{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002152","ANALYSIS_ID":"AN003525","VERSION":"1","CREATED_ON":"April 25, 2022, 9:33 am"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics analysis of mouse liver with or without SIRT5 deficiency","PROJECT_SUMMARY":"Lysine succinylation is a post-translational modification that has been implicated in the regulation of various metabolic pathways. However, the biological relevance of lysine succinylation remains largely uncertain due to methodological difficulties in determining high-impact succinylation sites. In the present study, multiple high stoichiometry lysine sites were identified in argininosuccinate synthase (ASS1), a key enzyme in urea cycle, are regulated by SIRT5. Metabolomics profiling confirms that SIRT5 deficiency decreases urea cycle activity in liver. Importantly, SIRT5 deficiency compromises ammonia tolerance, and reduces locomotor and exploratory activity in male mice upon high-ammonium diet (HAD) feeding. Therefore, lysine succinylation plays a functionally important role in ammonia metabolism.","INSTITUTE":"North Carolina State University","LAST_NAME":"Liu","FIRST_NAME":"Xiaojing","ADDRESS":"Polk Hall, RM 128","EMAIL":"xliu68@ncsu.edu","PHONE":"9195154387"},

"STUDY":{"STUDY_TITLE":"Metabolomics analysis of mouse liver with or without SIRT5 deficiency","STUDY_SUMMARY":"8 Wild-type (WT) and 8 Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were put on euthanized. Liver metabolites were extracted (5-10 mg) were extracted using 80% methanol/water as the extraction solvent. Metabolite extract was split into two tubes (one for polar metabolite analysis and the other one for acyl-CoA analysis), and then extraction solvent was evaporated using a speed vacuum concentrator. Dry pellets were stored in −80 °C freezer until ready for LC-MS analysis. For acyl-CoA analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate) per 6 mg tissue, and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v/v) per 3 mg tissue, and 3 μL was injected into the LC-MS.","INSTITUTE":"North Carolina State University","LAST_NAME":"Liu","FIRST_NAME":"Xiaojing","ADDRESS":"Polk Hall, RM 128","EMAIL":"xliu68@ncsu.edu","PHONE":"9195154387"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WT_1.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_2.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_3.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_4.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_5.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_6.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_7.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_8.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_1.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_2.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_3.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_4.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_5.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_6.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_7.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_8.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_1_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_1_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_2_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_2_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_3_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_3_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_4_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_4_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_5_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_5_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_6_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_6_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_7_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_7_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"WT_8_luna.raw",
"Factors":{"Sample Source":"Wild type"},
"Additional sample data":{"RAW_FILE_NAME":"WT_8_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_1_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_1_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_2_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_2_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_3_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_3_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_4_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_4_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_5_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_5_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_6_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_6_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_7_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_7_luna.raw"}
},
{
"Subject ID":"-",
"Sample ID":"KO_8_luna.raw",
"Factors":{"Sample Source":"SIRT5 knockout"},
"Additional sample data":{"RAW_FILE_NAME":"KO_8_luna.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Wild-type (WT) and Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were euthanized. Metabolites extracted from eight WT and eight Sirt5-/- mouse livers were analyzed by LC/MS. Intracellular metabolites and acyl-CoA from cells were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS.","SAMPLE_TYPE":"Liver"},

"TREATMENT":{"TREATMENT_SUMMARY":"Eight Wild-type (WT) and eight Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were euthanized. Mice had free access to food and water. Mouse body weight and food intake were monitored weekly."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Intracellular metabolites and acyl-CoA from mouse liver tissues were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"RPLC is for acyl-CoA and folate analysis.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Phenomenex Luna C18 (100 × 2.0 mm i.d., 3 μm)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"It was operated in the full-scan mode with a scan range of 150-1000 and the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch."},

"MS_METABOLITE_DATA":{
"Units":"ion counts",

"Data":[{"Metabolite":"Acetyl-CoA","WT_1_luna.raw":"60110.88995","WT_2_luna.raw":"87972.99815","WT_3_luna.raw":"110622.0071","WT_4_luna.raw":"37399.20485","WT_5_luna.raw":"75816.21825","WT_6_luna.raw":"78570.0305","WT_7_luna.raw":"156827.3572","WT_8_luna.raw":"115046.2322","KO_1_luna.raw":"104438.7855","KO_2_luna.raw":"130904.9864","KO_3_luna.raw":"123934.5468","KO_4_luna.raw":"92897.0235","KO_5_luna.raw":"67066.5548","KO_6_luna.raw":"251610.2753","KO_7_luna.raw":"219695.2732","KO_8_luna.raw":"102788.2088"},{"Metabolite":"Propanoyl-CoA","WT_1_luna.raw":"251192.5407","WT_2_luna.raw":"283657.4577","WT_3_luna.raw":"253898.3242","WT_4_luna.raw":"101890.3948","WT_5_luna.raw":"133475.949","WT_6_luna.raw":"154573.6164","WT_7_luna.raw":"292786.3928","WT_8_luna.raw":"258224.2054","KO_1_luna.raw":"200020.6025","KO_2_luna.raw":"188000.6967","KO_3_luna.raw":"264500.5872","KO_4_luna.raw":"242075.2135","KO_5_luna.raw":"183436.3836","KO_6_luna.raw":"145768.7216","KO_7_luna.raw":"85540.8074","KO_8_luna.raw":"207760.3752"},{"Metabolite":"Isobutyryl-CoA/Butyryl-CoA","WT_1_luna.raw":"11941.9782","WT_2_luna.raw":"37821.66515","WT_3_luna.raw":"43479.0201","WT_4_luna.raw":"20377.35695","WT_5_luna.raw":"34550.6236","WT_6_luna.raw":"29185.351","WT_7_luna.raw":"42086.1707","WT_8_luna.raw":"29323.8693","KO_1_luna.raw":"50594.36105","KO_2_luna.raw":"43762.79465","KO_3_luna.raw":"58589.78335","KO_4_luna.raw":"55996.721","KO_5_luna.raw":"49055.6859","KO_6_luna.raw":"92704.46725","KO_7_luna.raw":"86392.8519","KO_8_luna.raw":"99891.3808"},{"Metabolite":"Isovaleryl-CoA","WT_1_luna.raw":"33222.75845","WT_2_luna.raw":"54679.67005","WT_3_luna.raw":"44423.5976","WT_4_luna.raw":"39923.7524","WT_5_luna.raw":"41694.1866","WT_6_luna.raw":"36181.04285","WT_7_luna.raw":"42937.72975","WT_8_luna.raw":"25542.5475","KO_1_luna.raw":"38585.7297","KO_2_luna.raw":"42479.1005","KO_3_luna.raw":"40560.83205","KO_4_luna.raw":"43673.65815","KO_5_luna.raw":"27393.3082","KO_6_luna.raw":"46809.3263","KO_7_luna.raw":"46635.5004","KO_8_luna.raw":"67010.5233"},{"Metabolite":"Malonyl-CoA","WT_1_luna.raw":"2528.29315","WT_2_luna.raw":"3855.25895","WT_3_luna.raw":"4187.3277","WT_4_luna.raw":"1933.6341","WT_5_luna.raw":"2560.2491","WT_6_luna.raw":"2548.18855","WT_7_luna.raw":"2927.1663","WT_8_luna.raw":"2285.0596","KO_1_luna.raw":"2666.6056","KO_2_luna.raw":"989.93955","KO_3_luna.raw":"3630.84185","KO_4_luna.raw":"1056.2954","KO_5_luna.raw":"2810.6483","KO_6_luna.raw":"1174.13875","KO_7_luna.raw":"2039.4582","KO_8_luna.raw":"2908.1493"},{"Metabolite":"Succinyl-CoA","WT_1_luna.raw":"31740.4901","WT_2_luna.raw":"55764.61935","WT_3_luna.raw":"76203.88735","WT_4_luna.raw":"23176.69425","WT_5_luna.raw":"29296.37395","WT_6_luna.raw":"24085.9651","WT_7_luna.raw":"61805.0599","WT_8_luna.raw":"46364.92425","KO_1_luna.raw":"53245.54955","KO_2_luna.raw":"35899.35665","KO_3_luna.raw":"85962.7104","KO_4_luna.raw":"56693.14985","KO_5_luna.raw":"60097.67395","KO_6_luna.raw":"50155.34165","KO_7_luna.raw":"26213.9267","KO_8_luna.raw":"42139.2575"},{"Metabolite":"3-Hydroxyisovaleryl-CoA","WT_1_luna.raw":"117876.3706","WT_2_luna.raw":"98103.7607","WT_3_luna.raw":"63191.7958","WT_4_luna.raw":"24590.3491","WT_5_luna.raw":"45880.3207","WT_6_luna.raw":"31299.70505","WT_7_luna.raw":"44704.98895","WT_8_luna.raw":"10304.00595","KO_1_luna.raw":"73189.79505","KO_2_luna.raw":"19482.3833","KO_3_luna.raw":"36948.4766","KO_4_luna.raw":"34365.8971","KO_5_luna.raw":"26709.3477","KO_6_luna.raw":"17816.378","KO_7_luna.raw":"17799.3722","KO_8_luna.raw":"20351.6531"},{"Metabolite":"3-Hydroxyisobutyryl-CoA /3-Hydroxybutanoyl-CoA","WT_1_luna.raw":"18285.51715","WT_2_luna.raw":"18131.53285","WT_3_luna.raw":"19326.9032","WT_4_luna.raw":"10041.6199","WT_5_luna.raw":"9916.16645","WT_6_luna.raw":"9959.8095","WT_7_luna.raw":"15933.85745","WT_8_luna.raw":"9946.73015","KO_1_luna.raw":"21614.9482","KO_2_luna.raw":"18715.3517","KO_3_luna.raw":"16633.98025","KO_4_luna.raw":"13312.7388","KO_5_luna.raw":"12756.83335","KO_6_luna.raw":"24828.57025","KO_7_luna.raw":"10391.93845","KO_8_luna.raw":"11054.8804"},{"Metabolite":"Hexanoyl-CoA","WT_1_luna.raw":"3561.0412","WT_2_luna.raw":"8197.4813","WT_3_luna.raw":"14828.47585","WT_4_luna.raw":"3229.6589","WT_5_luna.raw":"7071.01285","WT_6_luna.raw":"7215.457","WT_7_luna.raw":"9311.64455","WT_8_luna.raw":"5278.8773","KO_1_luna.raw":"12793.9914","KO_2_luna.raw":"10674.4332","KO_3_luna.raw":"16103.1197","KO_4_luna.raw":"11249.9561","KO_5_luna.raw":"11053.43775","KO_6_luna.raw":"17611.8319","KO_7_luna.raw":"15641.63225","KO_8_luna.raw":"16511.1291"},{"Metabolite":"3-Oxo-methylisocapryloyl-CoA","WT_1_luna.raw":"11780.84755","WT_2_luna.raw":"22876.63855","WT_3_luna.raw":"20704.63355","WT_4_luna.raw":"16323.68395","WT_5_luna.raw":"10821.3739","WT_6_luna.raw":"6279.5153","WT_7_luna.raw":"16777.2449","WT_8_luna.raw":"6000.6913","KO_1_luna.raw":"7629.7073","KO_2_luna.raw":"10659.2073","KO_3_luna.raw":"15341.5077","KO_4_luna.raw":"10629.09675","KO_5_luna.raw":"6959.9283","KO_6_luna.raw":"10945.1816","KO_7_luna.raw":"8809.1672","KO_8_luna.raw":"8670.42605"},{"Metabolite":"5-Methyltetrahydrofolate","WT_1_luna.raw":"40721.24345","WT_2_luna.raw":"22611.43605","WT_3_luna.raw":"39310.49365","WT_4_luna.raw":"27816.7478","WT_5_luna.raw":"22547.6069","WT_6_luna.raw":"21778.4088","WT_7_luna.raw":"18314.1022","WT_8_luna.raw":"18251.86415","KO_1_luna.raw":"29511.5549","KO_2_luna.raw":"18725.8126","KO_3_luna.raw":"30533.68945","KO_4_luna.raw":"20498.54695","KO_5_luna.raw":"19657.90125","KO_6_luna.raw":"21088.06265","KO_7_luna.raw":"11793.45055","KO_8_luna.raw":"23208.9292"}],

"Metabolites":[{"Metabolite":"Acetyl-CoA","Chemical formula":"C23H38N7O17P3S"},{"Metabolite":"Propanoyl-CoA","Chemical formula":"C24H40N7O17P3S"},{"Metabolite":"Isobutyryl-CoA/Butyryl-CoA","Chemical formula":"C25H42N7O17P3S"},{"Metabolite":"Isovaleryl-CoA","Chemical formula":"C26H44N7O17P3S"},{"Metabolite":"Malonyl-CoA","Chemical formula":"C24H38N7O19P3S"},{"Metabolite":"Succinyl-CoA","Chemical formula":"C25H40N7O19P3S"},{"Metabolite":"3-Hydroxyisovaleryl-CoA","Chemical formula":"C26H44N7O18P3S"},{"Metabolite":"3-Hydroxyisobutyryl-CoA /3-Hydroxybutanoyl-CoA","Chemical formula":"C25H42N7O18P3S"},{"Metabolite":"Hexanoyl-CoA","Chemical formula":"C27H46N7O17P3S"},{"Metabolite":"3-Oxo-methylisocapryloyl-CoA","Chemical formula":"C30H50N7O18P3S"},{"Metabolite":"5-Methyltetrahydrofolate","Chemical formula":"C20H25N7O6"}]
}

}