Ion mobility spectrometry in cocoa polyphenol metabolomics workflow increases the resolution of molecular networks

Ion mobility spectrometry (IMS) may improve feature-based molecular networking (FBMN) for annotating polyphenol isomers co-eluted in chromatography. The study aimed to assess the added value of trapped ion mobility spectrometry (TIMS) in metabolomics with FBMN for cocoa polyphenols. Untargeted analyses were performed on black and brown cocoa beans using a UHPLC-TIMS-Q-TOF system, with or without TIMS. The processed data underwent statistical and FBMN analyses. TIMS nearly doubled discriminating features in black beans and increased them by 50 % in brown beans. It separated isomeric dimers, trimers, and C-(O-)glycosides (native or process-derived). The UHPLC-TIMS-HRMS-FBMN resolved these isomers into distinct molecular network clusters. New discriminant phenolics were reported compared to a previous non-IMS study: ethyl-bridged flavanols in black beans and dehydro(epi)catechins, (epi)catechin-C-glycosides, and B-type procyanidin trimer C-glycosides in brown beans. TIMS improved structural information from FBMN, enabling polyphenols isomer identification. This TIMS-based approach can improve the phenolic characterization of cocoa products.