{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000040","ANALYSIS_ID":"AN000061","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Isotopic Ratio Outlier Analysis Global Metabolomics ofCaenorhabditis elegans","PROJECT_TYPE":"IROA labeling study","PROJECT_SUMMARY":"We demonstrate the global metabolic analysis ofCaenorhabditis elegansstress using a mass-spectrometry-based technique called isotopic ratio outlier (IROA). In an IROA protocol, control and experimental samples are isotopically with 95 and 5%13C, and the two sample populations are mixed together for extraction, sample preparation, and LC-MS analysis.To illustrate the utility of for global metabolomics, we exposed wild-type (N2) worms to a heat shock (30 heat shock at 33 C), which causes significant, widespread changes in We collected and analyzed material from the exometabolome (all material that release in the supernatant) and the endometabolome (homogenized total extracts the worm bodies).","INSTITUTE":"University of Florida","DEPARTMENT":"Biochemistry & Molecular Biology","LABORATORY":"Edison","LAST_NAME":"Edison","FIRST_NAME":"Arthur","ADDRESS":"R3-226 Academic Research Building, Department of Biochemistry & Molecular PO Box 100245, Gainesville, FL 32610-0245","EMAIL":"aedison@ufl.edu","PHONE":"(352) 392-4535"},

"STUDY":{"STUDY_TITLE":"Heatshock response of C. elegans using IROA (I)","STUDY_SUMMARY":"-","INSTITUTE":"University of Florida","DEPARTMENT":"Biochemistry & Molecular Biology","LABORATORY":"Edison","LAST_NAME":"Stupp","FIRST_NAME":"Gregory","ADDRESS":"-","EMAIL":"stuppie@ufl.edu","PHONE":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Caenorhabditis elegans","TAXONOMY_ID":"6239","GENOTYPE_STRAIN":"N2","AGE_OR_AGE_RANGE":"Young Adult","GENDER":"Hermaphrodite","SPECIES_GROUP":"Invertebrate"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Control_1P",
"Factors":{"Heat shock":"control","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_2P",
"Factors":{"Heat shock":"control","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_3P",
"Factors":{"Heat shock":"control","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_4P",
"Factors":{"Heat shock":"control","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_1S",
"Factors":{"Heat shock":"control","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_2S",
"Factors":{"Heat shock":"control","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_3S",
"Factors":{"Heat shock":"control","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Control_4S",
"Factors":{"Heat shock":"control","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_1P",
"Factors":{"Heat shock":"heat shock","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_2P",
"Factors":{"Heat shock":"heat shock","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_3P",
"Factors":{"Heat shock":"heat shock","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_4P",
"Factors":{"Heat shock":"heat shock","Metabolome":"endometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_1S",
"Factors":{"Heat shock":"heat shock","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_2S",
"Factors":{"Heat shock":"heat shock","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_3S",
"Factors":{"Heat shock":"heat shock","Metabolome":"exometabolome"}
},
{
"Subject ID":"-",
"Sample ID":"Test_4S",
"Factors":{"Heat shock":"heat shock","Metabolome":"exometabolome"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"whole young adult C. elegans Heat shock | supernatant Heat shock | whole young C. elegans Control | supernatant Control","COLLECTION_METHOD":"centrifugation | Filtration (0.2 micron) | centrifugation | Filtration (0.2","VOLUMEORAMOUNT_COLLECTED":"225,000 worms | 10 mL worm water | 250,000 worms | 10 mL worm water"},

"TREATMENT":{"TREATMENT_SUMMARY":"Heat Shock: Two successive synchronous generations of wild-type C. elegans (N2) grown in S-complete buffer at 22C containing 5% 13C-labeled E. coli. Upon the young adult stage, the population was washed from E. coli using standard and was divided into four replicates. Each replicate was treated with a 30 min shock at 33 °C followed by incubation at 22C for 1.5 hours. Control: Two synchronous generations of wild-type C. elegans (N2) were grown in S-complete at 22C containing 95% 13C-labeled E. coli. Upon reaching the young adult stage, population was washed from E. coli using standard procedures.","TREATMENT":"Abiotic","TREATMENT_DOSE":"30C | 22C","TREATMENT_DOSEDURATION":"30C for 30 minutes; 1.5 hours at 22 C before harvest | 22C for 30 minutes; 1.5 at 22 C before harvest","ANIMAL_ACCLIMATION_DURATION":"-"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Supernatant (endometabolome) was separated from worm pellets (exometabolome) by The supernatant was filtered, lyophilized, and resuspended in 100 ?L of LC-MS H2O. Worm pellet (endometabolome)was separated from supernatant (exometabolome) centrifugation. The worm pellets were homogenized using a Biospec in 80% methanol, dried under nitrogen and resuspended in 100 ?L of LC-MS grade","PROCESSING_METHOD":"filtration with 0.2 micron nitrocellulose, frozen at -80C, lyophilized and in 100 ?L of LC-MS grade H2O. homogenization with Biospec Mini-Beadbeater-8 in methanol, dried under nitrogen and resuspended in 100 ?L of LC-MS grade H2O."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Three microliters of each sample were injected onto a Thermo Scientific Gold aQ × 2.1 mm, 1.9 ?m) column using a column temperature of 40 °C and a flow rate 600 ?L/min with a gradient of solvent A (0.1% formic acid in water) and solvent (0.1% formic acid in acetonitrile) from 100% solvent A for 1 min followed by a gradient to 20% B in 6 min, a linear gradient to 60% B in 2 min, a linear to 95% B in 4 min, held for 2 min, and a 3.5 min return to the starting The inlet to the Orbitrap was held at a temperature of 320 °C, and the S-lens Level was set to 35%. The FR resolution was set to 70?000 at m/z 200. The achieved was routinely less than 1.5 ppm, externally calibrated.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Accela 1250","COLUMN_NAME":"Thermo Scientific Gold aQ","COLUMN_TEMPERATURE":"40 °C","FLOW_GRADIENT":"A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) 100% solvent A for 1 min followed by a linear gradient to 20% B in 6 min, a gradient to 60% B in 2 min, a linear gradient to 95% B in 4 min, held for 2 and a 3.5 min return to the starting composition","SAMPLE_INJECTION":"3 ?L","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"0.1% formic acid in acetonitrile","ANALYTICAL_TIME":"18.5 min"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","DETECTOR_TYPE":"Thermo Scientific Q-Exactive Orbitrap/negative mode"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Samples were analyzed using a mass range of m/z 70-800 in positive and negative mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass equipped with an Open Accela autosampler and an Accela 1250 pump (San Jose, The Q-Exactive was equipped with a heated electrospray ionization (HESI) which operated at a spray temperature of 500 °C, a spray voltage of 3 kV, and and auxiliary gas flow rates of 60 and 10 arbitrary units, respectively. were extracted from the ms data using proprietary MATLAB IROA scripts. Ratios each feature (heatshock/control) were calculated for each replicate. Ratios normalized by setting the median log-fold change for each sample to zero","ION_SOURCE_TEMPERATURE":"500 °C","ION_SPRAY_VOLTAGE":"3 kV","MASS_ACCURACY":"1.5 ppm","SCAN_RANGE_MOVERZ":"70-1000"},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"11-Hydroxy-9-tridecenoic acid","Control_1P":"339201.6484","Control_2P":"504973.3936","Control_3P":"","Control_4P":"165897.3491","Control_1S":"","Control_2S":"","Control_3S":"","Control_4S":"","Test_1P":"309810.6045","Test_2P":"483307.2451","Test_3P":"","Test_4P":"321916.4082","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"1_2_3-Trihydroxybenzene","Control_1P":"378189.1230","Control_2P":"378410.4971","Control_3P":"384413.5249","Control_4P":"381762.8032","Control_1S":"393061.9033","Control_2S":"1264505.2170","Control_3S":"815168.2207","Control_4S":"1156875.1410","Test_1P":"215636.2212","Test_2P":"279763.1318","Test_3P":"315428.3252","Test_4P":"233294.0669","Test_1S":"348555.5088","Test_2S":"983568.3403","Test_3S":"677916.5039","Test_4S":"934619.8281"},{"Metabolite":"1H-Indole-3-carboxaldehyde","Control_1P":"989408.5845","Control_2P":"319926.9697","Control_3P":"1500061.4430","Control_4P":"1415962.5820","Control_1S":"311312.6973","Control_2S":"2405830.1520","Control_3S":"2781788.3890","Control_4S":"2278872.4950","Test_1P":"919406.8374","Test_2P":"341832.5220","Test_3P":"1568323.9550","Test_4P":"1432334.1910","Test_1S":"263113.0166","Test_2S":"1960409.3590","Test_3S":"2384321.5830","Test_4S":"2178006.7900"},{"Metabolite":"1-Methylguanosine","Control_1P":"440428.3750","Control_2P":"844112.6709","Control_3P":"1205561.9320","Control_4P":"1139819.2480","Control_1S":"571613.3408","Control_2S":"1392718.9830","Control_3S":"733520.9531","Control_4S":"1243806.9870","Test_1P":"519222.7520","Test_2P":"1074880.9000","Test_3P":"1399166.1880","Test_4P":"1236468.2100","Test_1S":"423407.5781","Test_2S":"734101.2715","Test_3S":"469759.3047","Test_4S":"829147.7188"},{"Metabolite":"1-Methylinosine","Control_1P":"490831.2744","Control_2P":"1475397.9890","Control_3P":"1476884.7500","Control_4P":"1447647.0970","Control_1S":"223015.9082","Control_2S":"297434.9277","Control_3S":"880792.8979","Control_4S":"1001780.9150","Test_1P":"717392.1533","Test_2P":"1888720.6020","Test_3P":"1876708.2640","Test_4P":"1733120.4640","Test_1S":"182179.3984","Test_2S":"218257.8574","Test_3S":"601132.2988","Test_4S":"564850.6387"},{"Metabolite":"1-Pyrroline-2-carboxylic acid","Control_1P":"197617.1367","Control_2P":"613949.6719","Control_3P":"252620.2891","Control_4P":"","Control_1S":"","Control_2S":"","Control_3S":"25932.9121","Control_4S":"","Test_1P":"129848.4326","Test_2P":"918070.5938","Test_3P":"196777.1641","Test_4P":"","Test_1S":"","Test_2S":"","Test_3S":"58251.1074","Test_4S":""},{"Metabolite":"1-(sn-Glycero-3-phospho)-1D-myo-inositol","Control_1P":"1226957.1470","Control_2P":"748676.1758","Control_3P":"988090.3789","Control_4P":"1085601.8330","Control_1S":"","Control_2S":"43621.6201","Control_3S":"","Control_4S":"","Test_1P":"1866173.1900","Test_2P":"1278613.2720","Test_3P":"1432501.2640","Test_4P":"1508010.2920","Test_1S":"","Test_2S":"217556.9048","Test_3S":"","Test_4S":""},{"Metabolite":"2-Aminobenzoic acid","Control_1P":"","Control_2P":"519327.3037","Control_3P":"137560.8345","Control_4P":"85765.6406","Control_1S":"","Control_2S":"754781.6538","Control_3S":"260054.3433","Control_4S":"182930.2544","Test_1P":"","Test_2P":"","Test_3P":"","Test_4P":"","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"2-Aminomuconic acid","Control_1P":"","Control_2P":"","Control_3P":"308868.3857","Control_4P":"79343.5977","Control_1S":"","Control_2S":"","Control_3S":"593493.3804","Control_4S":"69691.0381","Test_1P":"","Test_2P":"264087.8105","Test_3P":"844309.4551","Test_4P":"262142.7432","Test_1S":"","Test_2S":"291110.9297","Test_3S":"940234.8584","Test_4S":"297807.9492"},{"Metabolite":"2-Furoic acid","Control_1P":"1296893.0390","Control_2P":"601622.1055","Control_3P":"1070121.4450","Control_4P":"","Control_1S":"1421439.9650","Control_2S":"669749.2617","Control_3S":"1407002.5450","Control_4S":"","Test_1P":"72403.7607","Test_2P":"","Test_3P":"","Test_4P":"132705.0781","Test_1S":"94984.6592","Test_2S":"","Test_3S":"","Test_4S":"128234.2832"},{"Metabolite":"(±)-2-Hydroxy-4-(methylthio)butanoic acid","Control_1P":"78337.4980","Control_2P":"1511772.0170","Control_3P":"548538.9600","Control_4P":"559744.2607","Control_1S":"","Control_2S":"","Control_3S":"","Control_4S":"","Test_1P":"29620.5894","Test_2P":"923209.1230","Test_3P":"281818.2549","Test_4P":"374752.8022","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"2-Hydroxyadipic acid","Control_1P":"","Control_2P":"527369.4141","Control_3P":"388623.0859","Control_4P":"980826.5391","Control_1S":"","Control_2S":"527706.6406","Control_3S":"431865.6914","Control_4S":"585819.8359","Test_1P":"","Test_2P":"158117.9863","Test_3P":"","Test_4P":"227146.3203","Test_1S":"","Test_2S":"373933.5840","Test_3S":"","Test_4S":"375566.8359"},{"Metabolite":"2-Isopropylmalic acid","Control_1P":"","Control_2P":"","Control_3P":"","Control_4P":"","Control_1S":"","Control_2S":"","Control_3S":"","Control_4S":"","Test_1P":"2678054.1100","Test_2P":"3587536.0080","Test_3P":"4307725.5860","Test_4P":"4132961.3820","Test_1S":"3782821.8860","Test_2S":"4505194.1630","Test_3S":"5321418.1540","Test_4S":"6305505.5290"},{"Metabolite":"2-Ketobutyric acid","Control_1P":"631153.6836","Control_2P":"287749.6680","Control_3P":"86683.2539","Control_4P":"","Control_1S":"777347.4023","Control_2S":"295527.1621","Control_3S":"134487.9219","Control_4S":"","Test_1P":"182620.7188","Test_2P":"329619.2744","Test_3P":"","Test_4P":"386417.9199","Test_1S":"170059.1563","Test_2S":"581082.3555","Test_3S":"","Test_4S":"562149.4570"},{"Metabolite":"2-Keto-glutaramic acid","Control_1P":"","Control_2P":"50515.4453","Control_3P":"224004.8086","Control_4P":"142485.1953","Control_1S":"","Control_2S":"148500.8457","Control_3S":"622840.3438","Control_4S":"178158.4844","Test_1P":"21301.7417","Test_2P":"22562.8511","Test_3P":"224382.6826","Test_4P":"47680.9658","Test_1S":"75393.3975","Test_2S":"52406.1362","Test_3S":"375796.9053","Test_4S":"103845.5195"},{"Metabolite":"2-(Methylthio)pyrazine","Control_1P":"649794.3203","Control_2P":"841259.9258","Control_3P":"271601.2031","Control_4P":"371073.6201","Control_1S":"","Control_2S":"","Control_3S":"","Control_4S":"","Test_1P":"1012036.1680","Test_2P":"1237532.9360","Test_3P":"710651.9844","Test_4P":"455193.8525","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"3-(2-Hydroxyphenyl)propanoic acid","Control_1P":"809045.1523","Control_2P":"17267114.6000","Control_3P":"7834535.1760","Control_4P":"7870261.4310","Control_1S":"782996.4941","Control_2S":"17267138.1700","Control_3S":"8030996.6470","Control_4S":"8314693.0920","Test_1P":"","Test_2P":"","Test_3P":"","Test_4P":"","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"3-Dehydrocarnitine","Control_1P":"81354.3174","Control_2P":"453426.7314","Control_3P":"232594.3398","Control_4P":"","Control_1S":"60215.8994","Control_2S":"294371.1929","Control_3S":"130793.3066","Control_4S":"","Test_1P":"912811.3926","Test_2P":"1178349.6770","Test_3P":"1273019.2890","Test_4P":"849966.0996","Test_1S":"414418.1899","Test_2S":"613691.2334","Test_3S":"563772.4443","Test_4S":"426060.3037"},{"Metabolite":"3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid","Control_1P":"697933.1523","Control_2P":"501341.0352","Control_3P":"813494.1484","Control_4P":"310642.1592","Control_1S":"845073.3652","Control_2S":"603334.1885","Control_3S":"974714.2217","Control_4S":"472482.2793","Test_1P":"1931668.7210","Test_2P":"2884103.4510","Test_3P":"4289566.9140","Test_4P":"3412158.8150","Test_1S":"1823097.2160","Test_2S":"2718362.2550","Test_3S":"3606516.3960","Test_4S":"3433237.1000"},{"Metabolite":"3-Hydroxy-2-methyl-[R-(R_S)]-butanoic acid","Control_1P":"","Control_2P":"275622.1680","Control_3P":"154041.0063","Control_4P":"96798.6963","Control_1S":"","Control_2S":"526125.3867","Control_3S":"434842.1660","Control_4S":"239417.4971","Test_1P":"448047.7407","Test_2P":"792288.9624","Test_3P":"775214.0132","Test_4P":"1114795.5010","Test_1S":"786436.5049","Test_2S":"1142166.5390","Test_3S":"982917.6055","Test_4S":"1484409.0220"},{"Metabolite":"3-Hydroxyanthranilic acid","Control_1P":"357300.3320","Control_2P":"804925.4609","Control_3P":"1203915.3490","Control_4P":"859915.1328","Control_1S":"367699.2529","Control_2S":"980470.6167","Control_3S":"1577723.0770","Control_4S":"1201534.7970","Test_1P":"","Test_2P":"","Test_3P":"","Test_4P":"","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"3-Hydroxyisoheptanoic acid","Control_1P":"","Control_2P":"","Control_3P":"","Control_4P":"","Control_1S":"","Control_2S":"","Control_3S":"","Control_4S":"","Test_1P":"","Test_2P":"963048.2622","Test_3P":"1025698.6800","Test_4P":"848315.1172","Test_1S":"","Test_2S":"544476.9438","Test_3S":"520983.6396","Test_4S":"450542.2495"},{"Metabolite":"3-Methyladenine","Control_1P":"416812.0146","Control_2P":"259195.5996","Control_3P":"899747.1641","Control_4P":"585897.0381","Control_1S":"408052.6563","Control_2S":"254309.2500","Control_3S":"841112.4580","Control_4S":"573503.6206","Test_1P":"","Test_2P":"","Test_3P":"","Test_4P":"","Test_1S":"","Test_2S":"","Test_3S":"","Test_4S":""},{"Metabolite":"3-Methylguanine","Control_1P":"191863.0103","Control_2P":"138823.8428","Control_3P":"325880.3262","Control_4P":"180510.2261","Control_1S":"75978.8398","Control_2S":"57163.8057","Control_3S":"134282.0273","Control_4S":"59628.7686","Test_1P":"","Test_2P":"153138.9941","Test_3P":"405311.9639","Test_4P":"181381.2256","Test_1S":"","Test_2S":"60965.5020","Test_3S":"202324.0469","Test_4S":"73859.8066"},{"Metabolite":"4-Hydroxy-2-oxoglutaric acid","Control_1P":"330949.1895","Control_2P":"235463.0762","Control_3P":"135483.1523","Control_4P":"","Control_1S":"96970.1016","Control_2S":"482457.9531","Control_3S":"260259.1230","Control_4S":"","Test_1P":"","Test_2P":"57308.2227","Test_3P":"81080.8086","Test_4P":"52520.2813","Test_1S":"","Test_2S":"119396.7148","Test_3S":"119054.7334","Test_4S":"134048.8125"},{"Metabolite":"4-Hydroxybenzoic acid","Control_1P":"279811.9795","Control_2P":"581693.2031","Control_3P":"941396.2808","Control_4P":"606334.2422","Control_1S":"1207856.7740","Control_2S":"3609557.7290","Control_3S":"5606718.5210","Control_4S":"4781209.3990","Test_1P":"662973.2256","Test_2P":"2072698.6170","Test_3P":"2367939.7450","Test_4P":"2167518.3690","Test_1S":"2390522.4630","Test_2S":"6032916.2850","Test_3S":"6438854.6310","Test_4S":"6412491.8920"},{"Metabolite":"4-Hydroxybutyric 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}

}