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.

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Study IDST000972
Study TitleHigh Resolution GC-MS Metabolomics of Non-Human Primate Serum
Study TypeNon-human Primate Serum
Study SummaryRationale: 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
DepartmentCenter for Precision Medicine
LaboratoryMichael Olivier Laboratory
Last NameMisra
First NameBiswapriya
AddressNRC Building, Medical Center Boulevard
Emailbmisra@wakehealth.edu
Phone3522156040
Submit Date2018-05-16
Total Subjects1
Num Males1
Study CommentsNA
PublicationsHigh 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 AvailableYes
Raw Data File Type(s).raw, .cdf
Analysis Type DetailGC-MS
Release Date2018-05-30
Release Version1
Release CommentsEarlier release date was 2018-11-16, submitter requested to remove embargo on 30 May, 2018
Biswapriya Misra Biswapriya Misra
https://dx.doi.org/10.21228/M8QD6T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA058592S3_22D GC-ToF-MS
SA058593S3_32D GC-ToF-MS
SA058594S1_12D GC-ToF-MS
SA058595S2_32D GC-ToF-MS
SA058596S3_12D GC-ToF-MS
SA058597S1_22D GC-ToF-MS
SA058598S2_12D GC-ToF-MS
SA058599S1_32D GC-ToF-MS
SA058600S2_22D GC-ToF-MS
SA058601S8_1GC-Orbitrap-MS
SA058602S8_2GC-Orbitrap-MS
SA058603S8_3GC-Orbitrap-MS
SA058604S7_3GC-Orbitrap-MS
SA058605S6_1GC-Orbitrap-MS
SA058606S6_2GC-Orbitrap-MS
SA058607S6_3GC-Orbitrap-MS
SA058608S7_1GC-Orbitrap-MS
SA058609S7_2GC-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 MS (30 x 0.25mm, 0.25um) a Thermo Scientific™ TraceGOLD™ TG-5SILMS 30 m length × 0.25 mm i.d. × 0.25 µm
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 MS (30 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:a Thermo Scientific™ TraceGOLD™ TG-5SILMS 30 m length × 0.25 mm i.d. × 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
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
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