Summary of Study ST000972
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000665. The data can be accessed directly via it's Project DOI: 10.21228/M8QD6T This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST000972 |
| 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 |
| bmisra@wakehealth.edu | |
| Phone | 3522156040 |
| Submit Date | 2018-05-16 |
| Total Subjects | 1 |
| Num Males | 1 |
| Study Comments | NA |
| Publications | High Resolution GC/MS Metabolomics of Non‐Human Primate Serum: Biswapriya B. Misra, Ekong Bassey, Andrew C. Bishop, David T. Kusel, Laura A. Cox,Michael Olivier; Rapid Communications in Mass Spectrometry, DOI: https://doi.org/10.1002/rcm.8197 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2018-05-30 |
| Release Version | 1 |
| Release Comments | Earlier release date was 2018-11-16, submitter requested to remove embargo on 30 May, 2018 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000665 |
| Project DOI: | doi: 10.21228/M8QD6T |
| 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: | High Resolution GC/MS Metabolomics of Non‐Human Primate Serum: Biswapriya B. Misra, Ekong Bassey, Andrew C. Bishop, David T. Kusel, Laura A. Cox,Michael Olivier; Rapid Communications in Mass Spectrometry, DOI: https://doi.org/10.1002/rcm.8197 |
| Contributors: | Biswapriya B. Misra, Ekong Bassey, Andrew C. Bishop, David T. Kusel, Laura A. Cox, Michael Olivier |
Subject:
| Subject ID: | SU001011 |
| Subject Type: | Other |
| Subject Species: | Papio hamadryas |
| Taxonomy ID: | 9557 |
| Age Or Age Range: | 18 |
| Gender: | Male |
Factors:
Subject type: Other; Subject species: Papio hamadryas (Factor headings shown in green)
| mb_sample_id | local_sample_id | Platform Type |
|---|---|---|
| SA058592 | S3_2 | 2D GC-ToF-MS |
| SA058593 | S3_3 | 2D GC-ToF-MS |
| SA058594 | S1_1 | 2D GC-ToF-MS |
| SA058595 | S2_3 | 2D GC-ToF-MS |
| SA058596 | S3_1 | 2D GC-ToF-MS |
| SA058597 | S1_2 | 2D GC-ToF-MS |
| SA058598 | S2_1 | 2D GC-ToF-MS |
| SA058599 | S1_3 | 2D GC-ToF-MS |
| SA058600 | S2_2 | 2D GC-ToF-MS |
| SA058601 | S8_1 | GC-Orbitrap-MS |
| SA058602 | S8_2 | GC-Orbitrap-MS |
| SA058603 | S8_3 | GC-Orbitrap-MS |
| SA058604 | S7_3 | GC-Orbitrap-MS |
| SA058605 | S6_1 | GC-Orbitrap-MS |
| SA058606 | S6_2 | GC-Orbitrap-MS |
| SA058607 | S6_3 | GC-Orbitrap-MS |
| SA058608 | S7_1 | GC-Orbitrap-MS |
| SA058609 | S7_2 | GC-Orbitrap-MS |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO001005 |
| 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 ID: | TR001025 |
| Treatment Summary: | None |
Sample Preparation:
| Sampleprep ID: | SP001018 |
| 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 |
Combined analysis:
| Analysis ID | AN001592 | AN001593 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | GC | GC |
| Chromatography system | Leco Pegasus 4D GC | Thermo Trace 1310 |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) | Thermo Scientific TraceGOLD TG-5SILMS (30m x 0.25 mm,0.25um) |
| MS Type | EI | EI |
| MS instrument type | GC x GC-TOF | Orbitrap |
| MS instrument name | Leco Pegasus 4D GCxGC TOF | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE |
| Units | Arbitrary units | Arbitrary units |
Chromatography:
| Chromatography ID: | CH001117 |
| Chromatography Summary: | 1µL of derivatized sample into a split/splitless (SSL) injector at 250 °C using a splitless injection on a Thermo Scientific™ TRACE™ 1310 GC. Helium carrier gas at a flow rate of 1 mL/min was used for separation on a Thermo Scientific™ TraceGOLD™ TG-5SILMS 30 m length × 0.25 mm i.d. × 0.25 µm film thickness column. The initial oven temperature was held at 70 °C for 4 min, followed by an initial gradient of 20 °C/min ramp rate. The final temperature was 320 °C and held for 8 min. |
| Chromatography Comments: | 2D GC |
| Instrument Name: | Leco Pegasus 4D GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 250 |
| Internal Standard: | Adonitol, d4-succinic acid |
| Sample Injection: | 1 uL |
| Running Buffer: | Helium |
| Transferline Temperature: | 250 |
| Randomization Order: | Yes |
| Chromatography Type: | GC |
| Chromatography ID: | CH001118 |
| 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. |
| Instrument Name: | Thermo Trace 1310 |
| Column Name: | Thermo Scientific TraceGOLD TG-5SILMS (30m x 0.25 mm,0.25um) |
| Injection Temperature: | 250 |
| Internal Standard: | Adonitol, d4-succinic acid |
| Sample Injection: | 1 uL |
| Running Buffer: | Helium |
| Transferline Temperature: | 250 |
| Randomization Order: | Yes |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001470 |
| Analysis ID: | AN001592 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Fragment Voltage: | -70 eV |
| Fragmentation Method: | EI |
| Helium Flow: | 1 ml/min |
| Ion Source Temperature: | 250 |
| Mass Accuracy: | Unit resolution |
| Scan Range Moverz: | 40-600 |
| Scanning: | 200 scans/s |
| MS ID: | MS001471 |
| Analysis ID: | AN001593 |
| 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 |
