{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000784","ANALYSIS_ID":"AN001240","VERSION":"1","CREATED_ON":"July 6, 2017, 1:53 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics study of Prostate cancer for African American","PROJECT_TYPE":"MS quantitative analysis","PROJECT_SUMMARY":"Quantitative metabolomics studies on tissues, serum and urine of prostate cancer for African American.","INSTITUTE":"Baylor College of Medicine","LAST_NAME":"Sreekumar","FIRST_NAME":"Arun","ADDRESS":"One Baylor Plaza, Houston, TX, 77030, USA","EMAIL":"Arun.Sreekumar@bcm.edu","PHONE":"713-798-3305"},

"STUDY":{"STUDY_TITLE":"metabolome in a group of AA and EA matched pairs of prostate cancer (PCa) and benign adjacent tissues","STUDY_SUMMARY":"10 µL of suspended samples was injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM) of a total of 240 endogenous water soluble metabolites for steady-state analyses of samples. Those 240 compounds monitored were chosen due to their involvement in central pathways important in a number of malignancies. Source parameters were as follows: Gas temperature was 250 °C; Gas flow was 14 l/min; Nebulizer was 20psi; Sheath gas temperature was 350 °C; Sheath gas flow was 12 l/min; Capillary was 3000 V positive and 3000 V negative; Nozzle voltage was 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. Samples were delivered to the MS via normal phase chromatography using either a 4.6 mm i.d ×10 cm Amide XBridge HILIC column (Waters) or a Luna 3µ NH2 100A (Phenomenex) at 300 µL/min","INSTITUTE":"Baylor College of Medicine","LAST_NAME":"Sreekumar","FIRST_NAME":"Arun","ADDRESS":"One Baylor Plaza, Houston, TX, 77030, USA","EMAIL":"Arun.Sreekumar@bcm.edu","PHONE":"713-798-3305"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"1",
"Sample ID":"3609",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"1",
"Sample ID":"3608",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"2",
"Sample ID":"5050",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"2",
"Sample ID":"5057",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"4",
"Sample ID":"8678",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"4",
"Sample ID":"8680",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"7",
"Sample ID":"10188",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"7",
"Sample ID":"10184",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"9",
"Sample ID":"10506",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"9",
"Sample ID":"10512",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"10",
"Sample ID":"10524",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"10",
"Sample ID":"10526",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"14",
"Sample ID":"18476",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"14",
"Sample ID":"18473",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"15",
"Sample ID":"19051",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"15",
"Sample ID":"19053",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"16",
"Sample ID":"19205",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"16",
"Sample ID":"19204",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"17",
"Sample ID":"19338",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"17",
"Sample ID":"19337",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"18",
"Sample ID":"21274",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"18",
"Sample ID":"21275",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"19",
"Sample ID":"22346",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"19",
"Sample ID":"22343",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"20",
"Sample ID":"22693",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"20",
"Sample ID":"22694",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"21",
"Sample ID":"23979",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"21",
"Sample ID":"23977",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"24",
"Sample ID":"31703",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"24",
"Sample ID":"31708",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"25",
"Sample ID":"32567",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"25",
"Sample ID":"32564",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"26",
"Sample ID":"32595",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"26",
"Sample ID":"32594",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"29",
"Sample ID":"32871",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"29",
"Sample ID":"32870",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"30",
"Sample ID":"36673",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"30",
"Sample ID":"36668",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"33",
"Sample ID":"36916",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"33",
"Sample ID":"36914",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"34",
"Sample ID":"37654",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"34",
"Sample ID":"37653",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"35",
"Sample ID":"37687",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"35",
"Sample ID":"37689",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"37",
"Sample ID":"37976",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"37",
"Sample ID":"37977",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"42",
"Sample ID":"42957",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"42",
"Sample ID":"42955",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"43",
"Sample ID":"43779",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"43",
"Sample ID":"43782",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"46",
"Sample ID":"47605",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"46",
"Sample ID":"47603",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"48",
"Sample ID":"50742",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"48",
"Sample ID":"50739",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"49",
"Sample ID":"52012",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"49",
"Sample ID":"52014",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"50",
"Sample ID":"53131",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"50",
"Sample ID":"53132",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"51",
"Sample ID":"53247",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"51",
"Sample ID":"53248",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"55",
"Sample ID":"53983",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"55",
"Sample ID":"53984",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"56",
"Sample ID":"54182",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"56",
"Sample ID":"54184",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"69",
"Sample ID":"59701",
"Factors":{"Diagnosis":"Benign","Race":"AA"}
},
{
"Subject ID":"69",
"Sample ID":"59703",
"Factors":{"Diagnosis":"Cancer","Race":"AA"}
},
{
"Subject ID":"88",
"Sample ID":"17626",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"88",
"Sample ID":"17627",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"89",
"Sample ID":"17637",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"89",
"Sample ID":"17643",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"94",
"Sample ID":"19567",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"94",
"Sample ID":"19564",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"103",
"Sample ID":"23868",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"103",
"Sample ID":"23870",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"104",
"Sample ID":"24070",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"104",
"Sample ID":"24068",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"106",
"Sample ID":"39907",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"106",
"Sample ID":"25794",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"107",
"Sample ID":"25793",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"107",
"Sample ID":"25922",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"108",
"Sample ID":"25923",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"108",
"Sample ID":"25945",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"109",
"Sample ID":"25944",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"109",
"Sample ID":"26084",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"110",
"Sample ID":"26163",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"110",
"Sample ID":"26166",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"113",
"Sample ID":"31630",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"113",
"Sample ID":"36357",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"114",
"Sample ID":"39117",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"114",
"Sample ID":"39116",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
},
{
"Subject ID":"115",
"Sample ID":"36361",
"Factors":{"Diagnosis":"Benign","Race":"EA"}
},
{
"Subject ID":"115",
"Sample ID":"39910",
"Factors":{"Diagnosis":"Cancer","Race":"EA"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Frozen pathologically-verified prostate tissues were collected and stored at -140°C until analysis"},

"TREATMENT":{"TREATMENT_SUMMARY":"NA"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"For extraction of metabolome, 10 mg of tissue was homogenized in 1:4 ice cold water:methanol mixture containing equimolar mixture of 11 standard compounds [Epibrassinolide, [D3] Testosterone (mass difference from endogenous Testosterone = 3 Da), [15N] Anthranilic acid (mass difference from endogenous Anthranilic acid =1 Da), Zeatine, Jasmonic acid, Gibberelic acid, [D4] Estrone (mass difference from endogenous Estrone =4 Da), [15N]-Tryptophan (mass difference from endogenous Tryptophan =1 Da), [D4] Thymine (mass difference from endogenous Thymine =4 Da), [13C] Creatinine (mass difference from endogenous Creatinine =1 Da) and [15N] Arginine (mass difference from endogenous Arginine =1 Da)]. This was followed by sequential addition of ice cold chloroform and water in 3:1 ratio and separation of the organic (methanol and chloroform) and aqueous solvents (water:methanol:chloroform:water; ratio 1:4:3:1). The aqueous extract was de-proteinized using a 3 KDa molecular filter (Amicon Ultracel -3K Membrane, Millipore Corporation, Billerica, MA) and the filtrate containing metabolites was dried under vacuum (Genevac EZ-2plus, Gardiner, NY). Prior to mass spectrometry, the dried extract was resuspended in identical volume of injection solvent composed of water:methanol (50:50) and subjected to liquid chromatography (LC) mass spectrometry."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Flow rate was 0.3ml/min. Gradients were run starting from 85% buffer B (0.1% formic acid in acetonitrile) to 35% B from 0–3.5 minutes; 35% B to 2% B from 3.5–11.5 minutes; 2% B was held from 11.5–16.5 minutes; 2% B to 85% B from 16.5–17.5 minutes; 85% B was held for 7 minutes to re-equilibrate the column.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters XBridge Amide (100 x 4.6mm, 3.5um)","FLOW_RATE":"0.3ml/min","SOLVENT_A":"0.1% formic acid in HPLC grade water","SOLVENT_B":"0.1% formic acid in HPLC grade acetonitrile"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6490A QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"log transform with internal standard normalization",

"Data":[{"Metabolite":"Nicotinamide adenine 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Ions":"129/84.1"},{"Metabolite":"3-Hydroxykynurenine","Kegg ID":"C02794","Retention Time(min)":"6.5","Precursor Ion":"225.087","Product Ions":"162.1"},{"Metabolite":"Octanoylcarnitine","Kegg ID":"C02838","Retention Time(min)":"4.3","Precursor Ion":"288.2","Product Ions":"85/57.1"},{"Metabolite":"Butyrylcarnitine","Kegg ID":"C02862","Retention Time(min)":"4.3","Precursor Ion":"232.1543","Product Ions":"173/85"},{"Metabolite":"1-Methylnicotinamide","Kegg ID":"C02918","Retention Time(min)":"5.7","Precursor Ion":"138.08","Product Ions":"95.1/79.1"},{"Metabolite":"4-Acetamidobutanoate","Kegg ID":"C02946","Retention Time(min)":"5.2","Precursor Ion":"146.08","Product Ions":"86.1"},{"Metabolite":"Argininosuccinate","Kegg ID":"C03406","Retention Time(min)":"5.5","Precursor Ion":"291.1299","Product Ions":"70"},{"Metabolite":"S-ribosyl-L-homocysteine","Kegg ID":"C03539","Retention Time(min)":"6.6","Precursor Ion":"268.0849","Product Ions":"88"},{"Metabolite":"Dimethylarginine","Kegg 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}

}