{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000881","ANALYSIS_ID":"AN001437","VERSION":"1","CREATED_ON":"October 29, 2017, 8:18 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics analysis of leprosy patients with type 1 reaction","PROJECT_TYPE":"MS qualitative analysis and identification of polyunsaturated fatty acids in retrospective serum samples of leprosy patients with type 1 reaction","PROJECT_SUMMARY":"Type 1 reaction (T1R) is an acute inflammatory episode that causes severe neuronal damages in patients with leprosy. The factors that trigger this pathology is still unknown, and further studies are needed to understand T1R and to early prevent its start. It is well established that the host immune response is linked to T1R and previous studies indicated that the metabolism of the host also influences the adaptive immune response against M. leprae antigens. Therefore, metabolomics-based analyses of sera from 7 patients with and 9 without T1R were conducted via liquid chromatography–mass spectrometry. The main goal of this project was to determine whether the metabolism of polyunsaturated fatty acids (such as eicosanoids and omega-3 fatty acids) were perturbed in leprosy patients with T1R.","INSTITUTE":"Colorado State University","DEPARTMENT":"Department of Microbiology, Immunology, and Pathology","LABORATORY":"Belisle","LAST_NAME":"Belisle","FIRST_NAME":"John","ADDRESS":"Rampart Road, 1682 Campus Delivery","EMAIL":"cadriano@rams.colostate.edu","PHONE":"9704819160","FUNDING_SOURCE":"This work was supported by the New York Community Trust (grant to J. T. B. as co–principle investigator [PI]), by the Heiser Foundation (grant to J. T. B. as co-PI), and by the Brazilian Coordination for the Improvement of Higher Education Personnel through the Science without Borders program (10546-13-8, for the postdoctoral scholarship to C. A. M. S.).","PROJECT_COMMENTS":"The institutional review boards of Colorado State University approved the use of sera for the reported study.","PUBLICATIONS":"J Infect Dis. 2017 Feb 1;215(3):431-439. doi: 10.1093/infdis/jiw541.","CONTRIBUTORS":"Carlos A. M. Silva, Kristofor Webb, Barbara G. Andre, Maria Angela Marques, Fernanda Marques Carvalho, Cristiana Santos de Macedo, Roberta Olmo Pinheiro, Euzenir Nunes Sarno, Maria Cristina Vidal Pessolani, John T. Belisle."},

"STUDY":{"STUDY_TITLE":"Targeted metabolomics data of leprosy patients with type 1 reaction","STUDY_TYPE":"Targeted MS/MS analysis in retrospective serum samples of leprosy patients with type 1 reaction","STUDY_SUMMARY":"Targeted metabolomics-based analyses of pooled sera from 7 patients with T1R were conducted via LC-MS/MS.","INSTITUTE":"Colorado State University","DEPARTMENT":"Department of Microbiology, Immunology, and Pathology","LABORATORY":"Belisle","LAST_NAME":"Silva","FIRST_NAME":"Carlos","ADDRESS":"Rampart Road, 1682 Campus Delivery","EMAIL":"cadriano@rams.colostate.edu","PHONE":"9702154962","NUM_GROUPS":"02 (first group was leprosy patients with type 1 reaction, N=9; and second group was leprosy patients without type 1 reaction, N=7)","TOTAL_SUBJECTS":"16","NUM_MALES":"5 (3 were leprosy patients with type 1 reaction and 2 were leprosy patients without type 1 reaction)","NUM_FEMALES":"11 (4 were leprosy patients with type 1 reaction and 7 were leprosy patients without type 1 reaction)","STUDY_COMMENTS":"For this study we used retrospective sera samples.","PUBLICATIONS":"J Infect Dis. 2017 Feb 1;215(3):431-439. doi: 10.1093/infdis/jiw541."},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"13 - 66","GENDER":"Female and Male","HUMAN_ETHNICITY":"Brazillian","HUMAN_INCLUSION_CRITERIA":"Retrospective serum samples from leprosy patients diagnosed or not with type 1 reaction that were not receiving multidrug therapy or corticosteroid therapy at the time of blood collection.","HUMAN_EXCLUSION_CRITERIA":"Retrospective serum samples from leprosy patients that were under multidrug therapy and/or corticosteroid therapy at the time of blood collection were excluded from the study.","SUBJECT_COMMENTS":"The patients exhibited borderline tuberculoid, borderline borderline and borderline lepromatous forms of leprosy and was diagnosed or not with type 1 reaction."},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"S1",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"46","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S3",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"F","Bacillary index":"0.5","Age":"27","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BB"}
},
{
"Subject ID":"-",
"Sample ID":"S5",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"F","Bacillary index":"0.5","Age":"56","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BB"}
},
{
"Subject ID":"-",
"Sample ID":"S7",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"32","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S8",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"M","Bacillary index":"-","Age":"41","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S9",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"M","Bacillary index":"2","Age":"66","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BL"}
},
{
"Subject ID":"-",
"Sample ID":"S10",
"Factors":{"Type 1 reaction (T1R)":"Yes"},
"Additional sample data":{"Gender":"M","Bacillary index":"1.5","Age":"49","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BB"}
},
{
"Subject ID":"-",
"Sample ID":"S11",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"65","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S12",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"46","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S13",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"13","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S14",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"57","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S15",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"15","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S16",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"M","Bacillary index":"-","Age":"34","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S17",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"40","Serologic finding (+ or - for PGL-I)":"+","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S18",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"M","Bacillary index":"-","Age":"55","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
},
{
"Subject ID":"-",
"Sample ID":"S19",
"Factors":{"Type 1 reaction (T1R)":"No"},
"Additional sample data":{"Gender":"F","Bacillary index":"-","Age":"64","Serologic finding (+ or - for PGL-I)":"-","clinical form of leprosy":"BT"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The whole blood (10 mL) was collected in a Vacutainer tube from Becton Dickinson (BD). After collection of the whole blood, it was allowed the blood to clot by leaving it undisturbed at room temperature for 30 minutes. The clot was removed by centrifuging at 1,000–2,000 x g for 10 minutes in a refrigerated centrifuge (4 C). The resulting supernatant is designated serum. The serum samples were aliquoted in 100 microliters and stored in a serum bank at -80C. These samples were collected in the Leprosy Outpatient Unit (Oswaldo Cruz Foundation, Rio de Janeiro, Brazil) and then they were sent in dry ice to Colorado State University, where it was processed and analyzed for metabolomics. At Colorado State University the samples were stored at -80C until processing.","SAMPLE_TYPE":"Serum","COLLECTION_LOCATION":"Leprosy Outpatient Unit (Oswaldo Cruz Foundation, Rio de Janeiro, Brazil)","COLLECTION_DURATION":"30 minutes","STORAGE_CONDITIONS":"-80C","ADDITIVES":"no","BLOOD_SERUM_OR_PLASMA":"Serum"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment of the patients was performed"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Serum samples (7 serum samples from leprosy patients with T1R) were pooled prior the extraction. These pooled serum samples were incubated with 3 volumes of cold methanol (100%) for 1 hour at -20C. After this incubation, the samples were centrifuged for 30 minutes at 18,000 xg at 4C to clear the supernatant. The supernatant was then transferred and dried under vacuum. Samples were re-suspended in 80 μl of 50% methanol. Prior to the injections on the LC-MS instrument, the samples were centrifuged for 30 minutes at 18,000 xg at 4oC.","SAMPLEPREP_PROTOCOL_ID":"SP000100","SAMPLEPREP_PROTOCOL_FILENAME":"060613_Methanol_Serum_Extraction","SAMPLEPREP_PROTOCOL_COMMENTS":"Use always nitrile gloves. Do not use gloves with powder. Use pipette tips with aerosol barrier.","PROCESSING_METHOD":"Homogenization and solvent removal with Speed Vac","PROCESSING_STORAGE_CONDITIONS":"on ice","EXTRACTION_METHOD":"Cold Methanol extraction (3:1 methanol/water)","EXTRACT_ENRICHMENT":"no enrichment was performed","EXTRACT_CLEANUP":"Centrifugation","EXTRACT_STORAGE":"-80C","SAMPLE_RESUSPENSION":"50% methanol","SAMPLE_DERIVATIZATION":"no derivatization process was performed","SAMPLE_SPIKING":"Samples were spiked with the following commercial standards: arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid and leukotriene B4"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"This analysis was performed only on negative mode. The solvent gradient used for all chromatography was 2% solvent B for 3 min followed by a 15 min linear gradient of 2% to 98% solvent B, which was held for 0.3 min. Then returned to starting conditions over 1.2 min.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 quadrupole time-of-flight (Q-TOF) mass spectrometer.","COLUMN_NAME":"Waters Xbridge BEH C18 XP (100 x 2.1mm, 2.5um) Millford, MA, USA)","FLOW_GRADIENT":"0.25 mL/min","FLOW_RATE":"0.25 mL/min","COLUMN_TEMPERATURE":"50C","SOLVENT_A":"89% water, 5% acetonitrile, 5% isopropanol and 1% 500 mM ammonium acetate","SOLVENT_B":"49.5% acetonitrile, 49.5% isopropanol and 1% 500 mM ammonium acetate","INJECTION_TEMPERATURE":"4C","SAMPLE_INJECTION":"20uL","CAPILLARY_VOLTAGE":"2.8 kV"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Mycobacteria Research Laboratories","OPERATOR_NAME":"Kristofor Webb and Carlos AM Silva","SOFTWARE_VERSION":"Agilent Mass Hunter Workstation Software version, Qualitative Analysis, Version B.05.00","DATA_FORMAT":".d"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6510 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","CAPILLARY_VOLTAGE":"2.8kV","COLLISION_ENERGY":"20eV","COLLISION_GAS":"Nitrogen","DRY_GAS_FLOW":"10 L/min","DRY_GAS_TEMP":"310C","FRAGMENT_VOLTAGE":"120V","NEBULIZER":"45 psig","SCANNING_RANGE":"2 spectra per second","SKIMMER_VOLTAGE":"50V","MS_RESULTS_FILE":"ST000881_AN001437_Results.txt UNITS:arbitrary units"},

"MS_METABOLITE_DATA":{
"Units":"MS peak area",

"Data":[{"Metabolite":"arachidonic acid","S19":"7936921.548","S18":"5559891.47","S14":"4816532.524","S12":"8343606.247","S16":"8312042.446","S11":"4260880.609","S15":"4203527.537","S17":"5188449.248","S13":"4419431.369","S10":"32171297.07","S1":"7396863.005","S3":"20764686.47","S5":"3410989.698","S7":"11438085.37","S8":"17777816.43","S9":"40211943.32"},{"Metabolite":"docosahexaenoic acid","S19":"2918531.495","S18":"2126677.293","S14":"1160184.902","S12":"1768356.609","S16":"2376769.736","S11":"1799836.869","S15":"2066720.114","S17":"1819937.346","S13":"1333346.88","S10":"11359754.35","S1":"3289928.37","S3":"6517555.083","S5":"1566183.678","S7":"3224927.67","S8":"5951942.001","S9":"11531546.11"},{"Metabolite":"eicosapentaenoic acid","S19":"744377.0623","S18":"920976.3724","S14":"103139.337","S12":"832269.0022","S16":"893886.9039","S11":"1037429.957","S15":"330488.2954","S17":"371476.0546","S13":"339867.5464","S10":"12927592.16","S1":"1080763.992","S3":"2607795.945","S5":"792520.8231","S7":"1815303.276","S8":"2514850.163","S9":"5856024.135"},{"Metabolite":"leukotriene B4","S19":"NA","S18":"35897.19797","S14":"NA","S12":"64022.06455","S16":"31468.15348","S11":"NA","S15":"34383.10702","S17":"93400.19634","S13":"26461.06465","S10":"1481179.511","S1":"190631.8112","S3":"1525152.203","S5":"NA","S7":"1914268.658","S8":"1765671.804","S9":"2580232.762"}],

"Metabolites":[{"Metabolite":"arachidonic acid","retention index":"","quantified m/z":"303.23","PubChem ID":"444899","KEGG ID":"C00219","HMDB ID":"HMDB01043"},{"Metabolite":"docosahexaenoic acid","retention index":"","quantified m/z":"327.23","PubChem ID":"445580","KEGG ID":"C06429","HMDB ID":"HMDB02183"},{"Metabolite":"eicosapentaenoic acid","retention index":"","quantified m/z":"301.22","PubChem ID":"446284","KEGG ID":"C06428","HMDB ID":"HMDB01999"},{"Metabolite":"leukotriene B4","retention index":"","quantified m/z":"335.22","PubChem ID":"5280492","KEGG ID":"C02165","HMDB ID":"HMDB01085"}]
}

}