#METABOLOMICS WORKBENCH walsaks_20171202_172455 DATATRACK_ID:1274 STUDY_ID:ST000934 ANALYSIS_ID:AN001531 PROJECT_ID:PR000646 VERSION 1 CREATED_ON March 5, 2018, 2:53 pm #PROJECT PR:PROJECT_TITLE Identification of biomarkers in schistosomiasis and associated bladder cancer PR:PROJECT_TITLE and pathologies in Eggua, Nigeria PR:PROJECT_SUMMARY The aim of the project is to develop biomarkers that will aid the search for new PR:PROJECT_SUMMARY therapeutic or diagnostic targets for schistosomiasis and its induced bladder PR:PROJECT_SUMMARY pathologies or cancer. Blood and urine samples from individuals were collected PR:PROJECT_SUMMARY in Eggua, Nigeria for subsequent metabolomics, proteomics and genomics PR:PROJECT_SUMMARY characterization PR:INSTITUTE University of Ibadan, Nigeria PR:DEPARTMENT Zoology (Cell biology and Genetics unit) PR:LABORATORY Centre for Materials Characterization, National Chemical Laboratory, Pune, India PR:LAST_NAME Adewale PR:FIRST_NAME Adebayo PR:ADDRESS Cell Biology and Genetics unit, Department of zoology, University of ibadan, PR:ADDRESS Nigeria/ National Centre for Cell Science, Pune, India PR:EMAIL walsaks@gmail.com PR:PHONE 07030710368 #STUDY ST:STUDY_TITLE Metabolome profiles in urogenital schistosomiasis and associated pathologies ST:STUDY_SUMMARY Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were ST:STUDY_SUMMARY collected from volunteers in Eggua community, Nigeria, after ethical approval. ST:STUDY_SUMMARY LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools ST:STUDY_SUMMARY were used to detect important metabolites ST:INSTITUTE University of Ibadan, Nigeria ST:DEPARTMENT Zoology (Cell biology and Genetics unit) ST:LABORATORY Centre for Materials Characterization, National Chemical Laboratory, Pune, India ST:LAST_NAME Adebayo ST:FIRST_NAME Adewale ST:ADDRESS Cell Biology and Genetics unit, Department of zoology, University of ibadan, ST:ADDRESS Nigeria/ National Centre for Cell Science, Pune, India ST:EMAIL walsaks@gmail.com ST:PHONE 07030710368 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:HUMAN_ETHNICITY Yoruba SU:HUMAN_INCLUSION_CRITERIA apparent health, no recent treatment for any disease, no recent use of SU:HUMAN_INCLUSION_CRITERIA antibiotics, antimalarial or other drugs #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-0041 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-0042 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-0043 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-221 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-222 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-223 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-391 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-392 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-393 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-401 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-402 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-403 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-461 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-462 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS S-463 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=PLASMA; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-41 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-42 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-43 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-162 Status:INFECTED | Stage:ADVANCED SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-221 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-222 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-223 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-391 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-392 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-393 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-401 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-402 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-403 Status:CONTROL | Stage:CONTROL SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-461 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-462 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-463 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE SUBJECT_SAMPLE_FACTORS HOMO SAPIENS U-1122 Status:INFECTED | Stage:INFECTION-ONLY SAMPLE_TYPE=URINE; IONISATION=NEGATIVE #COLLECTION CO:COLLECTION_SUMMARY blood and urine samples collected from volunteers in the morning hours. Plasma CO:COLLECTION_SUMMARY was separated from blood. urine was examined for S. haematobium infection. CO:COLLECTION_SUMMARY Distended Bladder scans were carried out CO:COLLECTION_PROTOCOL_ID UI/EC/15/0019 CO:SAMPLE_TYPE blood and urine #TREATMENT TR:TREATMENT_SUMMARY Samples were categorised as infected, infected with pathologies, and controls. TR:TREATMENT_SUMMARY Infection with Schistosoma haematobium infection by examining urine under the TR:TREATMENT_SUMMARY microscopy to detect eggs and by amplifying Dra 1 region. Pathologies were TR:TREATMENT_SUMMARY determined ultrasonography #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Both urine and plasma samples were prepared using chilled methanol:water mixture SP:SAMPLEPREP_SUMMARY (4:1). Separation was achieved with 150mm x 2.1mm, 1.9μ Hypersil Gold column SP:SAMPLEPREP_SUMMARY with a 5μl injection volume. MS acquisition was performed on the Q-Exactive SP:SAMPLEPREP_SUMMARY hybrid quadrupole orbitrap mass spectrometer #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Both urine and plasma samples were prepared using chilled methanol:water mixture CH:CHROMATOGRAPHY_SUMMARY (4:1). Separation was achieved with 150mm x 2.1mm, 1.9μ Hypersil Gold column CH:CHROMATOGRAPHY_SUMMARY with a 5μl injection volume. Gradient elution was performed using 0.1% formic CH:CHROMATOGRAPHY_SUMMARY acid in water (A) and acetonitrile (B) as mobile phase after optimization. The CH:CHROMATOGRAPHY_SUMMARY column was washed between each sample for stability and to eliminate carry-over. CH:CHROMATOGRAPHY_SUMMARY The flow rate was 0.35 ml/min. MS acquisition was performed on the Q-Exactive CH:CHROMATOGRAPHY_SUMMARY hybrid quadrupole orbitrap mass spectrometer (ThermoFisher, MA, USA) operated in CH:CHROMATOGRAPHY_SUMMARY positive and negative electrospray ionization (ESI) modes. The scan range was 70 CH:CHROMATOGRAPHY_SUMMARY to 1000 m/z. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Q-Exactive hybrid quadrupole orbitrap mass spectrometer CH:COLUMN_NAME Hypersil Gold column #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST000934_AN001531_Results.txt UNITS:abundance of specific m/z (amu) #END