High-resolution gas chromatography/mass spectrometry metabolomics of non-human primate serum

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 1D-GC/Orbitrap-MS.

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 HRMS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a complementary approach, we also analyzed the same serum samples using two-dimensional gas chromatography/time-of-flight mass spectrometry (2D-GC/TOF-MS) for metabolite identification and quantification following established standard protocols.

Overall, the 2D-GC/TOF-MS (~5000 peaks per sample) and 1D-GC/Orbitrap-MS (~500 peaks per sample) analyses enabled identification and quantification of a total of 555 annotated metabolites from the NHP serum with a spectral similarity score R_sim  ≥ 900 and signal-to-noise (S/N) ratio of >25. A common set of 30 metabolites with HMDB and KEGG IDs was quantified in the serum samples by both platforms where 2D-GC/TOF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and 1D-GC/Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Thus, roughly 30-70% of the peaks remain unidentified or un-annotated across both platforms.

Our study provides insights into the benefits and limitations of the use of a higher mass resolution and mass accuracy instrument for untargeted GC/MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.