Know Your Onions

Call it Onion-omics: Kazuki Saito and Ryo Nakabayashi, along with colleagues from the RIKEN Plant Science Center, Yokohama, Japan, are probing bioactive compounds of the esteemed bulb and their potential medical application (1). “Chemical assignment is the most crucial issue facing mass spectrometry-based metabolomics,” says Saito, of the RIKEN Center for Sustainable Resource Science. “Most detected peaks are assigned as ‘unknowns’.”

Elemental composition can provide useful information for the discovery of medically-relevant specialized or secondary metabolites, such as polyketides, flavonoids, alkaloids, and sulfur-containing metabolites (S-metabolites) that are not directly involved in the normal growth, development, or reproduction of an organism. “These secondary metabolites are important natural substances with unique biological activities that can open up innovative paths in drug development,” Saito explains.

To start identifying some of those ‘unknown’ peaks, the group exploits the ‘spectral fingerprint’ of heteroatom-containing compounds using high-resolution mass spectrometry (HRMS). Saito admits that, while strategies that extract secondary metabolite groups by capturing specific features from metabolome data do exist, there is plenty of room for improvement. “In most cases, these secondary metabolites consist of C, H, N, O, and/or S. A first step toward better assignment of peaks is to precisely distinguish monoisotopic ions of N-, O-, and/or S-metabolites and then determine specific chemical information, such as the elemental composition and structure of the ions,” he says.

The group grew onion bulbs in standard and in carbon-13 atmospheric conditions. Comparison of the two HRMS data sets could, in theory, reveal the complete atomic make-up. And by comparing the data with that of known compounds, 67 sulfur-containing ions were identified. To obtain the data, liquid chromatography coupled to Fourier transform ion cyclotron resonance-mass spectrometry (LC-FTICR-MS) with C13 labelling was used. “LC–FTICR-MS has ultra-high performance on mass accuracy (< 1 ppm) and resolution power (> 250,000 FWHM) and can separate naturally occurring, stable isotope-labeled ions. Other HRMS platforms cannot fulfill those conditions,” he says, noting that the FTICR-MS system (commonly known as FTMS) used in the study, a Bruker soraliX, readily combines with LC systems from several vendors.

FTMS accelerates research by eliminating the need for multiple stable isotope-labeled plants. “The performance from [FTMS] provides a minimal number of candidates for elemental composition, meaning that we only needed single stable isotope-labeled plants”. To further speed up the cataloging of compounds, the group plans to add NMR into the mix, creating an automated structural assignment system. 

Saito is optimistic about the impact of the approach: “Heteroatom-targeted chemical assignment, coupled with modern approaches in natural products chemistry – for example, LC-SPE-NMR-MS – will undoubtedly enable great advances in the isolation and structure elucidation of targeted metabolites in plants and other organisms.”