{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001724","ANALYSIS_ID":"AN002809","VERSION":"1","CREATED_ON":"March 17, 2021, 9:48 am"}, "PROJECT":{"PROJECT_TITLE":"The effects of birth weight and breeding value for protein deposition on the urine 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 urine 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"}, "STUDY":{"STUDY_TITLE":"The effects of birth weight and breeding value for protein deposition on the urine metabolome in growing pigs (part-III)","STUDY_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 urine 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","TOTAL_SUBJECTS":"40","NUM_MALES":"40","PUBLICATIONS":"The effects of birth weight and breeding value for protein deposition on nitrogen efficiency in growing pigs"}, "SUBJECT":{"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"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"QC", "Sample ID":"QC.1_1", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-1_neg_1.mzXML QC-1_pos_1.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.2_1", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-1_neg_2.mzXML QC-1_pos_2.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.3_1", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample 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"Factors":{"Diet":"restricted","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"-0.558","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_53.mzXML Urin_pos_53.mzXML"} }, { "Subject ID":"MM9325", "Sample ID":"54", "Factors":{"Diet":"adequate","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"0.882","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_54.mzXML Urin_pos_54.mzXML"} }, { "Subject ID":"MM9188", "Sample ID":"55", "Factors":{"Diet":"restricted","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"8.689","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_55.mzXML Urin_pos_55.mzXML"} }, { "Subject ID":"MM9310", "Sample ID":"56", "Factors":{"Diet":"adequate","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"16.944","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_56.mzXML Urin_pos_56.mzXML"} }, { "Subject ID":"MM9006", "Sample ID":"57", "Factors":{"Diet":"adequate","Wght_birth_cat":"high"}, 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data":{"Breedvalue_animal":"8.842","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_65.mzXML Urin_pos_65.mzXML"} }, { "Subject ID":"MM9315", "Sample ID":"66", "Factors":{"Diet":"restricted","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"0.82","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_66.mzXML Urin_pos_66.mzXML"} }, { "Subject ID":"MM9410", "Sample ID":"67", "Factors":{"Diet":"restricted","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"14.929","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_67.mzXML Urin_pos_67.mzXML"} }, { "Subject ID":"MM9305", "Sample ID":"68", "Factors":{"Diet":"restricted","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"12.996","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_68.mzXML Urin_pos_68.mzXML"} }, { "Subject ID":"MM9247", "Sample ID":"69", "Factors":{"Diet":"adequate","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"-12.409","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_69.mzXML Urin_pos_69.mzXML"} }, { "Subject ID":"MM9152", "Sample ID":"70", "Factors":{"Diet":"adequate","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"-2.114","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_70.mzXML Urin_pos_70.mzXML"} }, { "Subject ID":"MM9296", "Sample ID":"71", "Factors":{"Diet":"adequate","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"0.786","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_71.mzXML Urin_pos_71.mzXML"} }, { "Subject ID":"MM9295", "Sample ID":"72", "Factors":{"Diet":"restricted","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"-3.789","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_72.mzXML Urin_pos_72.mzXML"} }, { "Subject ID":"MM9266", "Sample ID":"73", "Factors":{"Diet":"restricted","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"7.079","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_73.mzXML Urin_pos_73.mzXML"} }, { "Subject ID":"MM9187", "Sample ID":"74", "Factors":{"Diet":"adequate","Wght_birth_cat":"high"}, "Additional sample data":{"Breedvalue_animal":"7.204","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_74.mzXML Urin_pos_74.mzXML"} }, { "Subject ID":"MM9031", "Sample ID":"75", "Factors":{"Diet":"adequate","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"8.422","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_75.mzXML Urin_pos_75.mzXML"} }, { "Subject ID":"MM9117", "Sample ID":"76", "Factors":{"Diet":"adequate","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"-2.702","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_76.mzXML Urin_pos_76.mzXML"} }, { "Subject ID":"MM9121", "Sample ID":"77", "Factors":{"Diet":"restricted","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"-1.224","Breedvalue_cat":"low","RAW_FILE_NAME":"Urin_neg_77.mzXML Urin_pos_77.mzXML"} }, { "Subject ID":"MM9177", "Sample ID":"78", "Factors":{"Diet":"restricted","Wght_birth_cat":"low"}, "Additional sample data":{"Breedvalue_animal":"5.137","Breedvalue_cat":"high","RAW_FILE_NAME":"Urin_neg_78.mzXML Urin_pos_78.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.1_4", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-4_neg_1.mzXML QC-4_pos_1.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.2_4", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-4_neg_2.mzXML QC-4_pos_2.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.3_4", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-4_neg_3.mzXML QC-4_pos_3.mzXML"} }, { "Subject ID":"QC", "Sample ID":"QC.4_4", "Factors":{"Diet":"QC","Wght_birth_cat":"QC"}, "Additional sample data":{"Breedvalue_animal":"QC","Breedvalue_cat":"QC","RAW_FILE_NAME":"QC-4_neg_4.mzXML QC-4_pos_4.mzXML"} } ], "COLLECTION":{"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_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."}, "SAMPLEPREP":{"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."}, "CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","FLOW_RATE":"0.4 ml/min","COLUMN_TEMPERATURE":"30","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"0.1% formic acid in acetonitrile"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Bruker Impact HD","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST001724_AN002809_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"} }