#METABOLOMICS WORKBENCH OihaneAlboniga001_20200716_005253 DATATRACK_ID:2099 STUDY_ID:ST001427 ANALYSIS_ID:AN002385 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 autoscaling was MS:MS_COMMENTS applied. Then multivariate and univariate analysis were carried out. MS:ION_MODE POSITIVE MS:MS_RESULTS_FILE ST001427_AN002385_Results.txt UNITS:Peak Area Has m/z:Yes Has RT:Yes RT units:Seconds #END