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.
| Study ID | ST001427 |
| Study Title | HPLC-(Q)-TOF-MS based study of plasma metabolic profiles differences associated with age in paediatric population using animal model |
| Study 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. 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 Name | Alboniga |
| First Name | Oihane E. |
| Address | Barrio Sarriena s/n |
| oihaneelena.alboniga@ehu.eus | |
| Phone | 0034 946 012 686 |
| Submit Date | 2020-07-16 |
| Num Groups | 3 |
| Total Subjects | 36 |
| Num Males | 18 |
| Num Females | 18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-07-30 |
| Release Version | 1 |
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: | 9823 |
Factors:
Subject type: Mammal; Subject species: Sus scrofa (Factor headings shown in green)
| mb_sample_id | local_sample_id | Paediatric Group |
|---|---|---|
| SA120140 | C7 | child |
| SA120141 | C5 | child |
| SA120142 | C2 | child |
| SA120143 | C1 | child |
| SA120144 | C6 | child |
| SA120145 | C4 | child |
| SA120146 | C9 | child |
| SA120147 | C3 | child |
| SA120148 | C10 | child |
| SA120149 | C8 | child |
| SA120150 | C12 | child |
| SA120151 | C11 | child |
| SA120152 | B10 | infant |
| SA120153 | B9 | infant |
| SA120154 | B12 | infant |
| SA120155 | B6 | infant |
| SA120156 | B8 | infant |
| SA120157 | B3 | infant |
| SA120158 | B7 | infant |
| SA120159 | B5 | infant |
| SA120160 | B2 | infant |
| SA120161 | B4 | infant |
| SA120162 | B1 | infant |
| SA120163 | B11 | infant |
| SA120164 | A2 | newborn |
| SA120165 | A12 | newborn |
| SA120166 | A11 | newborn |
| SA120167 | A9 | newborn |
| SA120168 | A7 | newborn |
| SA120169 | A4 | newborn |
| SA120170 | A1 | newborn |
| SA120171 | A8 | newborn |
| SA120172 | A5 | newborn |
| SA120173 | A3 | newborn |
| SA120174 | A6 | newborn |
| SA120175 | A10 | newborn |
| SA120133 | QC1 | QC |
| SA120134 | QC3 | QC |
| SA120135 | QC5 | QC |
| SA120136 | QC6 | QC |
| SA120137 | QC7 | QC |
| SA120138 | QC2 | QC |
| SA120139 | QC4 | QC |
| 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 (100 x 2.1mm,3.5um) | Agilent Zorbax SB-C18 (100 x 2.1mm,3.5um) |
| 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 (100 x 2.1mm,3.5um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001753 |
| Instrument Name: | Agilent 1200 |
| Column Name: | Agilent Zorbax SB-C18 (100 x 2.1mm,3.5um) |
| 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 |
