“Expanding Non-Targeted Metabolomics with Multiplexed Chemical Labeling”

The world of natural substances is full of unknown molecules – many of which are difficult to identify using standard metabolomics methods. Often, crucial clues for deciphering their structure are missing.

A research team led by CMFI Pricipal Investigators Chambers Hughes and Dr Daniel Petras has now developed a clever solution: Multiplexed Chemical Metabolomics (MCheM). In this method, molecules are specifically labelled with chemical markers after separation in the mass spectrometer. Each label reacts with a specific functional group – for example, hydroxyl or amino groups – and produces characteristic mass shifts.

These ‘chemical fingerprints’ help to greatly narrow down the number of possible structures. The co-first author of the study, Dr Giovanni Andrea Vitale, applied MCheM analysis in the search for new specialised metabolites. In combination with open analysis tools such as MZmine, GNPS2 and SIRIUS, MCheM becomes a freely available tool for researchers worldwide – with the aim of gradually shedding light on the unknown in the metabolome.

Daniel Petras and Chambers Hughes have written a ‘Behind the Paper’ article on this topic for Springer Nature's Research Communities Blog.
 

Springer Nature - Behind the Paper

Original publication:

Vitale GA, Xia SN, Dührkop K, Zare Shahneh MR, Brötz-Oesterhelt H, Mast Y, Brungs C, Böcker S, Schmid R, Wang M, Hughes CC, Petras D. (2025) Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling. Nat Commun. 16(1):6911. doi: 10.1038/s41467-025-61240-z.