Summary of Study ST001723

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 IDST001723
Study TitleThe effects of birth weight and breeding value for protein deposition on the plasma metabolome in growing pigs (part-II)
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 Date2021-03-14
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:SU001800
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
SA162207Plasma_pos_59adequate high
SA162208Plasma_pos_58adequate high
SA162209Plasma_pos_53adequate high
SA162210Plasma_pos_89adequate high
SA162211Plasma_pos_51adequate high
SA162212Plasma_pos_94adequate high
SA162213Plasma_pos_40adequate high
SA162214Plasma_pos_29adequate high
SA162215Plasma_pos_34adequate high
SA162216Plasma_pos_104adequate high
SA162217Plasma_pos_36adequate high
SA162218Plasma_pos_41adequate high
SA162219Plasma_pos_22adequate high
SA162220Plasma_pos_93adequate high
SA162221Plasma_pos_23adequate high
SA162222Plasma_pos_44adequate high
SA162223Plasma_pos_84adequate low
SA162224Plasma_pos_25adequate low
SA162225Plasma_pos_105adequate low
SA162226Plasma_pos_32adequate low
SA162227Plasma_pos_83adequate low
SA162228Plasma_pos_30adequate low
SA162229Plasma_pos_27adequate low
SA162230Plasma_pos_101adequate low
SA162231Plasma_pos_87adequate low
SA162232Plasma_pos_98adequate low
SA162233Plasma_pos_46adequate low
SA162234Plasma_pos_55adequate low
SA162235Plasma_pos_88adequate low
SA162236Plasma_pos_48adequate low
SA162237Plasma_pos_99adequate low
SA162238Plasma_pos_100adequate low
SA162239Plasma_pos_57adequate low
SA162179QC-1_pos_1QC QC
SA162180QC-3_pos_4aQC QC
SA162181QC-4_pos_4aQC QC
SA162182QC-1_pos_3QC QC
SA162183QC-1_pos_3aQC QC
SA162184QC-2_pos_1QC QC
SA162185QC-2_pos_4aQC QC
SA162186QC-1_pos_4aQC QC
SA162187QC-3_pos_2QC QC
SA162188QC-2_pos_3aQC QC
SA162189QC-3_pos_3aQC QC
SA162190QC-4_pos_3aQC QC
SA162191QC-1_pos_1aQC QC
SA162192QC-2_pos_3QC QC
SA162193QC-3_pos_1QC QC
SA162194QC-2_pos_1aQC QC
SA162195QC-4_pos_1QC QC
SA162196QC-1_pos_2QC QC
SA162197QC-3_pos_1aQC QC
SA162198QC-4_pos_1aQC QC
SA162199QC-4_pos_3QC QC
SA162200QC-1_pos_2aQC QC
SA162201QC-4_pos_2QC QC
SA162202QC-3_pos_3QC QC
SA162203QC-4_pos_2aQC QC
SA162204QC-3_pos_2aQC QC
SA162205QC-2_pos_2aQC QC
SA162206QC-2_pos_2QC QC
SA162240Plasma_pos_95restricted high
SA162241Plasma_pos_92restricted high
SA162242Plasma_pos_91restricted high
SA162243Plasma_pos_85restricted high
SA162244Plasma_pos_56restricted high
SA162245Plasma_pos_38restricted high
SA162246Plasma_pos_39restricted high
SA162247Plasma_pos_43restricted high
SA162248Plasma_pos_33restricted high
SA162249Plasma_pos_31restricted high
SA162250Plasma_pos_21restricted high
SA162251Plasma_pos_24restricted high
SA162252Plasma_pos_49restricted high
SA162253Plasma_pos_42restricted high
SA162254Plasma_pos_60restricted high
SA162255Plasma_pos_54restricted high
SA162256Plasma_pos_108restricted low
SA162257Plasma_pos_107restricted low
SA162258Plasma_pos_35restricted low
SA162259Plasma_pos_28restricted low
SA162260Plasma_pos_81restricted low
SA162261Plasma_pos_86restricted low
SA162262Plasma_pos_26restricted low
SA162263Plasma_pos_103restricted low
SA162264Plasma_pos_102restricted low
SA162265Plasma_pos_96restricted low
SA162266Plasma_pos_50restricted low
SA162267Plasma_pos_45restricted low
SA162268Plasma_pos_97restricted low
SA162269Plasma_pos_82restricted low
SA162270Plasma_pos_37restricted low
SA162271Plasma_pos_52restricted low
SA162272Plasma_pos_90restricted low
SA162273Plasma_pos_47restricted low
Showing results 1 to 95 of 95

Collection:

Collection ID:CO001793
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:TR001813
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:SP001806
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 AN002807
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 POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH002074
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:MS002602
Analysis ID:AN002807
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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