.d
SUBJECT_SAMPLE_FACTORS           	-	A2	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071920.d 17072620.d
SUBJECT_SAMPLE_FACTORS           	-	A3	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071926.d 17072626.d
SUBJECT_SAMPLE_FACTORS           	-	A4	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071932.d 17072632.d
SUBJECT_SAMPLE_FACTORS           	-	A5	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071958.d 17072704.d
SUBJECT_SAMPLE_FACTORS           	-	A6	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071930.d 17072630.d
SUBJECT_SAMPLE_FACTORS           	-	A7	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071933.d 17072633.d
SUBJECT_SAMPLE_FACTORS           	-	A8	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Male; Sample Type=Plasma; RAW_FILE_NAME=17071952.d 17072653.d
SUBJECT_SAMPLE_FACTORS           	-	A9	Paediatric Group:newborn	Group Name=A; Age in days=< 5; Gender=Female; Sample Type=Plasma; RAW_FILE_NAME=17071934.d 17072634.d
SUBJECT_SAMPLE_FACTORS           	-	QC1	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071918.d 17072615.d
SUBJECT_SAMPLE_FACTORS           	-	QC2	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071929.d 17072624.d
SUBJECT_SAMPLE_FACTORS           	-	QC3	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071936.d 17072629.d
SUBJECT_SAMPLE_FACTORS           	-	QC4	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071947.d 17072636.d
SUBJECT_SAMPLE_FACTORS           	-	QC5	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071956.d 17072648.d
SUBJECT_SAMPLE_FACTORS           	-	QC6	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071963.d 17072702.d
SUBJECT_SAMPLE_FACTORS           	-	QC7	Paediatric Group:QC	Group Name=QC; Age in days=-; Gender=-; Sample Type=Plasma; RAW_FILE_NAME=17071974.d 17072714.d
#COLLECTION
CO:COLLECTION_SUMMARY            	Samples were obtained from mechanically ventilated newborn piglets or group A
CO:COLLECTION_SUMMARY            	(<5 days, n =12), infant piglets or group B (2 weeks, n =12) and child
CO:COLLECTION_SUMMARY            	piglets or group C (4 weeks, n =12) of Topig F-1 Large White x Landrace breed.
CO:COLLECTION_SUMMARY            	Whole blood samples were collected in K2-EDTA tubes, and they were immediately
CO:COLLECTION_SUMMARY            	centrifuged at 950 g for 10 min at room temperature in order to obtain plasma.
CO:COLLECTION_SUMMARY            	The supernatant was transferred to a cryovial and stored at -80 °C until
CO:COLLECTION_SUMMARY            	analysis.
CO:SAMPLE_TYPE                   	Blood (plasma)
#TREATMENT
TR:TREATMENT_SUMMARY             	Whole blood collected in K2-EDTA tubes were immediately centrifuged at 950 g for
TR:TREATMENT_SUMMARY             	10 min at room temperature in order to obtain plasma. The supernatant was
TR:TREATMENT_SUMMARY             	transferred to a cryovial and stored at -80 °C until analysis.
TR:TREATMENT_PROTOCOL_FILENAME   	OihaneAlboniga001_20200716_005253_PR_SP_SP.pdf
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	SP.pdf was included with all the details related to sample preparation.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	OihaneAlboniga001_20200716_005253_PR_SP_SP.pdf
#CHROMATOGRAPHY
CH:INSTRUMENT_NAME               	Agilent 1200
CH:COLUMN_NAME                   	Agilent Zorbax SB-C18 (100 x 2.1mm,3.5um)
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6530 QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	LC-MS.pdf with all the details related to the analysis of plasma samples is
MS:MS_COMMENTS                   	uploaded. Then, XCMS was used to process data by using the Isotopologue
MS:MS_COMMENTS                   	Parameters Optimization (IPO) package following the criteria reported by
MS:MS_COMMENTS                   	Albóniga et al. (Alboniga OE, Gonzalez O, Alonso RM, Xu Y, Goodacre R.
MS:MS_COMMENTS                   	Optimization of XCMS parameters for LC-MS metabolomics: An assessment of
MS:MS_COMMENTS                   	automated versus manual tuning and its effect on the final results.
MS:MS_COMMENTS                   	Metabolomics. 2020;16(1):14-020-1636-9) Finally, Plasma data matrix was
MS:MS_COMMENTS                   	processed with Matlab using the toolbox freely available online at
MS:MS_COMMENTS                   	https://github.com/Biospec/cluster-toolbox-v2.0. Intensity drop was corrected
MS:MS_COMMENTS                   	with the QC correction function included in the toolbox and then logarithm
MS:MS_COMMENTS                   	scaling was applied. Then multivariate and univariate analysis were carried out.
MS:ION_MODE                      	NEGATIVE
MS:MS_RESULTS_FILE               	ST001427_AN002386_Results.txt	UNITS:Peak Area	Has m/z:Yes	Has RT:Yes	RT units:Seconds
#END