Summary of Study ST001724

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 PR001104. The data can be accessed directly via it's Project DOI: 10.21228/M80M6C 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 IDST001724
Study TitleThe effects of birth weight and breeding value for protein deposition on the urine metabolome in growing pigs (part-III)
Study SummaryAn experiment was conducted with growing pigs, to determine the effects of birth weight (BiW) and estimated breeding value for protein deposition (EBV) on the metabolomic profile in urine samples collected under different dietary regimens: protein adequate (A) or protein restricted (R, 70% of A).
Institute
Aarhus University
DepartmentAnimal Science
LaboratoryMetabolomics LC-MS platform Aarhus University Foulum
Last NameHedemann
First NameMette
AddressBlichers Alle 20, Tjele, -, 8830, Denmark
EmailMette.Hedemann@anis.au.dk
Phone51448783
Submit Date2021-03-15
Total Subjects40
Num Males40
PublicationsThe effects of birth weight and breeding value for protein deposition on nitrogen efficiency in growing pigs
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2021-03-31
Release Version1
Mette Hedemann Mette Hedemann
https://dx.doi.org/10.21228/M80M6C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001104
Project DOI:doi: 10.21228/M80M6C
Project Title:The effects of birth weight and breeding value for protein deposition on the plasma metabolome in growing pigs
Project Summary:An experiment was conducted with growing pigs, to determine the effects of birth weight (BiW) and estimated breeding value for protein deposition (EBV) on the metabolomic profile in plasma samples collected under different dietary regimens: protein adequate (A) or protein restricted (R, 70% of A).
Institute:Aarhus University
Department:Animal Science
Laboratory:Metabolomics LC-MS platform Aarhus University Foulum
Last Name:Hedemann
First Name:Mette
Address:Blichers Alle 20, Tjele, -, 8830, Denmark
Email:Mette.Hedemann@anis.au.dk
Phone:51448783
Funding Source:European Union's H2020 Program
Project Comments:Feed-a-Gene, Grant agreement no 633531
Publications:The effects of birth weight and breeding value for protein deposition on nitrogen efficiency in growing pigs
Contributors:C.M.C. van der Peet-Schwering, L.M.G. Verschuren, R. Bergsma, M.S. Hedemann, G.P. Binnendijk, A.J.M. Jansman

Subject:

Subject ID:SU001801
Subject Type:Mammal
Subject Species:Sus scrofa
Taxonomy ID:9823
Age Or Age Range:0-125 days
Weight Or Weight Range:1-80 kg
Gender:Male
Animal Animal Supplier:Swine Innovation Centre Sterksel, the Netherlands
Animal Housing:Metabolism cages
Animal Light Cycle:12h light / 12h darknes
Animal Feed:Experimental diets (see publication)
Animal Water:Ad libitum
Animal Inclusion Criteria:Birth weight

Factors:

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

mb_sample_id local_sample_id Diet Wght_birth_cat
SA16229034adequate high
SA16229129adequate high
SA16229233adequate high
SA16229343adequate high
SA16229457adequate high
SA16229571adequate high
SA16229674adequate high
SA16229770adequate high
SA16229864adequate high
SA16229952adequate high
SA16230058adequate high
SA16230150adequate high
SA16230240adequate high
SA16230320adequate high
SA1623042adequate high
SA1623053adequate high
SA16230616adequate high
SA16230714adequate high
SA1623089adequate high
SA16230954adequate low
SA16231012adequate low
SA16231176adequate low
SA16231275adequate low
SA16231324adequate low
SA16231410adequate low
SA16231565adequate low
SA16231669adequate low
SA1623177adequate low
SA16231861adequate low
SA16231945adequate low
SA16232060adequate low
SA16232156adequate low
SA16232247adequate low
SA16232328adequate low
SA16232438adequate low
SA1623255adequate low
SA16232627adequate low
SA16232739adequate low
SA16232823adequate low
SA162274QC.1_1QC QC
SA162275QC.2_2QC QC
SA162276QC.4_2QC QC
SA162277QC.4_3QC QC
SA162278QC.1_2QC QC
SA162279QC.2_3QC QC
SA162280QC.3_3QC QC
SA162281QC.1_3QC QC
SA162282QC.3_2QC QC
SA162283QC.4_1QC QC
SA162284QC.3_4QC QC
SA162285QC.2_4QC QC
SA162286QC.3_1QC QC
SA162287QC.1_4QC QC
SA162288QC.2_1QC QC
SA162289QC.4_4QC QC
SA16232932restricted high
SA16233011restricted high
SA16233159restricted high
SA1623324restricted high
SA16233325restricted high
SA1623341restricted high
SA16233555restricted high
SA16233631restricted high
SA16233772restricted high
SA16233853restricted high
SA16233948restricted high
SA16234068restricted high
SA16234141restricted high
SA16234242restricted high
SA16234335restricted high
SA16234419restricted high
SA16234518restricted high
SA16234613restricted high
SA16234773restricted high
SA16234877restricted low
SA1623498restricted low
SA16235078restricted low
SA1623516restricted low
SA16235251restricted low
SA16235336restricted low
SA16235437restricted low
SA16235521restricted low
SA16235630restricted low
SA16235726restricted low
SA16235822restricted low
SA16235944restricted low
SA16236046restricted low
SA16236163restricted low
SA16236266restricted low
SA16236362restricted low
SA16236449restricted low
SA16236517restricted low
SA16236615restricted low
SA16236767restricted low
Showing results 1 to 94 of 94

Collection:

Collection ID:CO001794
Collection Summary:In both balance periods, at d4 between 0900 and 1000 h three 1.5 ml urine samples per pig were taken from the buckets with urine collected from 0800 h that morning. Before taking the urine samples, the urine was mixed. The samples were stored at -80°C pending analyses.
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001814
Treatment Summary:At an age of 14 weeks, 10 LBW-LEBV (BiW: 1.07 + 0.09 kg; EBV: -2.52 + 3.97 g/d, compared to an average crossbred pig with a protein deposition of 165 g/d), 10 LBW-HEBV (BiW: 1.02 + 0.13 kg; EBV: 10.47 + 4.26 g/d), 10 HBW-LEBV (BiW: 1.80 + 0.13 kg; EBV: - 2.15 + 2.28 g/d), and 10 HBW-HEBV (BiW: 1.80 + 0.15 kg; EBV: 11.18 + 3.68 g/d), male growing pigs (Synthetic boar x (Dutch Landrace x Large White)) were allotted to the experiment. The pigs were individually housed in metabolism cages (1.80 x 0.80 m) at a room temperature of 22oC. They were subjected to N- balance measurements in two sequential periods of 5 d using a restricted feeding regime. After a 6-d adaptation period to the metabolism cages, pigs were adapted for 5 days to the experimental diets before the start of the first 5-d balance period. Pigs were assigned to a protein adequate (A) or protein restricted (R, 70% of A) regime in a change-over design. LBW: Low birth weight; HBW: High birth weight; LEBV: Low estimated breeding value for protein deposition; HEBV: High estimated breeding value for protein deposition.

Sample Preparation:

Sampleprep ID:SP001807
Sampleprep Summary:In a 96-well plate, the urine samples (112.5 µL) were diluted with H2O (112.5 µL) and 25 µL acetonitrile (100%, ACN) containing an internal standard mix of glycocholic acid (glycine-1-13C) and p-chlorophenylalanine to a final concentration of 0.01 mg/mL was added. The samples were incubated for 20 min at 4°C and subsequently centrifuged (3700 rpm, 25 min, 4°C). The supernatant, 100 µL per well, was transferred to a 200 µL 96-well plate and a protective film was welded on the plate using a heat sealer, and the plate was centrifuged at 3700 rpm, 4°C for 25 min prior to the LC-MS analysis. Samples were kept in the autosampler at 10°C, and the injection volume was 3 µl.

Combined analysis:

Analysis ID AN002808 AN002809
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Bruker Impact HD Bruker Impact HD
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002075
Chromatography Summary:Chromatographic separation was performed on a Dionex UltiMate 3000RSL Binary UHPLC System (Thermo Scientific Dionex, Sunnyvale, CA) equipped with a HSS T3 C18 UHPLC column, 1.8 µm, 100x2.1 mm (Waters Corporation, Milford, MA). The column was maintained at 30°C. Samples were kept in the autosampler at 10°C, and the injection volume was 3 µl. The mobile phases were 0.1% formic acid in Milli-Q water (A) and 0.1% formic acid in acetonitrile (B). The gradient program for the urine samples was as follows: 0-8 min, linear gradient from 5-70% B; 8-8.5 min, linear gradient from 70-100% B; 8.5-9.5 min, 100% B and return to initial conditions in 0.2 min. The column was re-equilibrated at 5% B for 2 min at the beginning of each run and the flow rate was set to 400 µL/min.
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:30
Flow Rate:0.4 ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002603
Analysis ID:AN002808
Instrument Name:Bruker Impact HD
Instrument Type:QTOF
MS Type:ESI
MS Comments:The eluent was introduced into the mass spectrometer by electrospray ionization, with capillary set in the positive and negative mode to 4500 and 3600 V, respectively. End-plate offset voltage was set to 500 V. Nitrogen was used as both nebulizer and drying gas with a gas pressure of 1.8 bar. Drying gas temperature and flow were 200 °C and 8.0 L/min, respectively. Spectra were acquired over the scan range of 50−1000 m/z. A solution of lithium formate clusters (5 mM) (water/isopropanol/formic acid in a 50:50:0.2 v/v/v ratio) was injected prior to each chromatographic run as an external calibrant.
Ion Mode:NEGATIVE
  
MS ID:MS002604
Analysis ID:AN002809
Instrument Name:Bruker Impact HD
Instrument Type:QTOF
MS Type:ESI
MS Comments:The eluent was introduced into the mass spectrometer by electrospray ionization, with capillary set in the positive and negative mode to 4500 and 3600 V, respectively. End-plate offset voltage was set to 500 V. Nitrogen was used as both nebulizer and drying gas with a gas pressure of 1.8 bar. Drying gas temperature and flow were 200 °C and 8.0 L/min, respectively. Spectra were acquired over the scan range of 50−1000 m/z. A solution of lithium formate clusters (5 mM) (water/isopropanol/formic acid in a 50:50:0.2 v/v/v ratio) was injected prior to each chromatographic run as an external calibrant.
Ion Mode:POSITIVE
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