Summary of study ST001427

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 PR000979. The data can be accessed directly via it's Project DOI: 10.21228/M84X3K 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 IDST001427
Study TitleHPLC-(Q)-TOF-MS based study of plasma metabolic profiles differences associated with age in paediatric population using animal model
Study SummaryA deep knowledge about the biological development of children is essential for an appropriate drug administration and dosage in paediatrics. Even though the advances made in developmental biology the information available about organ maturation in the early stages of life is limited. This fact, together with the scarcity of clinical trials in children, sometimes leads to the use of off-label drugs. The best approximation to study organ maturation is analysing tissue samples but their collection requires a very invasive method. For this reason, a surrogate matrix such as plasma, which represents a snapshot of global organ/tissue metabolism, may be a suitable alternative. To test this hypothesis, plasma metabolic profiles from piglets of different ages (newborns, infants, and children) obtained by HPLC-(Q)-TOF-MS at positive and negative ionization modes were here studied. The multiblock principal component analysis used in this work proved to be a useful tool to improve the clustering within groups compared to classical principal component analysis. Furthermore, the separation observed among groups was better resolved by using partial least squares-discriminant analysis, which was validated by bootstrapping and permutation testing. Finally, 27 relevant features in positive and 74 features in negative ionization mode were selected by univariate analysis. Among the significant metabolies, an acylcarnitine and eight glycerophospholipids were annotated. The findings indicate that changes with age in the lipid metabolism, where lysophosphatidylcholine and lysophoshatidylethanolamine are included, might be related with the organ maturation state.
Institute
University of the Basque Country
Last NameAlboniga
First NameOihane E.
AddressBarrio Sarriena s/n
Emailoihaneelena.alboniga@ehu.eus
Phone0034 946 012 686
Submit Date2020-07-16
Num Groups3
Total Subjects36
Num Males18
Num Females18
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailLC-MS
Release Date2020-07-30
Release Version1
Oihane E. Alboniga Oihane E. Alboniga
https://dx.doi.org/10.21228/M84X3K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000979
Project DOI:doi: 10.21228/M84X3K
Project Title:LC-MS based metabolomics to study paediatric population using animal model
Project Summary:A deep knowledge about the biological development of children is essential for an appropriate drug administration and dosage in paediatrics. Even though the advances made in developmental biology the information available about organ maturation in the early stages of life is limited. This fact, together with the scarcity of clinical trials in children, sometimes leads to the use of off-label drugs. The best approximation to study organ maturation is analysing tissue samples but their collection requires a very invasive method. For this reason, a surrogate matrix such as plasma, which represents a snapshot of global organ/tissue metabolism, may be a suitable alternative.
Institute:University of the Basque Country
Last Name:Alboniga
First Name:Oihane E.
Address:Barrio Sarriena s/n
Email:oihaneelena.alboniga@ehu.eus
Phone:0034 946 012 686

Subject:

Subject ID:SU001501
Subject Type:Mammal
Subject Species:Sus scrofa
Taxonomy ID:1758

Factors:

Subject type: Mammal; Subject species: Sus scrofa (Factor headings shown in green)

mb_sample_id local_sample_id Paediatric Group
SA120140C7child
SA120141C5child
SA120142C2child
SA120143C1child
SA120144C6child
SA120145C4child
SA120146C9child
SA120147C3child
SA120148C10child
SA120149C8child
SA120150C12child
SA120151C11child
SA120152B10infant
SA120153B9infant
SA120154B12infant
SA120155B6infant
SA120156B8infant
SA120157B3infant
SA120158B7infant
SA120159B5infant
SA120160B2infant
SA120161B4infant
SA120162B1infant
SA120163B11infant
SA120164A2newborn
SA120165A12newborn
SA120166A11newborn
SA120167A9newborn
SA120168A7newborn
SA120169A4newborn
SA120170A1newborn
SA120171A8newborn
SA120172A5newborn
SA120173A3newborn
SA120174A6newborn
SA120175A10newborn
SA120133QC1QC
SA120134QC3QC
SA120135QC5QC
SA120136QC6QC
SA120137QC7QC
SA120138QC2QC
SA120139QC4QC
Showing results 1 to 43 of 43

Collection:

Collection ID:CO001496
Collection Summary:Samples were obtained from mechanically ventilated newborn piglets or group A (<5 days, n =12), infant piglets or group B (2 weeks, n =12) and child piglets or group C (4 weeks, n =12) of Topig F-1 Large White x Landrace breed. Whole blood samples were collected in K2-EDTA tubes, and they were immediately centrifuged at 950 g for 10 min at room temperature in order to obtain plasma. The supernatant was transferred to a cryovial and stored at -80 °C until analysis.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001516
Treatment Summary:Whole blood collected in K2-EDTA tubes were immediately centrifuged at 950 g for 10 min at room temperature in order to obtain plasma. The supernatant was transferred to a cryovial and stored at -80 °C until analysis.
Treatment Protocol Filename:OihaneAlboniga001_20200716_005253_PR_SP_SP.pdf

Sample Preparation:

Sampleprep ID:SP001509
Sampleprep Summary:SP.pdf was included with all the details related to sample preparation.
Sampleprep Protocol Filename:OihaneAlboniga001_20200716_005253_PR_SP_SP.pdf

Combined analysis:

Analysis ID AN002385 AN002386
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1200 Agilent 1200
Column Agilent Zorbax SB-C18 (2.1 x 100 mm, 3.5 µm) Agilent Zorbax SB-C18 (2.1 x 100 mm, 3.5 µm)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak Area Peak Area

Chromatography:

Chromatography ID:CH001752
Instrument Name:Agilent 1200
Column Name:Agilent Zorbax SB-C18 (2.1 x 100 mm, 3.5 µm)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001753
Instrument Name:Agilent 1200
Column Name:Agilent Zorbax SB-C18 (2.1 x 100 mm, 3.5 µm)
Chromatography Type:Reversed phase

MS:

MS ID:MS002227
Analysis ID:AN002385
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:LC-MS.pdf with all the details related to the analysis of plasma samples is uploaded. Then, XCMS was used to process data by using the Isotopologue Parameters Optimization (IPO) package following the criteria reported by Albóniga et al. (Alboniga OE, Gonzalez O, Alonso RM, Xu Y, Goodacre R. Optimization of XCMS parameters for LC-MS metabolomics: An assessment of automated versus manual tuning and its effect on the final results. Metabolomics. 2020;16(1):14-020-1636-9) Finally, Plasma data matrix was processed with Matlab using the toolbox freely available online at https://github.com/Biospec/cluster-toolbox-v2.0. Intensity drop was corrected with the QC correction function included in the toolbox and then autoscaling was applied. Then multivariate and univariate analysis were carried out.
Ion Mode:POSITIVE
  
MS ID:MS002228
Analysis ID:AN002386
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:LC-MS.pdf with all the details related to the analysis of plasma samples is uploaded. Then, XCMS was used to process data by using the Isotopologue Parameters Optimization (IPO) package following the criteria reported by Albóniga et al. (Alboniga OE, Gonzalez O, Alonso RM, Xu Y, Goodacre R. Optimization of XCMS parameters for LC-MS metabolomics: An assessment of automated versus manual tuning and its effect on the final results. Metabolomics. 2020;16(1):14-020-1636-9) Finally, Plasma data matrix was processed with Matlab using the toolbox freely available online at https://github.com/Biospec/cluster-toolbox-v2.0. Intensity drop was corrected with the QC correction function included in the toolbox and then logarithm scaling was applied. Then multivariate and univariate analysis were carried out.
Ion Mode:NEGATIVE
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