{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000466","ANALYSIS_ID":"AN000729","VERSION":"1","CREATED_ON":"September 12, 2016, 1:31 pm"},

"PROJECT":{"PROJECT_TITLE":"Streptococcus mutans Amino Acid/Organic Acid Profile","PROJECT_SUMMARY":"Determination of metabolite profiles of S. mutans strains UA159 (WT) and ΔspxA1 in response to oxidative stress","INSTITUTE":"Univeristy of Florida","DEPARTMENT":"Oral Biology","LABORATORY":"Lemos-Abranches","LAST_NAME":"Lemos","FIRST_NAME":"Jose","ADDRESS":"1395 Center Drive, PO Box 100424 Gainesville, FL 32610","EMAIL":"jlemos@dental.ufl.edu","PHONE":"352-273-8843","FUNDING_SOURCE":"UF start-up funds"},

"STUDY":{"STUDY_TITLE":"Streptococcus mutans organic acids/amino acid profiles, effect of oxidative stress; pilot","STUDY_TYPE":"Amino acid/organic acid profiles of wild-type and mutant strain in response to H2O2 treatment over time.","STUDY_SUMMARY":"S. mutans UA159 and ΔspxA1 will be grown in BHI to OD600 = 0.4. Each culture will be split in to 4 samples. For the first sample, 3E10 cells will immediately be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. The remaining three samples will be treated with H2O2 to 0.5 mM, and the harvesting process repeated after 15, 30 and 60 minutes.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"Lemos-Abranches","LAST_NAME":"Hardin","FIRST_NAME":"Emily","ADDRESS":"1395 Center Drive, PO Box 100424, Gainesville, FL 32610","EMAIL":"ehardin@ufl.edu","PHONE":"352-273-8844","NUM_GROUPS":"6","TOTAL_SUBJECTS":"6"},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Streptococcus mutans","TAXONOMY_ID":"1309","GENOTYPE_STRAIN":"UA159"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"UA159_0",
"Sample ID":"Lemos_010",
"Factors":{"Strain":"WT","Exposure to H2O2":"0.00"}
},
{
"Subject ID":"UA159_15min",
"Sample ID":"Lemos_011",
"Factors":{"Strain":"WT","Exposure to H2O2":"15 min"}
},
{
"Subject ID":"UA159_30 min",
"Sample ID":"Lemos_012",
"Factors":{"Strain":"WT","Exposure to H2O2":"30 min"}
},
{
"Subject ID":"UA159_60 min",
"Sample ID":"Lemos_013",
"Factors":{"Strain":"WT","Exposure to H2O2":"60 min"}
},
{
"Subject ID":"spxA1_0",
"Sample ID":"Lemos_014",
"Factors":{"Strain":"ΔspxA1","Exposure to H2O2":"0.00"}
},
{
"Subject ID":"spxA1_60 min",
"Sample ID":"Lemos_017",
"Factors":{"Strain":"ΔspxA1","Exposure to H2O2":"60 min"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Upon reaching OD600 = 0.4, the culture is split into 4 samples. Three are treated with H2O2 (0.5 mM). The other is harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS (~1 mL), centrifuged for 30 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis. This process will be repeated with the remaining three samples after 15, 30 and 60 minutes treatment with H2O2.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"0.5 mM H2O2 for 15, 30 and 60 minutes. Control has 0 H2O2 added."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Amino acids|Organic acids","SAMPLEPREP_PROTOCOL_FILENAME":"SB_AA_Assay.pdf;SB_OA_Assay.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Organic acids","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Quantiva QQQ","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2mm, 1.7um)","METHODS_FILENAME":"SB_OA_Assay.pdf"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Quantiva QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"nmol/mg protein",

"Data":[{"Metabolite":"Lactate","Lemos_010":"38.11410827","Lemos_011":"37.92547892","Lemos_012":"34.49595534","Lemos_013":"12.75296215","Lemos_014":"56.07148179","Lemos_017":"53.19175841"},{"Metabolite":"Pyruvate","Lemos_010":"1.518795621","Lemos_011":"1.768367821","Lemos_012":"1.500451299","Lemos_013":"0.745049277","Lemos_014":"2.55928227","Lemos_017":"2.568756137"},{"Metabolite":"Succinate","Lemos_010":"0.46892125","Lemos_011":"0.476350026","Lemos_012":"0.554115095","Lemos_013":"0.44869083","Lemos_014":"0.531215577","Lemos_017":"0.224579712"},{"Metabolite":"Fumarate","Lemos_010":"0.010669337","Lemos_011":"0.06533411","Lemos_012":"0.103272586","Lemos_013":"0.078208839","Lemos_014":"0.117524568","Lemos_017":"0.104726182"},{"Metabolite":"Malate","Lemos_010":"","Lemos_011":"","Lemos_012":"","Lemos_013":"","Lemos_014":"","Lemos_017":""},{"Metabolite":"a-KG","Lemos_010":"0.085819743","Lemos_011":"0.075291412","Lemos_012":"0.087048149","Lemos_013":"0.062269822","Lemos_014":"1.175718779","Lemos_017":"0.34426083"},{"Metabolite":"Citrate","Lemos_010":"0.409795849","Lemos_011":"0.607818473","Lemos_012":"0.671669804","Lemos_013":"0.396595419","Lemos_014":"0.323044238","Lemos_017":"0.369449066"}],

"Metabolites":[{"Metabolite":"Lactate","retention index":"3.98","quantified m/z":"196.1","PubChem ID":"107689","KEGG ID":""},{"Metabolite":"Pyruvate","retention index":"6.68","quantified m/z":"299.1","PubChem ID":"1060","KEGG ID":""},{"Metabolite":"Succinate","retention index":"5.44","quantified m/z":"329.1","PubChem ID":"1110","KEGG ID":""},{"Metabolite":"Fumarate","retention index":"5.59","quantified m/z":"327.1","PubChem ID":"444972","KEGG ID":""},{"Metabolite":"Malate","retention index":"5.28","quantified m/z":"345.1","PubChem ID":"525","KEGG ID":""},{"Metabolite":"a-KG","retention index":"6.59","quantified m/z":"462.2","PubChem ID":"164533","KEGG ID":""},{"Metabolite":"Citrate","retention index":"5.95","quantified m/z":"508.25","PubChem ID":"311","KEGG ID":""}]
}

}