#METABOLOMICS WORKBENCH schrodm_20230112_095057 DATATRACK_ID:3687 STUDY_ID:ST002440 ANALYSIS_ID:AN003977 PROJECT_ID:PR001572 VERSION 1 CREATED_ON January 13, 2023, 7:27 am #PROJECT PR:PROJECT_TITLE Impacts of interactions between environmental chemical exposures and diet on gut PR:PROJECT_TITLE microbiota and microbiota-derived metabolites in mothers and children PR:PROJECT_TYPE C18 Reversed-Phase Broad Spectrum Metabolomics PR:PROJECT_SUMMARY This project is funded by the NIH Environmental influences on Child Health PR:PROJECT_SUMMARY Outcomes (ECHO) OIF program, and uses data from two cohorts: MAAP and MARCH. PR:PROJECT_SUMMARY This project will examine associations with PFAS exposures and gut microbiota PR:PROJECT_SUMMARY form and function in mothers and children over time. Untargeted metabolomics PR:PROJECT_SUMMARY will be used as a means to assess changes in microbiota-derived metabolites. PR:INSTITUTE NC HHEAR Hub PR:DEPARTMENT Untargeted Analysis PR:LABORATORY Sumner Lab PR:LAST_NAME Li PR:FIRST_NAME Yuanyuan PR:ADDRESS Nutrition Research Institute, UNC-CH, 500 Laureate Way, Kannapolis, NC 28081 PR:EMAIL yuanyli4@unc.edu PR:PHONE 984-377-0693 PR:FUNDING_SOURCE This research was supported by the Environmental influences on Child Health PR:FUNDING_SOURCE Outcomes (ECHO) OIF program, Office of The Director, National Institutes of PR:FUNDING_SOURCE Health. The content is solely the responsibility of the authors and does not PR:FUNDING_SOURCE necessarily represent the official views of the National Institutes of Health. PR:FUNDING_SOURCE MAAP is an ECHO cohort which is supported by the following ECHO Program PR:FUNDING_SOURCE Collaborators: ECHO Coordinating Center: Duke Clinical Research Institute, PR:FUNDING_SOURCE Durham, North Carolina: Smith PB, Newby KL, Benjamin DK; U2C OD023375; ECHO Data PR:FUNDING_SOURCE Analysis Center: Johns Hopkins University Bloomberg School of Public Health, PR:FUNDING_SOURCE Baltimore, Maryland: Jacobson LP; Research Triangle Institute, Durham, North PR:FUNDING_SOURCE Carolina: Catellier.D U24 OD023382; North Carolina Human Health Exposure PR:FUNDING_SOURCE Analysis Resource Hub: Research Triangle Institute: Fennell T, University of PR:FUNDING_SOURCE North Carolina at Chapel Hill: Sumner S, University of North Carolina at PR:FUNDING_SOURCE Charlotte: Du X; U2C ES030857; Human Health Exposure Analysis Resource PR:FUNDING_SOURCE Coordinating Center: Westat, Inc., Rockville, Maryland: O’Brien B; U24 PR:FUNDING_SOURCE ES026539 #STUDY ST:STUDY_TITLE Impacts of interactions between environmental chemical exposures and diet on gut ST:STUDY_TITLE microbiota and microbiota-derived metabolites in mothers and children (MAAP ST:STUDY_TITLE Cohort) ST:STUDY_TYPE Prospective Cohort Study ST:STUDY_SUMMARY In 2014, the Microbes, Allergy, Asthma and Pets (MAAP) study (P01 AI089473) was ST:STUDY_SUMMARY launched. All women ages 18-49 years scheduled for prenatal visits at Henry Ford ST:STUDY_SUMMARY Health, expected to deliver during the recruitment period at a Henry Ford Health ST:STUDY_SUMMARY hospital, and whose residence was in a predefined area of Detroit and ST:STUDY_SUMMARY metropolitan Detroit suburbs were potentially eligible. There were no medical ST:STUDY_SUMMARY insurance requirements. Between 2014 and 2016, 141 women were enrolled; their ST:STUDY_SUMMARY infant was followed through age 18 months (with continuing follow-up through ST:STUDY_SUMMARY early/mid childhood underway through the NIH ECHO program under the CREW birth ST:STUDY_SUMMARY cohort consortium (5UG3OD023282, Gern PI). Blood and stool samples were obtained ST:STUDY_SUMMARY from the mother prenatally and stool specimens were obtained from the infant at ST:STUDY_SUMMARY 5 time points (1-week, 1-, 3-, 6- and 18-months) with 16S sequencing already ST:STUDY_SUMMARY completed. Blood was also obtained from the infant at pre-defined intervals. ST:STUDY_SUMMARY Please contact Andrea Cassidy-Bushrow at acassid1@hfhs.org for questions related ST:STUDY_SUMMARY to the subject characteristics and outcomes. This research was supported by the ST:STUDY_SUMMARY Environmental influences on Child Health Outcomes (ECHO) OIF program, Office of ST:STUDY_SUMMARY The Director, National Institutes of Health. The content is solely the ST:STUDY_SUMMARY responsibility of the authors and does not necessarily represent the official ST:STUDY_SUMMARY views of the National Institutes of Health. MAAP is an ECHO cohort which is ST:STUDY_SUMMARY supported by the following ECHO Program Collaborators: ECHO Coordinating Center: ST:STUDY_SUMMARY Duke Clinical Research Institute, Durham, North Carolina: Smith PB, Newby KL, ST:STUDY_SUMMARY Benjamin DK; U2C OD023375 ECHO Data Analysis Center: Johns Hopkins University ST:STUDY_SUMMARY Bloomberg School of Public Health, Baltimore, Maryland: Jacobson LP; Research ST:STUDY_SUMMARY Triangle Institute, Durham, North Carolina: Catellier.D U24 OD023382 North ST:STUDY_SUMMARY Carolina Human Health Exposure Analysis Resource Hub: Research Triangle ST:STUDY_SUMMARY Institute: Fennell T, University of North Carolina at Chapel Hill: Sumner S, ST:STUDY_SUMMARY University of North Carolina at Charlotte: Du X; U2C ES030857 Human Health ST:STUDY_SUMMARY Exposure Analysis Resource Coordinating Center: Westat, Inc., Rockville, ST:STUDY_SUMMARY Maryland: O’Brien B; U24 ES026539 ST:INSTITUTE Wayne State University ST:DEPARTMENT Pharmacology ST:LAST_NAME Petriello ST:FIRST_NAME Michael ST:ADDRESS 6135 Woodward Ave, Detroit, MI 48202 ST:EMAIL michael.petriello@wayne.edu ST:PHONE 313-577-1089 ST:TOTAL_SUBJECTS 31 ST:STUDY_COMMENTS ECHO Project EC0549, HHEAR Project E020-0012 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS N/A MAAP_HHEAR_1 Sample Type:HHEAR Pool RAW_FILE_NAME=MAAP_HHEAR_1 SUBJECT_SAMPLE_FACTORS N/A MAAP_HHEAR_2 Sample Type:HHEAR Pool RAW_FILE_NAME=MAAP_HHEAR_2 SUBJECT_SAMPLE_FACTORS N/A MAAP_HHEAR_3 Sample Type:HHEAR Pool RAW_FILE_NAME=MAAP_HHEAR_3 SUBJECT_SAMPLE_FACTORS N/A MAAP_HHEAR_4 Sample Type:HHEAR Pool RAW_FILE_NAME=MAAP_HHEAR_4 SUBJECT_SAMPLE_FACTORS N/A MAAP_NIST_1 Sample Type:NIST Pool RAW_FILE_NAME=MAAP_NIST_1 SUBJECT_SAMPLE_FACTORS N/A MAAP_NIST_2 Sample Type:NIST Pool RAW_FILE_NAME=MAAP_NIST_2 SUBJECT_SAMPLE_FACTORS N/A MAAP_NIST_3 Sample Type:NIST Pool RAW_FILE_NAME=MAAP_NIST_3 SUBJECT_SAMPLE_FACTORS N/A MAAP_NIST_4 Sample Type:NIST Pool RAW_FILE_NAME=MAAP_NIST_4 SUBJECT_SAMPLE_FACTORS EO-7NXJ0-P-00-11302 MAAP_S_1 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_1 SUBJECT_SAMPLE_FACTORS EO-7N015-P-00-11302 MAAP_S_2 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_2 SUBJECT_SAMPLE_FACTORS EO-7NVJ2-P-00-11302 MAAP_S_3 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_3 SUBJECT_SAMPLE_FACTORS EO-7NR03-P-00-11302 MAAP_S_4 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_4 SUBJECT_SAMPLE_FACTORS EO-7N4A6-P-00-11302 MAAP_S_5 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_5 SUBJECT_SAMPLE_FACTORS EO-7P2K2-P-00-11302 MAAP_S_6 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_6 SUBJECT_SAMPLE_FACTORS EO-7N528-P-00-11302 MAAP_S_7 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_7 SUBJECT_SAMPLE_FACTORS EO-7N981-P-00-11302 MAAP_S_8 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_8 SUBJECT_SAMPLE_FACTORS EO-7NKQ8-P-00-11302 MAAP_S_9 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_9 SUBJECT_SAMPLE_FACTORS EO-7NHF5-P-00-11302 MAAP_S_10 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_10 SUBJECT_SAMPLE_FACTORS EO-7NMG8-P-00-11302 MAAP_S_11 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_11 SUBJECT_SAMPLE_FACTORS EO-7N1M3-P-00-11302 MAAP_S_12 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_12 SUBJECT_SAMPLE_FACTORS EO-7N353-P-00-11302 MAAP_S_13 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_13 SUBJECT_SAMPLE_FACTORS EO-7N841-P-00-11302 MAAP_S_14 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_14 SUBJECT_SAMPLE_FACTORS EO-7NZ54-P-00-11302 MAAP_S_15 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_15 SUBJECT_SAMPLE_FACTORS EO-7NQ53-P-00-11302 MAAP_S_16 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_16 SUBJECT_SAMPLE_FACTORS EO-7NJ92-P-00-11302 MAAP_S_17 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_17 SUBJECT_SAMPLE_FACTORS EO-7NKK1-P-00-11302 MAAP_S_18 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_18 SUBJECT_SAMPLE_FACTORS EO-7NR94-P-00-11302 MAAP_S_19 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_19 SUBJECT_SAMPLE_FACTORS EO-7N2H3-P-00-11302 MAAP_S_20 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_20 SUBJECT_SAMPLE_FACTORS EO-7NXP7-P-00-11302 MAAP_S_21 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_21 SUBJECT_SAMPLE_FACTORS EO-7N338-P-00-11302 MAAP_S_22 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_22 SUBJECT_SAMPLE_FACTORS EO-7NL33-P-00-11302 MAAP_S_23 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_23 SUBJECT_SAMPLE_FACTORS EO-7NGG4-P-00-11302 MAAP_S_24 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_24 SUBJECT_SAMPLE_FACTORS EO-7N2C4-P-00-11302 MAAP_S_25 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_25 SUBJECT_SAMPLE_FACTORS EO-7NR29-P-00-11302 MAAP_S_26 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_26 SUBJECT_SAMPLE_FACTORS EO-7NW08-P-00-11302 MAAP_S_27 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_27 SUBJECT_SAMPLE_FACTORS EO-7P0D9-P-00-11302 MAAP_S_28 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_28 SUBJECT_SAMPLE_FACTORS EO-7NYH4-P-00-11302 MAAP_S_29 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_29 SUBJECT_SAMPLE_FACTORS EO-7NR11-P-00-11302 MAAP_S_30 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_30 SUBJECT_SAMPLE_FACTORS EO-7P2Q9-P-00-11302 MAAP_S_31 Sample Type:Study Sample RAW_FILE_NAME=MAAP_S_31 SUBJECT_SAMPLE_FACTORS N/A MAAP_SP_1 Sample Type:Study Pool RAW_FILE_NAME=MAAP_SP_1 SUBJECT_SAMPLE_FACTORS N/A MAAP_SP_2 Sample Type:Study Pool RAW_FILE_NAME=MAAP_SP_2 SUBJECT_SAMPLE_FACTORS N/A MAAP_SP_3 Sample Type:Study Pool RAW_FILE_NAME=MAAP_SP_3 SUBJECT_SAMPLE_FACTORS N/A MAAP_SP_4 Sample Type:Study Pool RAW_FILE_NAME=MAAP_SP_4 #COLLECTION CO:COLLECTION_SUMMARY In 2014, the Microbes, Allergy, Asthma and Pets (MAAP) study (P01 AI089473) was CO:COLLECTION_SUMMARY launched. All women ages 18-49 years scheduled for prenatal visits at Henry Ford CO:COLLECTION_SUMMARY Health, expected to deliver during the recruitment period at a Henry Ford Health CO:COLLECTION_SUMMARY hospital, and whose residence was in a predefined area of Detroit and CO:COLLECTION_SUMMARY metropolitan Detroit suburbs were potentially eligible. There were no medical CO:COLLECTION_SUMMARY insurance requirements. Between 2014 and 2016, 141 women were enrolled; their CO:COLLECTION_SUMMARY infant was followed through age 18 months (with continuing follow-up through CO:COLLECTION_SUMMARY early/mid childhood underway through the NIH ECHO program under the CREW birth CO:COLLECTION_SUMMARY cohort consortium (5UG3OD023282, Gern PI). Blood and stool samples were obtained CO:COLLECTION_SUMMARY from the mother prenatally and stool specimens were obtained from the infant at CO:COLLECTION_SUMMARY 5 time points (1-week, 1-, 3-, 6- and 18-months) with 16S sequencing already CO:COLLECTION_SUMMARY completed. Blood was also obtained from the infant at pre-defined intervals. CO:COLLECTION_SUMMARY Please contact Andrea Cassidy-Bushrow at acassid1@hfhs.org for questions related CO:COLLECTION_SUMMARY to the subject characteristics and outcomes. CO:SAMPLE_TYPE Blood (plasma) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY N/A #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Study samples (500-1000 µL aliquots) were shipped from the Henry Ford Health SP:SAMPLEPREP_SUMMARY System to the NC HHEAR Hub on dry ice. The NC HHEAR Hub thawed and aliquoted the SP:SAMPLEPREP_SUMMARY study samples at 50 µL per aliquot. An additional 10 µL was taken from each SP:SAMPLEPREP_SUMMARY study sample, mixed, and distributed at 50 µL per aliquot, which were used as SP:SAMPLEPREP_SUMMARY QC study pools throughout the study. HHEAR reference plasma (50 µL each) and SP:SAMPLEPREP_SUMMARY NIST plasma (1950) reference material (50 µL each) were provided by the NC SP:SAMPLEPREP_SUMMARY HHEAR Hub. LC-MS grade water (50 µL) was used as blank. All samples were thawed SP:SAMPLEPREP_SUMMARY at 4°C overnight before the preparation. Samples, including study samples, SP:SAMPLEPREP_SUMMARY study pool samples, HHEAR reference plasma, NIST reference plasma, and blanks SP:SAMPLEPREP_SUMMARY were mixed with 400 µL methanol containing 500 ng/mL tryptophan-d5 as internal SP:SAMPLEPREP_SUMMARY standard and vortexed by a multiple tube vortex mixer for 2 min at 5000 rpm at SP:SAMPLEPREP_SUMMARY room temperature. All samples were centrifuged at 16,000 rcf for 10 min at 4°C. SP:SAMPLEPREP_SUMMARY The supernatant (350 µL) was transferred into a pre-labeled 2.0 mL Lo-bind SP:SAMPLEPREP_SUMMARY Eppendorf tube, dried by a SpeedVac overnight, and stored at -80° C. For SP:SAMPLEPREP_SUMMARY immediate analysis, 100 µL of water-methanol solution (95:5, v/v) was used to SP:SAMPLEPREP_SUMMARY reconstitute the dried extracts. Samples were thoroughly mixed on a multiple SP:SAMPLEPREP_SUMMARY tube vortex mixer for 10 min at 5000 rpm at room temperature and then SP:SAMPLEPREP_SUMMARY centrifuged at 4°C for 10 min at 16,000 rcf. The supernatant was transferred to SP:SAMPLEPREP_SUMMARY pre-labeled autosampler vials for data acquisition by LC-MS. SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACTION_METHOD Vortex with methanol containing 500ng/ml tryptophan-d5 as internal standard SP:EXTRACT_STORAGE -80℃ SP:SAMPLE_RESUSPENSION Water-Methanol (95:5, v/v) SP:SAMPLE_SPIKING Tryptophan-d5 stock solution at 500 ng/mL #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% methanol; 0.1% formic acid CH:FLOW_GRADIENT Time(min) Flow Rate %A %B Curve 1. 0 0.4 99.0 1.0 5 2. 1.00 0.4 99.0 1.0 5 3. CH:FLOW_GRADIENT 16.00 0.4 1.0 99.0 5 4. 19.00 0.4 1.0 99.0 5 5. 19.50 0.4 99.0 1.0 5 6. 22.00 CH:FLOW_GRADIENT 0.4 99.0 1.0 5 CH:FLOW_RATE 0.4 mL/min CH:COLUMN_TEMPERATURE 50 CH:COLUMN_PRESSURE 6000-10000 psi CH:INJECTION_TEMPERATURE 8 CH:INTERNAL_STANDARD Tryptophan-d5 CH:ANALYTICAL_TIME 22 min CH:WEAK_WASH_SOLVENT_NAME 10:90 Methanol:Water with 0.1% FA solution CH:STRONG_WASH_SOLVENT_NAME 75:25 2-Propanol:Water with 0.1% FA solution #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF-X Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Xcalibur 4.1.31.9 for data acquisition; Progenesis QI 2.4 for data preprocessing MS:CAPILLARY_TEMPERATURE 320 °C MS:CAPILLARY_VOLTAGE 3.5 kV MS:COLLISION_ENERGY 20-45, ramp MS:COLLISION_GAS N2 MS:DRY_GAS_TEMP 400°C MS:FRAGMENTATION_METHOD CID MS:DESOLVATION_GAS_FLOW 55 MS:MS_RESULTS_FILE ST002440_AN003977_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END