{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000466","ANALYSIS_ID":"AN000728","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":"Amino acids","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6490","COLUMN_NAME":"Waters AccQ Tag (100 x 2mm, 1.7um)","METHODS_FILENAME":"SB_AA_Assay.pdf"},

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

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

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

"Data":[{"Metabolite":"Alanine","Lemos_010":"13.4968173","Lemos_011":"13.77484535","Lemos_012":"17.08474808","Lemos_013":"11.44786287","Lemos_014":"29.57921822","Lemos_017":"27.80150967"},{"Metabolite":"Arginine","Lemos_010":"0.727122952","Lemos_011":"0.93160068","Lemos_012":"1.487828796","Lemos_013":"1.178842015","Lemos_014":"13.91608989","Lemos_017":"16.93600365"},{"Metabolite":"Asparagine","Lemos_010":"1.279478236","Lemos_011":"1.628887762","Lemos_012":"2.069656943","Lemos_013":"2.224827051","Lemos_014":"3.26275759","Lemos_017":"7.785364418"},{"Metabolite":"Aspartic Acid","Lemos_010":"4.455220825","Lemos_011":"6.984646068","Lemos_012":"9.881306129","Lemos_013":"5.568899683","Lemos_014":"20.26276077","Lemos_017":"19.34355353"},{"Metabolite":"Citrulline","Lemos_010":"6.310064266","Lemos_011":"8.581588219","Lemos_012":"8.964833713","Lemos_013":"6.238985801","Lemos_014":"0.176973847","Lemos_017":"0.131098646"},{"Metabolite":"Glutamic Acid","Lemos_010":"17.10642159","Lemos_011":"24.37329968","Lemos_012":"21.11184161","Lemos_013":"15.2096646","Lemos_014":"92.45672307","Lemos_017":"49.25100429"},{"Metabolite":"Glutamine","Lemos_010":"2.531073596","Lemos_011":"7.180627198","Lemos_012":"5.92838685","Lemos_013":"3.511570294","Lemos_014":"6.258616833","Lemos_017":"32.17249124"},{"Metabolite":"Glycine","Lemos_010":"4.404880679","Lemos_011":"3.490639013","Lemos_012":"6.156741627","Lemos_013":"3.869487452","Lemos_014":"7.282333173","Lemos_017":"7.485359965"},{"Metabolite":"Histidine","Lemos_010":"0.586065066","Lemos_011":"0.637094911","Lemos_012":"0.833566217","Lemos_013":"0.640196052","Lemos_014":"1.007666776","Lemos_017":"1.454040575"},{"Metabolite":"Isoleucine","Lemos_010":"1.392103942","Lemos_011":"1.917462191","Lemos_012":"2.249132637","Lemos_013":"1.519424174","Lemos_014":"2.00070069","Lemos_017":"3.156461297"},{"Metabolite":"Leucine","Lemos_010":"4.119419121","Lemos_011":"7.778756768","Lemos_012":"6.827787797","Lemos_013":"4.803071231","Lemos_014":"10.34482415","Lemos_017":"12.07748425"},{"Metabolite":"Lysine","Lemos_010":"8.086046824","Lemos_011":"12.85291899","Lemos_012":"16.39849601","Lemos_013":"8.784116838","Lemos_014":"24.36911396","Lemos_017":"28.16432389"},{"Metabolite":"Methionine","Lemos_010":"0.964918644","Lemos_011":"1.249392478","Lemos_012":"1.421942208","Lemos_013":"0.976152554","Lemos_014":"1.442880753","Lemos_017":"2.198434199"},{"Metabolite":"Ornithine","Lemos_010":"3.072268435","Lemos_011":"3.612224813","Lemos_012":"4.246898133","Lemos_013":"2.245134481","Lemos_014":"0.368238481","Lemos_017":"0.451957404"},{"Metabolite":"Phenylalanine","Lemos_010":"1.52883581","Lemos_011":"1.889360051","Lemos_012":"2.492716603","Lemos_013":"1.422059683","Lemos_014":"2.041916121","Lemos_017":"2.798384215"},{"Metabolite":"Proline","Lemos_010":"1.450537447","Lemos_011":"1.050247783","Lemos_012":"1.117216511","Lemos_013":"0.671405546","Lemos_014":"2.036416928","Lemos_017":"1.908432913"},{"Metabolite":"Serine","Lemos_010":"1.201237763","Lemos_011":"2.257184921","Lemos_012":"2.551346905","Lemos_013":"1.775937567","Lemos_014":"2.378835817","Lemos_017":"3.716613361"},{"Metabolite":"Threonine","Lemos_010":"2.707296961","Lemos_011":"3.475857255","Lemos_012":"4.598548885","Lemos_013":"2.550898527","Lemos_014":"8.081660248","Lemos_017":"7.673625587"},{"Metabolite":"Tryptophan","Lemos_010":"0.378391222","Lemos_011":"0.390840699","Lemos_012":"0.464721524","Lemos_013":"0.353727692","Lemos_014":"0.471037662","Lemos_017":"0.60111904"},{"Metabolite":"Tyrosine","Lemos_010":"0.644789168","Lemos_011":"0.693982476","Lemos_012":"0.965012788","Lemos_013":"0.615679833","Lemos_014":"0.961151331","Lemos_017":"0.966145347"},{"Metabolite":"Valine","Lemos_010":"2.021256555","Lemos_011":"3.032133437","Lemos_012":"3.323429924","Lemos_013":"1.812314893","Lemos_014":"1.869078353","Lemos_017":"1.427014083"}],

"Metabolites":[{"Metabolite":"Alanine","retention index":"4.16","quantified m/z":"260.17","PubChem ID":"5950","KEGG ID":""},{"Metabolite":"Arginine","retention index":"2.68","quantified m/z":"345.21","PubChem ID":"6322","KEGG ID":""},{"Metabolite":"Asparagine","retention index":"2.25","quantified m/z":"303.13","PubChem ID":"6267","KEGG ID":""},{"Metabolite":"Aspartic Acid","retention index":"2.99","quantified m/z":"304.11","PubChem ID":"5960","KEGG ID":""},{"Metabolite":"Citrulline","retention index":"3.33","quantified m/z":"346.21","PubChem ID":"9750","KEGG ID":""},{"Metabolite":"Glutamic Acid","retention index":"3.35","quantified m/z":"318.11","PubChem ID":"33032","KEGG ID":""},{"Metabolite":"Glutamine","retention index":"2.65","quantified m/z":"317.21","PubChem ID":"5961","KEGG ID":""},{"Metabolite":"Glycine","retention index":"2.81","quantified m/z":"246.08","PubChem ID":"750","KEGG ID":""},{"Metabolite":"Histidine","retention index":"2.07","quantified m/z":"326.21","PubChem ID":"6274","KEGG ID":""},{"Metabolite":"Isoleucine","retention index":"8.15","quantified m/z":"302.21","PubChem ID":"6306","KEGG ID":""},{"Metabolite":"Leucine","retention index":"8.26","quantified m/z":"302.21","PubChem ID":"6106","KEGG ID":""},{"Metabolite":"Lysine","retention index":"6.66","quantified m/z":"487.21","PubChem ID":"5962","KEGG ID":""},{"Metabolite":"Methionine","retention index":"6.87","quantified m/z":"320.21","PubChem ID":"6137","KEGG ID":""},{"Metabolite":"Ornithine","retention index":"5.93","quantified m/z":"473.22","PubChem ID":"6262","KEGG ID":""},{"Metabolite":"Phenylalanine","retention index":"8.40","quantified m/z":"336.21","PubChem ID":"6140","KEGG ID":""},{"Metabolite":"Proline","retention index":"4.84","quantified m/z":"286.16","PubChem ID":"145742","KEGG ID":""},{"Metabolite":"Serine","retention index":"2.60","quantified m/z":"276.11","PubChem ID":"5951","KEGG ID":""},{"Metabolite":"Threonine","retention index":"3.74","quantified m/z":"290.11","PubChem ID":"6288","KEGG ID":""},{"Metabolite":"Tryptophan","retention index":"8.54","quantified m/z":"375.21","PubChem ID":"6305","KEGG ID":""},{"Metabolite":"Tyrosine","retention index":"6.66","quantified m/z":"352.21","PubChem ID":"6057","KEGG ID":""},{"Metabolite":"Valine","retention index":"7.09","quantified m/z":"288.21","PubChem ID":"6287","KEGG ID":""}]
}

}