Summary of Study ST001722

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.

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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 IDST001722
Study TitleThe effects of birth weight and breeding value for protein deposition on the plasma metabolome in growing pigs (part-I)
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 plasma 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 Date2021-03-12
Total Subjects40
Num Males40
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

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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:SU001799
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
SA162101Plasma_neg_111adequate high
SA162102Plasma_neg_53adequate high
SA162103Plasma_neg_112adequate high
SA162104Plasma_neg_29adequate high
SA162105Plasma_neg_104adequate high
SA162106Plasma_neg_34adequate high
SA162107Plasma_neg_51adequate high
SA162108Plasma_neg_59adequate high
SA162109Plasma_neg_58adequate high
SA162110Plasma_neg_115adequate high
SA162111Plasma_neg_22adequate high
SA162112Plasma_neg_93adequate high
SA162113Plasma_neg_94adequate high
SA162114Plasma_neg_41adequate high
SA162115Plasma_neg_36adequate high
SA162116Plasma_neg_89adequate high
SA162117Plasma_neg_23adequate high
SA162118Plasma_neg_40adequate high
SA162119Plasma_neg_44adequate high
SA162120Plasma_neg_25adequate low
SA162121Plasma_neg_84adequate low
SA162122Plasma_neg_105adequate low
SA162123Plasma_neg_88adequate low
SA162124Plasma_neg_99adequate low
SA162125Plasma_neg_98adequate low
SA162126Plasma_neg_100adequate low
SA162127Plasma_neg_83adequate low
SA162128Plasma_neg_87adequate low
SA162129Plasma_neg_101adequate low
SA162130Plasma_neg_110adequate low
SA162131Plasma_neg_116adequate low
SA162132Plasma_neg_27adequate low
SA162133Plasma_neg_117adequate low
SA162134Plasma_neg_48adequate low
SA162135Plasma_neg_46adequate low
SA162136Plasma_neg_57adequate low
SA162137Plasma_neg_55adequate low
SA162138Plasma_neg_32adequate low
SA162139Plasma_neg_30adequate low
SA162069QC-1_neg_1QC QC
SA162070QC-1_neg_1aQC QC
SA162071QC-2_neg_1QC QC
SA162072QC-3_neg_1QC QC
SA162073QC-4_neg_1QC QC
SA162074QC-3_neg_4aQC QC
SA162075QC-2_neg_4aQC QC
SA162076QC-2_neg_3aQC QC
SA162077QC-3_neg_3aQC QC
SA162078QC-4_neg_3aQC QC
SA162079QC-1_neg_4aQC QC
SA162080QC-1_neg_2QC QC
SA162081QC-2_neg_2QC QC
SA162082QC-1_neg_4QC QC
SA162083QC-2_neg_4QC QC
SA162084QC-3_neg_4QC QC
SA162085QC-4_neg_4QC QC
SA162086QC-4_neg_3QC QC
SA162087QC-3_neg_3QC QC
SA162088QC-3_neg_2QC QC
SA162089QC-4_neg_2QC QC
SA162090QC-1_neg_3QC QC
SA162091QC-2_neg_3QC QC
SA162092QC-1_neg_3aQC QC
SA162093QC-4_neg_4aQC QC
SA162094QC-1_neg_2aQC QC
SA162095QC-4_neg_1aQC QC
SA162096QC-3_neg_1aQC QC
SA162097QC-2_neg_1aQC QC
SA162098QC-4_neg_2aQC QC
SA162099QC-3_neg_2aQC QC
SA162100QC-2_neg_2aQC QC
SA162140Plasma_neg_24restricted high
SA162141Plasma_neg_21restricted high
SA162142Plasma_neg_109restricted high
SA162143Plasma_neg_113restricted high
SA162144Plasma_neg_114restricted high
SA162145Plasma_neg_95restricted high
SA162146Plasma_neg_85restricted high
SA162147Plasma_neg_54restricted high
SA162148Plasma_neg_56restricted high
SA162149Plasma_neg_60restricted high
SA162150Plasma_neg_49restricted high
SA162151Plasma_neg_38restricted high
SA162152Plasma_neg_42restricted high
SA162153Plasma_neg_43restricted high
SA162154Plasma_neg_33restricted high
SA162155Plasma_neg_31restricted high
SA162156Plasma_neg_39restricted high
SA162157Plasma_neg_92restricted high
SA162158Plasma_neg_91restricted high
SA162159Plasma_neg_37restricted low
SA162160Plasma_neg_35restricted low
SA162161Plasma_neg_90restricted low
SA162162Plasma_neg_118restricted low
SA162163Plasma_neg_97restricted low
SA162164Plasma_neg_47restricted low
SA162165Plasma_neg_50restricted low
SA162166Plasma_neg_119restricted low
SA162167Plasma_neg_45restricted low
SA162168Plasma_neg_52restricted low
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Collection:

Collection ID:CO001792
Collection Summary:At the end of each feeding regime, blood samples were collected from the jugular vein. Per sampling moment, two 9-mL plasma tubes (Vacuette, Greiner Bio-One, Kremsmünster, Austria) per pig were filled and allowed to clot for 1 h at room temperature. Plasma was collected after centrifugation for 15 min at 2,000 ∙ g and was stored at -80°C pending analyses.
Sample Type:Blood (plasma)
Collection Method:Jugular vein puncture
Collection Frequency:At the end of feeding period
Volumeoramount Collected:2 x 9 ml blood
Storage Conditions:-80℃
Collection Vials:Vacuette

Treatment:

Treatment ID:TR001812
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.

Sample Preparation:

Sampleprep ID:SP001805
Sampleprep Summary:Plasma samples (150 µL) were pipetted into a 96-well plate and 450 µL acetonitrile 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 per well. The samples were mixed immediately and placed at 4°C for 10 min for protein precipitation. After centrifugation (3700 rpm for 25 min at 4°C), the supernatant was transferred to a filter plate fixed on top of a 96-well collection plate in a manifold with a pressure gauge. Vacuum was then applied to the filter plate, and the solvent containing plasma components was collected into the 96-well collection plate. The collection plate was placed in a vacuum centrifuge and the samples were evaporated to dryness (ca. 2.5 h, 805 × g and 30°C). A volume of 150 µL of water/acetonitrile/formic acid (95/5/0.1%) was added to the dried extracts in the collection plate. The dried collection plate was then sealed with a piece of aluminum laminate (#186002789, Waters), centrifuged (3700 rpm for 25 min at 4°C), and kept in the auto-sampler at 10°C for the UPLC-QTOF/MS analysis. The injection volume was 3 µl.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002806
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTOF
MS instrument name Bruker Impact HD
Ion Mode NEGATIVE
Units peak area

Chromatography:

Chromatography ID:CH002073
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 for both sample types 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 plasma samples was as follows: 0-12 min, linear gradient from 5-100% B; 12-13 min, 100% B and return to initial conditions in 0.2 min. In all cases, the column was re-equilibrated at 5% B for 2 min at the beginning of each run. The flow rate was 0.4 ml/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:MS002601
Analysis ID:AN002806
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
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