{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001946","ANALYSIS_ID":"AN003168","VERSION":"1","CREATED_ON":"October 12, 2021, 9:53 am"}, "PROJECT":{"PROJECT_TITLE":"Bipolar Disorder metabolomics analysis","PROJECT_TYPE":"MS untargeted analysis","PROJECT_SUMMARY":"MS untargeted analysis using FiehnLib and GOLM metabolite database for data curation","INSTITUTE":"University of Campinas","DEPARTMENT":"Chemistry Institute, Department of Analytical Chemistry","LABORATORY":"Laboratory of Bioanalytics and Integrated Omics (LaBIOmics)","LAST_NAME":"Ribeiro","FIRST_NAME":"Henrique","ADDRESS":"Rua Sérgio Buarque de Holanda,s/n","EMAIL":"hcarachoribeiro@gmail.com","PHONE":"+55 19 3521 3018","FUNDING_SOURCE":"CAPES","CONTRIBUTORS":"Henrique Caracho Ribeiro, Alessandra Sussulini, Matej Oresic, Alex Dickens, Partho Sen"}, "STUDY":{"STUDY_TITLE":"Bipolar disorder metabolomics analysis using FiehnLib and GMD for curation","STUDY_TYPE":"Untargeted GC analysis","STUDY_SUMMARY":"In this study we analyzed the blood serum from 14 controls and 14 BD patients using GC-MS under the conditions required for the use of FiehnLib library with GMD as secondary library for curation on a untargeted metabolomics approach","INSTITUTE":"new","DEPARTMENT":"Chemistry Institute, Department of Analytical Chemistry","LABORATORY":"Laboratory of Bioanalytics and Integrated Omics (LaBIOmics)","LAST_NAME":"Ribeiro","FIRST_NAME":"Henrique","ADDRESS":"Rua Sérgio Buarque de Holanda,s/n","EMAIL":"hcarachoribeiro@gmail.com","PHONE":"+55 19 3521 3018","NUM_GROUPS":"2","TOTAL_SUBJECTS":"28","NUM_MALES":"11","NUM_FEMALES":"17"}, "SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"19-79","WEIGHT_OR_WEIGHT_RANGE":"49-93","HEIGHT_OR_HEIGHT_RANGE":"1.5-1.9","GENDER":"Male and female","HUMAN_ETHNICITY":"Brazilian","HUMAN_MEDICATIONS":"BD patients used a wide range of different medications, mostly mood stabilizers and antipsychotics","HUMAN_INCLUSION_CRITERIA":"Controls: Any adult over 18 years respecting the excusion criteria / BD: Any adult over 18 years old with BD diagnosed by a psychiatrist, respecting exclusion criteria psychiat","HUMAN_EXCLUSION_CRITERIA":"Controls : negative history of any psychiatric disorder or use of any kind of psychiatric medication / BD : concomitant diseases such as AIDS, hepatitis, endocrinal or metabolic diseases, substance use (except nicotine dependence), and pregnancy or postpartum period"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"B01", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B01.cdf","Sex":"F","Age":"19","Height":"1.63","Weight":"69","BMI":"25.97012","Medication":"valproic acid"} }, { "Subject ID":"-", "Sample ID":"B02", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B02.cdf","Sex":"F","Age":"60","Height":"1.5","Weight":"77","BMI":"34.22222","Medication":"valproic acid, quetiapine, clonazepam"} }, { "Subject ID":"-", "Sample ID":"B03", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B03.cdf","Sex":"M","Age":"45","Height":"1.5","Weight":"55","BMI":"24.44444","Medication":"quetiapine"} }, { "Subject ID":"-", "Sample ID":"B05", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B05.cdf","Sex":"F","Age":"59","Height":"1.59","Weight":"93","BMI":"36.78652","Medication":"quetiapine, clonazepam,"} }, { "Subject ID":"-", "Sample ID":"B06", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B06.cdf","Sex":"F","Age":"19","Height":"1.59","Weight":"49","BMI":"19.38214","Medication":"lavontringine, valproic acid"} }, { "Subject ID":"-", "Sample ID":"B07", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B07.cdf","Sex":"F","Age":"40","Height":"1.5","Weight":"73","BMI":"32.44444","Medication":"lavontringine, Haldol, Clonazepam"} }, { "Subject ID":"-", "Sample ID":"B08", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B08.cdf","Sex":"M","Age":"52","Height":"1.58","Weight":"74.5","BMI":"29.84297","Medication":"lavontringine,Aripiprazole, Sertaline, Bupropione"} }, { "Subject ID":"-", "Sample ID":"B09", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B09.cdf","Sex":"M","Age":"24","Height":"1.83","Weight":"82","BMI":"24.48565","Medication":"lithium"} }, { "Subject ID":"-", "Sample ID":"B10", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B10.cdf","Sex":"M","Age":"66","Height":"1.66","Weight":"66","BMI":"23.95123","Medication":"lithium, quetiapine, carbamazepine, clozapine"} }, { "Subject ID":"-", "Sample ID":"B11", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B11.cdf","Sex":"M","Age":"19","Height":"1.8","Weight":"84","BMI":"25.92593","Medication":"lithium, olanzapine, clonazepam,"} }, { "Subject ID":"-", "Sample ID":"B12", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B12.cdf","Sex":"F","Age":"40","Height":"1.7","Weight":"80","BMI":"27.68166","Medication":"lithium, carbamazepine, biperidene"} }, { "Subject ID":"-", "Sample ID":"B14", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B14.cdf","Sex":"F","Age":"19","Height":"1.68","Weight":"51","BMI":"18.06973","Medication":"risperidone, lithium, quetiapine"} }, { "Subject ID":"-", "Sample ID":"B15", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B15.cdf","Sex":"M","Age":"71","Height":"1.68","Weight":"64","BMI":"22.67574","Medication":"olanzapine, carbolithium, clonazepam"} }, { "Subject ID":"-", "Sample ID":"B16", "Factors":{"Condition":"Bipolar"}, "Additional sample data":{"RAW_FILE_NAME":"B16.cdf","Sex":"M","Age":"34","Height":"1.89","Weight":"85","BMI":"23.79553","Medication":"clonazepam"} }, { "Subject ID":"-", "Sample ID":"D01", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D01.cdf","Sex":"M","Age":"33","Height":"1.78","Weight":"82","BMI":"25.88057","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D02", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D02.cdf","Sex":"F","Age":"34","Height":"1.7","Weight":"72","BMI":"24.91349","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D03", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D03.cdf","Sex":"F","Age":"25","Height":"1.6","Weight":"61","BMI":"23.82813","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D04", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D04.cdf","Sex":"F","Age":"33","Height":"1.66","Weight":"59","BMI":"21.41094","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D05", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D05.cdf","Sex":"F","Age":"49","Height":"1.65","Weight":"62","BMI":"22.77319","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D06", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D06.cdf","Sex":"M","Age":"34","Height":"1.71","Weight":"70","BMI":"23.93899","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D07", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D07.cdf","Sex":"M","Age":"28","Height":"1.85","Weight":"85","BMI":"24.83565","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D08", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D08.cdf","Sex":"F","Age":"43","Height":"1.63","Weight":"72","BMI":"27.09925","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D09", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D09.cdf","Sex":"F","Age":"31","Height":"1.58","Weight":"58","BMI":"23.23346","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D10", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D10.cdf","Sex":"F","Age":"51","Height":"1.64","Weight":"68","BMI":"25.28257","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D11", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D11.cdf","Sex":"F","Age":"79","Height":"1.49","Weight":"56","BMI":"25.22409","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D12", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D12.cdf","Sex":"F","Age":"60","Height":"1.55","Weight":"67","BMI":"27.88762","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D13", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D13.cdf","Sex":"F","Age":"52","Height":"1.67","Weight":"78","BMI":"27.96802","Medication":"NA"} }, { "Subject ID":"-", "Sample ID":"D14", "Factors":{"Condition":"Control"}, "Additional sample data":{"RAW_FILE_NAME":"D14.cdf","Sex":"M","Age":"47","Height":"1.67","Weight":"72","BMI":"25.81663","Medication":"NA"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"The blood was collected in a Vacutainer tube, left at ambient temperature for 30 minutes, and then stored on ice for the blood to coagulate. Afterward, the samples were centrifuged at 3500 g for 15 minutes at 4 °C. The blood serum was collected and transferred to microtubes, stored at -80 °C for further analysis.","SAMPLE_TYPE":"Blood (serum)","STORAGE_CONDITIONS":"-80℃"}, "TREATMENT":{"TREATMENT_SUMMARY":"Samples were aliquoted into 100uL microtubes, and treated with sodium azide 0.01% (m/v), then stored in biofreezer at -80 °C until further analysis."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The metabolites from serum samples were extracted by a simple protein precipitation method, using 50 µL of serum and 150 µL of MeOH and 150 µL of pentadecanoic acid as the internal standard. The mixture was vortexed, centrifuged at 15000 RPM, subsequently separating and discarding the protein phase. The aqueous phase was then dried in a SpeedVac at room temp and the dried samples were then submitted to a two-step derivatization, where 10 µL of methoxamine hydrochloride pyridine solution (40 mg mL-1) was added to the sample, kept at 30 ºC for 90 minutes. After the first derivatization step, 90 µL of MSTFA with 1 % (v/v) of TMCS (trimethylchlorosilane) was added, with the sample being kept at 37 ºC for 30 minutes."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The following GC/MS conditions were used. An HP 5890 Series II oven was ramped by 10°C/min from 60°C (1 min initial time) to 325°C (10 min final time), resulting in a 37.5 min run time with cooling down to 60°C. 10 µL was injected into the Agilent split/splitless injector at 250°C in splitless mode. A 30 m long HP5-MS column with 10 m Duragard precolumn was used with 0.25 mm diameter and 0.25 µm film thickness. A constant flow rate of 1 mL/min helium was used as carrier gas. The quadrupole mass spectrometer was switched on after a 5.90 min solvent delay time, scanning from 50-600 u. The source temperature was set to 230°C and the quadrupole temperature was 150°C.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"HP/Agilent 5890 Series II","COLUMN_NAME":"HP5-MS (30m x 0.25mm x 0.25 um) + Duragard precolumn (10m)"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"HP 5970 Series Quadrupole Mass Selective Detector","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"The GC-MS conditions were the same as required to use the FiehnLib library (Kind et al., 2009). The data obtained were exported as ‘.AIA’ format in GC Chemstation then transformed in ‘.d’ using Agilent GC-MS translator and finally converted in ‘.abf’ format using MS-DIAL ABF file converter. The ‘.abf’ files were then analyzed in MS-DIAL (version 4.16) for peak picking, deconvolution and peak identification. The peak table containing the identifications from FiehnLib and the respective intensities in total ion chromatogram (TIC) from each metabolite were exported and analyzed using R statistical programming language (version 3.60) to evaluate the relative standard deviations (RSD) from each metabolite on the QC samples. Metabolites with RSD > 30 % were discarded due to excessive deviation through the batch. We opted to perform a second curation of the identifications using Golm Metabolite Database (GMD) since was observed a deviation of ± 0.2 minutes on the identifications comparing to the value shown in the library, caused possibly by the equipment. Metabolites that presented inconsistencies between both platforms were considered unknown, where some of these were just identified by their functional groups using one of GMD functionalities."}, "MS_METABOLITE_DATA":{ "Units":"Intensities after normalization by Internal standard and log2 transformed", "Data":[{"Metabolite":"2-hydroxybutyric acid","B01":"-4.291787269","B02":"-5.960556484","B03":"-7.37580976","B05":"-5.050733293","B06":"-5.999947127","B07":"-5.609993306","B08":"-6.664762451","B09":"-5.311903669","B10":"-5.760213824","B11":"-4.998479368","B12":"-7.094877372","B14":"-5.843149015","B15":"-5.449306618","B16":"-5.036755076","D01":"-4.165527683","D02":"-7.193933663","D03":"-5.794194329","D04":"-6.476506231","D05":"-7.649934735","D06":"-7.721924827","D07":"-5.6489022","D08":"-6.089193224","D09":"-4.860101255","D10":"-6.566052037","D11":"-6.042578044","D12":"-5.843007114","D13":"-6.103902871","D14":"-5.882757412"},{"Metabolite":"2-ketocaproic acid","B01":"-9.555766098","B02":"-9.442951992","B03":"-9.505383113","B05":"-10.10498044","B06":"-9.348091176","B07":"-9.721112261","B08":"-9.857213547","B09":"-9.763498617","B10":"-9.641556981","B11":"-8.671339869","B12":"-9.631635901","B14":"-9.82248855","B15":"-9.946175523","B16":"-9.453865865","D01":"-11.24230362","D02":"-9.926344092","D03":"-9.603739993","D04":"-9.54908833","D05":"-9.466449983","D06":"-9.684305608","D07":"-9.334464604","D08":"-9.512994312","D09":"-9.435550971","D10":"-9.26995078","D11":"-9.428656278","D12":"-9.320325229","D13":"-9.522510925","D14":"-9.436709763"},{"Metabolite":"2-ketoisocaproic acid","B01":"-7.660550554","B02":"-7.996327111","B03":"-8.143495619","B05":"-8.007404623","B06":"-7.999711983","B07":"-7.73275498","B08":"-7.843729396","B09":"-8.078942299","B10":"-7.709137321","B11":"-11.41301303","B12":"-7.62404971","B14":"-7.60285828","B15":"-7.702567368","B16":"-7.138557983","D01":"-6.949429493","D02":"-7.916101031","D03":"-7.763223024","D04":"-7.43277112","D05":"-7.98327073","D06":"-7.928377169","D07":"-7.697230655","D08":"-7.20130282","D09":"-7.474618949","D10":"-7.703797781","D11":"-7.746675815","D12":"-7.395868042","D13":"-7.933236267","D14":"-7.431348329"},{"Metabolite":"2-ketoisocaproic acid 2","B01":"-8.399399574","B02":"-8.86843943","B03":"-9.432432014","B05":"-9.111640469","B06":"-8.837697351","B07":"-9.339080637","B08":"-9.364415438","B09":"-8.374541008","B10":"-9.000527482","B11":"-8.235205028","B12":"-9.155884579","B14":"-8.85423848","B15":"-8.526092973","B16":"-8.591349983","D01":"-8.121258881","D02":"-9.855880595","D03":"-9.124193332","D04":"-8.565615115","D05":"-9.217364925","D06":"-8.887799617","D07":"-8.21736484","D08":"-8.721606296","D09":"-8.900838741","D10":"-9.277651032","D11":"-9.799104338","D12":"-8.852534315","D13":"-9.712516518","D14":"-8.725362474"},{"Metabolite":"3-hydroxypyridine","B01":"-8.752754247","B02":"-7.504229533","B03":"-9.042469844","B05":"-10.00464923","B06":"-7.427206222","B07":"-9.061180233","B08":"-8.183464792","B09":"-9.534165115","B10":"-8.320435553","B11":"-23.68645607","B12":"-8.162041874","B14":"-7.617265612","B15":"-7.622657147","B16":"-7.538378586","D01":"-21.40554194","D02":"-8.311446036","D03":"-7.503032041","D04":"-7.65980369","D05":"-7.850049093","D06":"-7.542041417","D07":"-7.685351","D08":"-7.599272076","D09":"-7.657306643","D10":"-7.256935867","D11":"-7.517485148","D12":"-7.476177475","D13":"-7.607917617","D14":"-7.488969179"},{"Metabolite":"3-indoleacetic acid","B01":"-10.80256566","B02":"-10.31679194","B03":"-12.73090854","B05":"-14.02294118","B06":"-8.088130966","B07":"-12.91363499","B08":"-8.151201814","B09":"-13.40210543","B10":"-8.884184307","B11":"-11.42953034","B12":"-12.02869488","B14":"-9.422959068","B15":"-7.898037945","B16":"-8.070041458","D01":"-21.40554194","D02":"-10.50573969","D03":"-9.887793837","D04":"-10.96156173","D05":"-10.00887851","D06":"-9.417029562","D07":"-9.351554858","D08":"-8.661595589","D09":"-9.925290949","D10":"-9.468871597","D11":"-8.988235345","D12":"-9.885795382","D13":"-9.849889186","D14":"-8.851727506"},{"Metabolite":"alpha tocophereol","B01":"-11.2011205","B02":"-9.890970613","B03":"-11.10781841","B05":"-12.49378005","B06":"-10.1919192","B07":"-10.32494964","B08":"-10.80971312","B09":"-10.39118543","B10":"-10.20459552","B11":"-11.04109575","B12":"-11.91821021","B14":"-9.981315715","B15":"-10.02405922","B16":"-9.788921623","D01":"-21.40554194","D02":"-10.7053026","D03":"-9.381874751","D04":"-10.63502411","D05":"-9.516286865","D06":"-10.74191448","D07":"-9.429950826","D08":"-9.61202884","D09":"-10.25981378","D10":"-9.806369629","D11":"-9.712410423","D12":"-10.13617912","D13":"-10.41961905","D14":"-10.52608553"},{"Metabolite":"arachidic acid","B01":"-7.170294023","B02":"-6.747216923","B03":"-7.842756952","B05":"-8.8421406","B06":"-6.492505786","B07":"-8.081084909","B08":"-7.09710936","B09":"-8.361335969","B10":"-7.086403143","B11":"-7.557409766","B12":"-8.288726151","B14":"-6.547018242","B15":"-6.612825499","B16":"-6.781524805","D01":"-9.348408851","D02":"-7.33040369","D03":"-6.537600558","D04":"-7.067983341","D05":"-6.626065","D06":"-7.338816841","D07":"-6.350726427","D08":"-6.613665239","D09":"-6.742339267","D10":"-6.524158778","D11":"-6.60617075","D12":"-6.350312843","D13":"-6.424084775","D14":"-6.506330804"},{"Metabolite":"aspartic acid","B01":"-10.62801592","B02":"-10.06301178","B03":"-14.33160798","B05":"-22.7815132","B06":"-11.18152901","B07":"-14.38733897","B08":"-10.0506801","B09":"-14.61233014","B10":"-12.00304996","B11":"-13.78837548","B12":"-14.60192734","B14":"-8.331205561","B15":"-8.592201367","B16":"-7.948657085","D01":"-21.40554194","D02":"-9.762569829","D03":"-9.645847674","D04":"-13.03368663","D05":"-10.45198453","D06":"-13.28815127","D07":"-8.799752939","D08":"-8.784169933","D09":"-8.070165447","D10":"-10.53674709","D11":"-10.78081912","D12":"-8.935966917","D13":"-9.060821473","D14":"-10.93944889"},{"Metabolite":"aspartic acid 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