Metabolomics Benefits from Orbitrap GC–MS—Comparison of Low- and High-Resolution GC–MS

Abstract

The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC)–mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC)–MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC–MS in comparison to a commonly used unit-mass resolution single-quadrupole GC–MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC–MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC–MS technology for metabolomics studies are shown here.

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms

“…Using an in-house R-script [ 50 ], detected masses were deconvoluted via peak-shape comparison to potential metabolites and reduced in number to only include potential metabolites containing ≥20 fragments. Potential metabolites present in blanks and media controls (<fivefold increase or decrease relative to bacterial samples) were removed (Table S3 ).…”

Omics-Driven Biotechnology for Industrial Applications

“…Besides, the application of ion mobility and high resolution MS has improved the identification of isomers, thereby enabling a more accurate assessment of their biological roles (Ren et al, 2018 ; Rathahao-Paris et al, 2019 ). Moreover, new developments in orbitrap MS systems have improved metabolites annotation and coverage in GC- and LC-MS studies (Simirgiotis et al, 2017 ; Misra et al, 2018 ; Manier et al, 2019 ; Stettin et al, 2020 ).…”

Open, High-Resolution EI+ Spectral Library of Anthropogenic Compounds

“…Since commercial release in 2015, the high-resolution gas chromatography Orbitrap mass spectrometer (GC Orbitrap MS) has been evidenced as a valuable tool in metabolomics ( 1 – 6 ), environmental ( 7 – 10 ), clinical ( 11 ), and forensic analysis ( 12 ). The enhanced mass accuracy and greater achievable linear dynamic range ( 13 ), when operating in full-scan mode, makes GC Orbitrap MS particularly suited to chemical characterization of complex samples with unknown composition.…”

“…However, high-resolution electron ionization mass spectral (HR-[EI+]-MS) libraries are currently limited ( 1 ), particularly for environmental chemicals. This hinders the application of GC Orbitrap MS without prior generation of in-house spectral libraries, which requires substantial resources; or the purchase of commercial libraries that are often tied to proprietary data formats and software.…”