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• Honey proteomic signatures were obtained from SWATH-MS approach. • Honey from different geographical and botanical sources were clearly discriminated. • Discriminate the adulteration of honey and syrup in different proportions. Honey is widely consumed by humans, due to its multiple applications as a food constituent and its therapeutic effects. This study reports on the discrimination of honey products from different geographical and botanical sources, as well as honey products containing distinct forms of syrup used in honey adulteration. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS)-based proteomic analysis combined with chemometrics was successfully applied in identifying characteristic proteins that can be used as biomarkers of the original source of honey. Honey samples from different producing regions (Tainan, Changhua, and Taichung), countries (Taiwan and Thailand), and distinct botanical sources (longan and litchi) were clearly distinguished by the developed orthogonal projections to latent structures discriminant analysis (OPLS-DA) model with good fitness and prediction ability. Furthermore, we successfully discriminated the adulteration of honey with syrup in different proportions (even with honey content as low as 20%) with this proteomic SWATH-MS platform. [ABSTRACT FROM AUTHOR]