{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001848","ANALYSIS_ID":"AN002992","VERSION":"1","CREATED_ON":"June 28, 2021, 1:50 pm"},

"PROJECT":{"PROJECT_TITLE":"Untargeted mass spectrometry reveals impact of high fat diet on peripheral amino acid regulation in a mouse model of Alzheimer’s Disease","PROJECT_TYPE":"Untargeted Metabolomics analysis","PROJECT_SUMMARY":"Recent research regarding amino acid metabolism has shown that there may be a link between obesity and Alzheimer’s Disease (AD). This work reports a metabolomics study using untargeted mass spectrometry-based metabolomic strategies to investigate the metabolic changes that occur in AD and obesity. APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type litter mater controls were fed either a high-fat diet (HFD, 60% kcal from lard), low-fat diet (LFD, 10% kcal from lard) from 2 months of age, or reversal diet (REV, high-fat followed by low-fat from 9.5 months).","INSTITUTE":"Vanderbilt University","DEPARTMENT":"Chemistry","LABORATORY":"Center for Innovative Technology","LAST_NAME":"Codreanu","FIRST_NAME":"Simona","ADDRESS":"3009, Liberty Hills Drive","EMAIL":"SIMONA.CODREANU@VANDERBILT.EDU","PHONE":"6153477458"},

"STUDY":{"STUDY_TITLE":"Untargeted mass spectrometry reveals impact of high fat diet on peripheral amino acid regulation in a mouse model of Alzheimer’s Disease","STUDY_SUMMARY":"APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type litter mater controls were fed either a high-fat diet (HFD, 60% kcal from lard), low-fat diet (LFD, 10% kcal from lard) from 2 months of age, or reversal diet (REV, high-fat followed by low-fat from 9.5 months).","INSTITUTE":"Vanderbilt University","DEPARTMENT":"Chemistry","LABORATORY":"Center for Innovative Technology","LAST_NAME":"Codreanu","FIRST_NAME":"Simona","ADDRESS":"3009, Liberty Hills Drive","EMAIL":"SIMONA.CODREANU@VANDERBILT.EDU","NUM_GROUPS":"6","TOTAL_SUBJECTS":"36","NUM_MALES":"18","NUM_FEMALES":"18","STUDY_TYPE":"untargeted metabolomics analysis","PHONE":"6153477458"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"APPSwe/PS1ΔE9 (APP/PSEN1)","AGE_OR_AGE_RANGE":"12 month","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"958_S01",
"Sample ID":"S01",
"Factors":{"gender":"M","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_WT_958_S01"}
},
{
"Subject ID":"960_S02",
"Sample ID":"S02",
"Factors":{"gender":"M","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_WT_960_S02"}
},
{
"Subject ID":"907_S03",
"Sample ID":"S03",
"Factors":{"gender":"M","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_WT_907_S03"}
},
{
"Subject ID":"959_S04",
"Sample ID":"S04",
"Factors":{"gender":"M","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_APP_959_S04"}
},
{
"Subject ID":"904_S05",
"Sample ID":"S05",
"Factors":{"gender":"M","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_APP_904_S05"}
},
{
"Subject ID":"903_S06",
"Sample ID":"S06",
"Factors":{"gender":"M","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_LFD_APP_903_S06"}
},
{
"Subject ID":"1092_S07",
"Sample ID":"S07",
"Factors":{"gender":"M","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_WT_1092_S07"}
},
{
"Subject ID":"909_S08",
"Sample ID":"S08",
"Factors":{"gender":"M","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_WT_909_S08"}
},
{
"Subject ID":"908_S09",
"Sample ID":"S09",
"Factors":{"gender":"M","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_WT_908_S09"}
},
{
"Subject ID":"1091_S10",
"Sample ID":"S10",
"Factors":{"gender":"M","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_APP_1091_S10"}
},
{
"Subject ID":"1090_S11",
"Sample ID":"S11",
"Factors":{"gender":"M","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_APP_1090_S11"}
},
{
"Subject ID":"1162_S12",
"Sample ID":"S12",
"Factors":{"gender":"M","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_HFD_APP_1162_S12"}
},
{
"Subject ID":"695_S13",
"Sample ID":"S13",
"Factors":{"gender":"M","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_WT_695_S13"}
},
{
"Subject ID":"696_S14",
"Sample ID":"S14",
"Factors":{"gender":"M","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_WT_696_S14"}
},
{
"Subject ID":"983_S15",
"Sample ID":"S15",
"Factors":{"gender":"M","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_WT_983_S15"}
},
{
"Subject ID":"694_S16",
"Sample ID":"S16",
"Factors":{"gender":"M","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_APP_694_S16"}
},
{
"Subject ID":"697_S17",
"Sample ID":"S17",
"Factors":{"gender":"M","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_APP_697_S17"}
},
{
"Subject ID":"981_S18",
"Sample ID":"S18",
"Factors":{"gender":"M","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_M_REV_APP_981_S18"}
},
{
"Subject ID":"961_S19",
"Sample ID":"S19",
"Factors":{"gender":"F","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_WT_961_S19"}
},
{
"Subject ID":"962_S20",
"Sample ID":"S20",
"Factors":{"gender":"F","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_WT_962_S20"}
},
{
"Subject ID":"964_S21",
"Sample ID":"S21",
"Factors":{"gender":"F","genotype":"WT","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_WT_964_S21"}
},
{
"Subject ID":"963_S22",
"Sample ID":"S22",
"Factors":{"gender":"F","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_APP_963_S22"}
},
{
"Subject ID":"965_S23",
"Sample ID":"S23",
"Factors":{"gender":"F","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_APP_965_S23"}
},
{
"Subject ID":"984_S24",
"Sample ID":"S24",
"Factors":{"gender":"F","genotype":"APP","treatment":"LFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_LFD_APP_984_S24"}
},
{
"Subject ID":"749_S25",
"Sample ID":"S25",
"Factors":{"gender":"F","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_WT_749_S25"}
},
{
"Subject ID":"753_S26",
"Sample ID":"S26",
"Factors":{"gender":"F","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_WT_753_S26"}
},
{
"Subject ID":"1015_S27",
"Sample ID":"S27",
"Factors":{"gender":"F","genotype":"WT","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_WT_1015_S27"}
},
{
"Subject ID":"750_S28",
"Sample ID":"S28",
"Factors":{"gender":"F","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_APP_750_S28"}
},
{
"Subject ID":"751_S29",
"Sample ID":"S29",
"Factors":{"gender":"F","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_APP_751_S29"}
},
{
"Subject ID":"752_S30",
"Sample ID":"S30",
"Factors":{"gender":"F","genotype":"APP","treatment":"HFD"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_HFD_APP_752_S30"}
},
{
"Subject ID":"691_S31",
"Sample ID":"S31",
"Factors":{"gender":"F","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_WT_691_S31"}
},
{
"Subject ID":"692_S32",
"Sample ID":"S32",
"Factors":{"gender":"F","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_WT_692_S32"}
},
{
"Subject ID":"693_S33",
"Sample ID":"S33",
"Factors":{"gender":"F","genotype":"WT","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_WT_693_S33"}
},
{
"Subject ID":"954_S34",
"Sample ID":"S34",
"Factors":{"gender":"F","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_APP_954_S34"}
},
{
"Subject ID":"956_S35",
"Sample ID":"S35",
"Factors":{"gender":"F","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_APP_956_S35"}
},
{
"Subject ID":"877_S36",
"Sample ID":"S36",
"Factors":{"gender":"F","genotype":"APP","treatment":"REV"},
"Additional sample data":{"RAW_FILE_NAME":"SC_20190826_RPLCp_FMS_Liv_F_REV_APP_877_S36"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Liver samples from male and female APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice and wild-type (WT) littermates were collected after sacrifice at 12 months. These mice are a subset of mice for which behavioral and biochemical data have already been published, including weight change and diabetic state as assessed by glucose tolerance tests.After sacrifice, liver tissue samples were taken and put immediately on dry ice and stored at −80°C until used in the analytical workflow described herein.","SAMPLE_TYPE":"Liver","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Briefly, at 2-months of age, standard lab chow (Purina 5001, 4% kcal/fat) was replaced with either HFD in which 60% kcal are derived from lard, 20% from carbohydrate and 20% from protein, or low-fat diet (LFD) control in which 10% kcal are derived from lard and additional calories are derived from corn starch, with 70% from carbohydrates and 20% from protein.33 For the reversal group (REV), a subset of mice on the HFD was provided with a LFD, at 9.5 months of age, for the study duration.33 All other mice were maintained on their original experimental diets until the end of the study, which was an additional 10 weeks."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"For liver samples, frozen tissues were first individually pulverized using a mortar and pestle followed by lysing in 1 mL ice-cold lysis buffer ((1:1:2, ACN:MeOH:ammonium bicarbonate (0.1 M, pH 8.0) (LC-MS grade)). Individual samples were sonicated using a probe tip sonicator, 10 pulses, at 30% power, and cooled on ice between samples. A bicinchoninic acid (BCA) protein assay was used to determine the protein concentration for each individual sample and adjusted to a total amount of protein of 200 µg. For untargeted MS studies, SIL-ISs biotin-D2 and phenylalanine-D8 were added to each sample to assess sample processing steps (metabolite extraction and reconstitution). Following lysis and addition of SIL-ISs, protein precipitation was performed by adding 800 µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min. The supernatant containing metabolites were dried in vacuo and metabolite extracts were stored frozen at -80 °C until ready to use.","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"Following lysis and standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum.","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Hypersil Gold Hypersil Gold, 1.9 mm, 2.1 mm x 100 mm","FLOW_GRADIENT":"0.250","FLOW_RATE":"0.25 mL/min","COLUMN_TEMPERATURE":"40","SOLVENT_A":"100% water, 0.1% Formic Acid","SOLVENT_B":"100% acetonitrile, 0.1% Formic Acid","INJECTION_TEMPERATURE":"8","SAMPLE_INJECTION":"5"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"XCalibur software for data acquisition Progenesis QI 2.0 for data processing","MS_RESULTS_FILE":"ST001848_AN002992_Results.txt UNITS:time_m/z Has m/z:Yes Has RT:Yes RT units:Minutes"}

}