Proteogenomic investigation of plant constituents in herbal beverages

Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. While high-throughput sequencing (HTS) of DNA barcodes is a promising method to identify adulterants, its practical application is hampered by technical challenges. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components. Consequently, HTS results require independent confirmation using an orthogonal method based on very different physical principles than DNA sequencing. To address this, we evaluated the suitability of a multi-omic approach that coupled DNA barcode HTS analysis with proteomic analysis, to enhance the detection of food fraud in herbal beverages. To resolve discrepancies between genomic and proteomic findings, we employed traditional botanical morphology as an arbiter. Among the samples studied, the combined approach revealed two main adulterations of Epilobium with Lythrum - a substitution potentially hazardous to consumers - as well as several minor substitutions, all confirmed by orthogonal methods. Our findings demonstrate that proteomic analysis provides enhanced confidence for verifying the presence or absence of plant components identified by HTS. However, its effective application is guided by prior sequencing to define specific targets for subsequent proteomic verification. This study established that a multimodal analytical approach is not only beneficial, but essential for the reliable and comprehensive characterization of components in complex plant mixtures.