{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000972","ANALYSIS_ID":"AN001593","VERSION":"1","CREATED_ON":"May 22, 2018, 1:17 pm"}, "PROJECT":{"PROJECT_TITLE":"High Resolution GC-MS Metabolomics of Non-Human Primate Serum","PROJECT_TYPE":"Method Development in Metabolomics","PROJECT_SUMMARY":"Rationale: Metabolomics analyses using gas chromatography mass spectrometry (GC-MS) - based metabolomics are heavily impeded by the lack of high-resolution mass spectrometers and limited spectral libraries to complement the excellent chromatography that GC platforms offer, a challenge that is being addressed with the implementation of high resolution (HR) platforms such as GC-Orbitrap-MS. Methods: We used serum samples from a non-human primate (NHP), a baboon (Papio hamadryas), with suitable quality controls to quantify the chemical space using an advanced HR MS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a comparative approach, we also analyzed the same serum samples using a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) for metabolite identification and quantification following established standard protocols. Results: Overall, the 2D GC-ToF-MS and GC-Orbitrap-MS analyses enabled identification and quantification of 555 total metabolites from the NHP serum with a spectral similarity score Rsim ≥ 900 and S/R ratio of > 25. A common set of 30 metabolites with HMDB and KEGG IDs were quantified in the serum samples by both platforms where the 2D GC-ToF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and the GC-Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Conclusions: Our study provides insights into the benefits and limitations of the use of a higher mass accuracy instrument for untargeted GC-MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.","INSTITUTE":"Wake Forest School of Medicine","DEPARTMENT":"Center for Precision Medicine","LABORATORY":"Michael Olivier Laboratory","LAST_NAME":"Misra","FIRST_NAME":"Biswapriya","ADDRESS":"NRC Building, Room G#43, Medical Center Boulevard, Winston Salem, NC, USA","EMAIL":"bmisra@wakehealth.edu","PHONE":"3522156040","FUNDING_SOURCE":"NA","PROJECT_COMMENTS":"NA","PUBLICATIONS":"In process","CONTRIBUTORS":"Biswapriya B. Misra, Ekong Bassey, Andrew C. Bishop, David T. Kusel, Laura A. Cox, Michael Olivier"}, "STUDY":{"STUDY_TITLE":"High Resolution GC-MS Metabolomics of Non-Human Primate Serum","STUDY_TYPE":"Non-human Primate Serum","STUDY_SUMMARY":"Rationale: Metabolomics analyses using gas chromatography mass spectrometry (GC-MS) - based metabolomics are heavily impeded by the lack of high-resolution mass spectrometers and limited spectral libraries to complement the excellent chromatography that GC platforms offer, a challenge that is being addressed with the implementation of high resolution (HR) platforms such as GC-Orbitrap-MS. Methods: We used serum samples from a non-human primate (NHP), a baboon (Papio hamadryas), with suitable quality controls to quantify the chemical space using an advanced HR MS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a comparative approach, we also analyzed the same serum samples using a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) for metabolite identification and quantification following established standard protocols. Results: Overall, the 2D GC-ToF-MS and GC-Orbitrap-MS analyses enabled identification and quantification of 555 total metabolites from the NHP serum with a spectral similarity score Rsim ≥ 900 and S/R ratio of > 25. A common set of 30 metabolites with HMDB and KEGG IDs were quantified in the serum samples by both platforms where the 2D GC-ToF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and the GC-Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Conclusions: Our study provides insights into the benefits and limitations of the use of a higher mass accuracy instrument for untargeted GC-MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.","INSTITUTE":"Wake Forest School of Medicine","DEPARTMENT":"Center for Precision Medicine","LABORATORY":"Michael Olivier Laboratory","LAST_NAME":"Misra","FIRST_NAME":"Biswapriya","ADDRESS":"NRC Building, Medical Center Boulevard","EMAIL":"bmisra@wakehealth.edu","PHONE":"3522156040","TOTAL_SUBJECTS":"1","NUM_MALES":"1","STUDY_COMMENTS":"NA","PUBLICATIONS":"In process"}, "SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Papio hamadryas","TAXONOMY_ID":"9557","AGE_OR_AGE_RANGE":"18","GENDER":"Male"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"S1_1", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S1_2", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S1_3", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S2_1", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S2_2", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S2_3", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S3_1", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S3_2", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S3_3", "Factors":{"Platform Type":"2D GC-ToF-MS"} }, { "Subject ID":"-", "Sample ID":"S6_1", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S6_2", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S6_3", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S7_1", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S7_2", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S7_3", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S8_1", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S8_2", "Factors":{"Platform Type":"GC-Orbitrap-MS"} }, { "Subject ID":"-", "Sample ID":"S8_3", "Factors":{"Platform Type":"GC-Orbitrap-MS"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"All procedures involving animals were reviewed and approved by the Texas Biomedical Research Institute’s Institutional Animal Care and Use Committee and conducted in AAALAC approved facilities. For this study, we utilized a healthy adult male olive baboon (Papio hamadryas) maintained as part of the baboon colony at the Southwest National Primate Research Center, located on the campus of the Texas Biomedical Research Institute, San Antonio, Texas. The male baboon used in this study was 18 yrs. old. The baboon had been raised and maintained on a standard monkey chow diet (high complex carbohydrates; low fat) prior to the fasting blood collection. All procedures involving animals were reviewed and approved by the Texas Biomedical Research Institute’s Institutional Animal Care and Use Committee (IACUC). Freshly collected serum samples were stored in aliquots at -80 C until analysis.","SAMPLE_TYPE":"Blood (serum)","COLLECTION_LOCATION":"Southwest National Primate Research Center, San Antonio, Texas, USA","COLLECTION_FREQUENCY":"1","COLLECTION_DURATION":"NA","VOLUMEORAMOUNT_COLLECTED":"40 mL","STORAGE_CONDITIONS":"-80℃","COLLECTION_TUBE_TEMP":"4 C","ADDITIVES":"None"}, "TREATMENT":{"TREATMENT_SUMMARY":"None"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Aliquots of serum (30 µL) samples were subjected to sequential solvent extraction once each with 1 mL of acetonitrile: isopropanol: water (3:3:2) and 500 µL of acetonitrile: water (1:1) mixtures at 4 C.22 Adonitol and d4-succinic acid (both 5 µL from 10 mg/ml stock) were added to each aliquots as two internal standards prior to the extraction. The pooled extracts (~ 1500 µL) from the two steps were dried under vacuum at 4 C prior to chemical derivatization. Dummy extractions performed on blank tubes served as extraction blanks to account for background (extraction) noise and other sources of contamination. Six (S1, S2, S3, S6, S7, S8) samples were then sequentially derivatized with methoxyamine hydrochloride (MeOX) and 1% TMCS in N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) as described elsewhere.23,24 Steps involved addition of 10 μL of MeOX (20 mg mL-1) in pyridine incubated under shaking at 55 °C for 60 min followed by trimethylsilylation at 60 °C for 60 min after adding 90 μL MSTFA.","PROCESSING_METHOD":"Fiehn et al., 2008","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"Fiehn et al., 2008","EXTRACT_ENRICHMENT":"None","EXTRACT_CLEANUP":"None","EXTRACT_STORAGE":"-80℃","SAMPLE_DERIVATIZATION":"Methoxyamination + silylation (MSTFA)","SAMPLE_SPIKING":"Adonitol, d4-succinic acid"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples were injected in splitless mode using an autosampler (VCTS, Gerstel™, Linthicum, MD, USA) consisting of an Agilent© 7890 B gas chromatograph (Agilent Technologies, Palo Alto, CA, USA) in line with a Pegasus ® 4D ToF-MS instrument (Leco Corp., San Jose, CA, USA) equipped with an electron impact (EI) ionization source. Injection temperature was set at 250 °C (front inlet) and the helium (carrier gas) flow rate was set to 1 mL min-1. Separation on the GC was achieved using two columns, a primary Rxi®-5Sil MS capillary column (Cat. No. 13623-6850, Restek, Bellefonte, PA, USA) (30 m × 0.25 mm × 0.25 μm) in line with a secondary Rxi®-17Sil capillary column (Cat. No. 40201-6850, Restek, Bellefonte, PA, USA) (2 m × 0.15 mm × 0.15 μm). The temperature program for the primary column started isothermal at 70 °C for 1 min followed by a 6 °C min-1 ramp to 310 °C and a final 11 min hold at 310 °C. The secondary oven temperature was programmed with an offset of 5°C whereas the modulator temperature offset was 15° C relative to the first oven temperature. The modulation temperature (second-dimension separation time) was 4 s divided into a hot and cold pulse times of 0.60 s and 1.4 s, respectively between the two stages.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Thermo Trace 1310","COLUMN_NAME":"a Thermo Scientificâ„¢ TraceGOLDâ„¢ TG-5SILMS 30 m length × 0.25 mm i.d. × 0.25 µm 0.25 µm","INJECTION_TEMPERATURE":"250","INTERNAL_STANDARD":"Adonitol, d4-succinic acid","SAMPLE_INJECTION":"1 uL","RUNNING_BUFFER":"Helium","TRANSFERLINE_TEMPERATURE":"250","RANDOMIZATION_ORDER":"Yes"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"ThermoFisher Scientific","OPERATOR_NAME":"Ekong Bassey","DETECTOR_TYPE":"Orbitrap","SOFTWARE_VERSION":"Tracefinder™ 4.1","DATA_FORMAT":".RAW"}, "MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"EI","ION_MODE":"POSITIVE","FRAGMENT_VOLTAGE":"-70 eV","FRAGMENTATION_METHOD":"EI","HELIUM_FLOW":"1 ml/min","ION_SOURCE_TEMPERATURE":"250","MASS_ACCURACY":"60,000 resolution (FWHM at m/z 200","SCAN_RANGE_MOVERZ":"50-650","MS_RESULTS_FILE":"ST000972_AN001593_Results.txt UNITS:Arbitrary units"}, "MS_METABOLITE_DATA":{ "Units":"Arbitrary units", "Data":[{"Metabolite":"Cholesterol","S6_1":"909334669","S6_2":"908832248","S6_3":"933549867","S7_1":"887555438","S7_2":"1052059898","S7_3":"1046267800","S8_1":"1027202906","S8_2":"993828515","S8_3":"1034958520"},{"Metabolite":"Epinephrine","S6_1":"186622123","S6_2":"231162651","S6_3":"266222802","S7_1":"","S7_2":"506239448","S7_3":"237000342","S8_1":"226126548","S8_2":"81136320","S8_3":"266623619"},{"Metabolite":"Citric 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