{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000242","ANALYSIS_ID":"AN000378","VERSION":"1","CREATED_ON":"2016-09-17"},
"PROJECT":{"PROJECT_TITLE":"Metabolimic Analysis of Conditioned Macrophage Media","PROJECT_TYPE":"Untargeted LC-MS Metabolomics","PROJECT_SUMMARY":"We are studying the secreted components from pro-inflammatory macrophages, M1. We use a macrophage at the opposite end of the macrophage phenotype as a control, the anti-inflammatory macrophage, coined M2. M1 macrophage media has a <3 kD factor that reduces survival of a cell of interest in primary This factor is not present in M2 macrophage conditioned media <3 kD, as there no effect on primary cell numbers. The goal of this project is to analyze the present in the M1 conditioned <3 kD media and compare to the M2 conditioned < media.","INSTITUTE":"Mayo Clinic","DEPARTMENT":"Physiology and Biomedical Engineering","LAST_NAME":"Farrugia","FIRST_NAME":"Gianrico","ADDRESS":"200 First Street SW, Rochester, MN 55905","EMAIL":"Dasari.Surendra@mayo.edu","PHONE":"507-284-0513"},
"STUDY":{"STUDY_TITLE":"Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole medium","STUDY_TYPE":"differential metabolomics","STUDY_SUMMARY":"Media was flash frozen with N2 and stored at -80 C. Samples can be stored at C until use. ~1 ml aliquots. The following media has been provided to the core in biological triplicates.Complete (Whole) Media:1) Whole unconditioned (Defined culture media, M199)2) Whole M1 medium3) Whole M2 medium","INSTITUTE":"Mayo Clinic","DEPARTMENT":"Physiology and Biomedical Engineering","LAST_NAME":"Farrugia","FIRST_NAME":"Gianrico","ADDRESS":"-","EMAIL":"Dasari.Surendra@mayo.edu","PHONE":"-","NUM_GROUPS":"1"},
"SUBJECT":{"SUBJECT_TYPE":"Human macrophages","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"2",
"Sample ID":"ms5047-2-1",
"Factors":{"Sample Status":"Whole M1 medium"}
},
{
"Subject ID":"2",
"Sample ID":"ms5047-2-2",
"Factors":{"Sample Status":"Whole M1 medium"}
},
{
"Subject ID":"2",
"Sample ID":"ms5047-2-3",
"Factors":{"Sample Status":"Whole M1 medium"}
},
{
"Subject ID":"3",
"Sample ID":"ms5047-3-1",
"Factors":{"Sample Status":"Whole M2 medium"}
},
{
"Subject ID":"3",
"Sample ID":"ms5047-3-2",
"Factors":{"Sample Status":"Whole M2 medium"}
},
{
"Subject ID":"3",
"Sample ID":"ms5047-3-3",
"Factors":{"Sample Status":"Whole M2 medium"}
},
{
"Subject ID":"1",
"Sample ID":"ms5047-1-1",
"Factors":{"Sample Status":"Whole unconditioned medium (Defined culture media, M199)"}
},
{
"Subject ID":"1",
"Sample ID":"ms5047-1-2",
"Factors":{"Sample Status":"Whole unconditioned medium (Defined culture media, M199)"}
},
{
"Subject ID":"1",
"Sample ID":"ms5047-1-3",
"Factors":{"Sample Status":"Whole unconditioned medium (Defined culture media, M199)"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Whole media","SAMPLE_TYPE":"Media"},
"TREATMENT":{"TREATMENT_SUMMARY":"Media was flash frozen with N2 and stored at -80 C. Samples can be stored -80 C until use. ~1 ml aliquots. The following media has been provided to metabolomics core in biological triplicates. Complete (Whole) Media: 1) unconditioned macrophage medium (Defined culture media, M199) 2) Whole M1 medium 3) Whole M2 macrophage medium"},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Quality-control samples used in the study were prepared from pooled samples with a selection of standards. All samples (200 μL) were thawed on ice at 4°C by deproteinization with methanol (1:4 ratio of plasma to methanol) and for 10 s, followed by incubation at −20°C for 2 h. The samples were then at 15,871g for 30 min at 4°C. The supernatants were lyophilized (Savant, NY) and stored at −20°C prior to analysis. The samples were reconstituted in H2O/acetonitrile and passed through a Microcon YM3 filter (Millipore The supernatants were transferred to analytical vials, stored in the at 4°C, and analyzed within 48 h of reconstitution in buffer."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"C18","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"high-strength silica 2.1 150 mm, 1.8 m; Waters","CHROMATOGRAPHY_COMMENTS":"Metabolite separation was achieved using an Acquity UPLC system (Waters, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and min, 100% B. The injection volume of each sample was 5 L and column was at 50C."},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Agilent 6220 TOF","INSTRUMENT_TYPE":"TOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"HILIC-NESI (-ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both and negative electrospray ionization (ESI) modes using a scan range of m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and ppm, respectively. The instrument settings were as follows: nebulizer gas 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run 15.0 min."},
"MS_METABOLITE_DATA":{
"Units":"Peak area",
"Data":[{"Metabolite":"1-Hydroxy-2-naphthoic acid","ms5047-2-1":"14.9905","ms5047-2-2":"15.8698","ms5047-2-3":"14.4234","ms5047-3-1":"14.1172","ms5047-3-2":"8.6375","ms5047-3-3":"14.0731","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"2^-Deoxyuridine","ms5047-2-1":"14.2698","ms5047-2-2":"14.0351","ms5047-2-3":"8.6692","ms5047-3-1":"15.7710","ms5047-3-2":"14.2820","ms5047-3-3":"15.1798","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"3_3^-Dichloro-4_4^-diaminodiphenyl ether","ms5047-2-1":"16.2645","ms5047-2-2":"16.5139","ms5047-2-3":"16.1155","ms5047-3-1":"16.5005","ms5047-3-2":"15.3178","ms5047-3-3":"16.2620","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"3_5-Dinitroguaiacol","ms5047-2-1":"4.3290","ms5047-2-2":"0.0000","ms5047-2-3":"0.0000","ms5047-3-1":"0.0000","ms5047-3-2":"4.3527","ms5047-3-3":"0.0000","ms5047-1-1":"14.0904","ms5047-1-2":"13.8754","ms5047-1-3":"9.6653"},{"Metabolite":"4-Acetamido-2-amino-6-nitrotoluene","ms5047-2-1":"4.3830","ms5047-2-2":"4.3248","ms5047-2-3":"0.0000","ms5047-3-1":"7.8703","ms5047-3-2":"11.6211","ms5047-3-3":"8.3402","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"4-Bromophenylthiourea","ms5047-2-1":"18.3467","ms5047-2-2":"18.5571","ms5047-2-3":"12.2280","ms5047-3-1":"0.0000","ms5047-3-2":"0.0000","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"4-Hydroxybenzaldehyde","ms5047-2-1":"15.5274","ms5047-2-2":"10.3444","ms5047-2-3":"14.9791","ms5047-3-1":"4.6972","ms5047-3-2":"15.4330","ms5047-3-3":"15.5160","ms5047-1-1":"16.7106","ms5047-1-2":"17.2710","ms5047-1-3":"16.8540"},{"Metabolite":"Acyclovir","ms5047-2-1":"11.4211","ms5047-2-2":"5.6062","ms5047-2-3":"10.7000","ms5047-3-1":"0.0000","ms5047-3-2":"16.5286","ms5047-3-3":"5.5764","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Camoensine","ms5047-2-1":"17.8896","ms5047-2-2":"17.5241","ms5047-2-3":"15.9600","ms5047-3-1":"18.1888","ms5047-3-2":"16.8938","ms5047-3-3":"13.8565","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Cefuroxime","ms5047-2-1":"16.8466","ms5047-2-2":"15.6369","ms5047-2-3":"15.2519","ms5047-3-1":"16.0274","ms5047-3-2":"15.7150","ms5047-3-3":"4.6949","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Chondroitin sulfate","ms5047-2-1":"18.7509","ms5047-2-2":"18.2225","ms5047-2-3":"17.8460","ms5047-3-1":"19.4624","ms5047-3-2":"18.7762","ms5047-3-3":"4.8114","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Cyclopiazonic Acid","ms5047-2-1":"14.2730","ms5047-2-2":"15.0206","ms5047-2-3":"14.3839","ms5047-3-1":"12.6888","ms5047-3-2":"15.0925","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Cytarabine","ms5047-2-1":"14.0238","ms5047-2-2":"13.7526","ms5047-2-3":"4.0476","ms5047-3-1":"16.7958","ms5047-3-2":"13.8816","ms5047-3-3":"16.4612","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Decarbamoylgonyautoxin 1","ms5047-2-1":"16.3753","ms5047-2-2":"16.4550","ms5047-2-3":"10.5778","ms5047-3-1":"17.4123","ms5047-3-2":"15.6806","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Deoxycytidine","ms5047-2-1":"13.8180","ms5047-2-2":"13.1932","ms5047-2-3":"4.1449","ms5047-3-1":"14.9717","ms5047-3-2":"12.1398","ms5047-3-3":"13.7792","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Diclobutrazol","ms5047-2-1":"14.8348","ms5047-2-2":"15.0272","ms5047-2-3":"10.1299","ms5047-3-1":"14.7282","ms5047-3-2":"0.0000","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Dihydroneopterin phosphate","ms5047-2-1":"14.6390","ms5047-2-2":"14.2369","ms5047-2-3":"13.7394","ms5047-3-1":"0.0000","ms5047-3-2":"13.6803","ms5047-3-3":"4.5238","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"dTDP-D-galacturonate","ms5047-2-1":"15.5606","ms5047-2-2":"15.6261","ms5047-2-3":"15.2994","ms5047-3-1":"16.6186","ms5047-3-2":"14.9860","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Erythrono-1_4-lactone","ms5047-2-1":"19.1907","ms5047-2-2":"19.8667","ms5047-2-3":"19.4814","ms5047-3-1":"17.3908","ms5047-3-2":"16.4108","ms5047-3-3":"16.8625","ms5047-1-1":"15.4789","ms5047-1-2":"15.7690","ms5047-1-3":"15.6419"},{"Metabolite":"F-Honaucin A","ms5047-2-1":"6.8712","ms5047-2-2":"14.5071","ms5047-2-3":"7.1991","ms5047-3-1":"22.7766","ms5047-3-2":"22.6256","ms5047-3-3":"21.2151","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Fumaric acid","ms5047-2-1":"9.8673","ms5047-2-2":"0.0000","ms5047-2-3":"0.0000","ms5047-3-1":"0.0000","ms5047-3-2":"8.6446","ms5047-3-3":"4.8681","ms5047-1-1":"14.9490","ms5047-1-2":"15.3700","ms5047-1-3":"14.9371"},{"Metabolite":"Glutaconic acid","ms5047-2-1":"21.4854","ms5047-2-2":"21.8890","ms5047-2-3":"21.1770","ms5047-3-1":"19.5318","ms5047-3-2":"17.8028","ms5047-3-3":"5.0408","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Gly Asp Asp","ms5047-2-1":"13.3718","ms5047-2-2":"12.6621","ms5047-2-3":"3.9903","ms5047-3-1":"12.6682","ms5047-3-2":"3.9104","ms5047-3-3":"8.4560","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"griseorhodin A","ms5047-2-1":"5.2931","ms5047-2-2":"13.7882","ms5047-2-3":"10.3424","ms5047-3-1":"14.1641","ms5047-3-2":"13.9362","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Iprobenfos","ms5047-2-1":"14.4449","ms5047-2-2":"14.0974","ms5047-2-3":"4.4164","ms5047-3-1":"13.7610","ms5047-3-2":"8.2334","ms5047-3-3":"13.7494","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Jaceidin 7-neohesperidoside","ms5047-2-1":"14.1104","ms5047-2-2":"14.1338","ms5047-2-3":"9.2497","ms5047-3-1":"15.8055","ms5047-3-2":"7.9862","ms5047-3-3":"4.0140","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"L-4-Hydroxy-3-methoxy-a-methylphenylalanine","ms5047-2-1":"15.1411","ms5047-2-2":"14.4660","ms5047-2-3":"13.5868","ms5047-3-1":"14.2700","ms5047-3-2":"14.5908","ms5047-3-3":"8.2177","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Lys Trp Lys","ms5047-2-1":"13.1817","ms5047-2-2":"9.2143","ms5047-2-3":"9.0492","ms5047-3-1":"0.0000","ms5047-3-2":"13.3676","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Methyl oxalate","ms5047-2-1":"19.2024","ms5047-2-2":"19.8583","ms5047-2-3":"19.4814","ms5047-3-1":"17.3908","ms5047-3-2":"16.4082","ms5047-3-3":"16.8625","ms5047-1-1":"15.4789","ms5047-1-2":"15.7690","ms5047-1-3":"15.6356"},{"Metabolite":"N-Formylmethionylphenylalanine","ms5047-2-1":"15.5779","ms5047-2-2":"15.9940","ms5047-2-3":"14.3999","ms5047-3-1":"16.8279","ms5047-3-2":"13.7972","ms5047-3-3":"9.1836","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Nicotinamide N-oxide","ms5047-2-1":"14.8357","ms5047-2-2":"14.4198","ms5047-2-3":"0.0000","ms5047-3-1":"15.2438","ms5047-3-2":"8.9224","ms5047-3-3":"14.3615","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Oryzalin","ms5047-2-1":"18.5895","ms5047-2-2":"18.6488","ms5047-2-3":"16.1608","ms5047-3-1":"19.8514","ms5047-3-2":"16.6583","ms5047-3-3":"11.3090","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Oxolinic Acid","ms5047-2-1":"14.5171","ms5047-2-2":"14.4137","ms5047-2-3":"13.5932","ms5047-3-1":"13.4184","ms5047-3-2":"14.1563","ms5047-3-3":"13.8238","ms5047-1-1":"3.8047","ms5047-1-2":"0.0000","ms5047-1-3":"3.9282"},{"Metabolite":"Pectolinarigenin 7-(4^^^-acetylrutinoside)","ms5047-2-1":"13.3823","ms5047-2-2":"13.1263","ms5047-2-3":"8.1519","ms5047-3-1":"14.5399","ms5047-3-2":"7.9607","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Penicillin G","ms5047-2-1":"18.0901","ms5047-2-2":"19.6458","ms5047-2-3":"18.2760","ms5047-3-1":"21.0266","ms5047-3-2":"16.8779","ms5047-3-3":"13.6913","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Phe4Cl-Ser-OH","ms5047-2-1":"4.3829","ms5047-2-2":"8.8142","ms5047-2-3":"4.3744","ms5047-3-1":"13.0162","ms5047-3-2":"0.0000","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Phenolsulfonphthalein","ms5047-2-1":"13.0332","ms5047-2-2":"12.9990","ms5047-2-3":"8.8046","ms5047-3-1":"0.0000","ms5047-3-2":"7.7140","ms5047-3-3":"13.0741","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Phenylacetylglycine","ms5047-2-1":"21.8392","ms5047-2-2":"21.1445","ms5047-2-3":"20.8784","ms5047-3-1":"20.6766","ms5047-3-2":"22.0451","ms5047-3-3":"17.4101","ms5047-1-1":"13.8860","ms5047-1-2":"15.8503","ms5047-1-3":"10.2432"},{"Metabolite":"p-Hydroxyprimidone","ms5047-2-1":"16.0666","ms5047-2-2":"15.6464","ms5047-2-3":"14.0807","ms5047-3-1":"16.2764","ms5047-3-2":"14.9924","ms5047-3-3":"0.0000","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Prochlorperazine","ms5047-2-1":"16.0785","ms5047-2-2":"16.3620","ms5047-2-3":"16.2497","ms5047-3-1":"0.0000","ms5047-3-2":"16.3975","ms5047-3-3":"4.7261","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Ribothymidine","ms5047-2-1":"15.9253","ms5047-2-2":"15.9467","ms5047-2-3":"15.5751","ms5047-3-1":"17.3086","ms5047-3-2":"15.4326","ms5047-3-3":"17.3708","ms5047-1-1":"0.0000","ms5047-1-2":"0.0000","ms5047-1-3":"0.0000"},{"Metabolite":"Sericetin 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