LC-ESI(±)-LTQ MSⁿ-Based Metabolomic Profiling of Coffee: Fragmentation Pathways for Identification of Major Polar...

Coffee is characterized by a complex chemical matrix that significantly influences its organoleptic properties and market value. This complexity is driven by factors such as botanical species, geographical origin, cultivation conditions, and post-harvest processing methods. Metabolomic studies aim to elucidate how these factors impact the biosynthesis of metabolites that contribute to the sensory qualities of high-quality coffee. Among various analytical techniques, liquid chromatography-mass spectrometry (LC-MS) is particularly effective for separating, identifying, and quantifying these compounds. Most metabolomic studies employ high-resolution mass spectrometry (HRMS) for its superior mass accuracy (<1 ppm), whereas the interpretation of low-resolution data requires additional effort, often relying on literature references and proposed fragmentation mechanisms. In this study, we applied LC-ESI(±)LTQ MSⁿ to comprehensively profile coffee metabolites, identifying 60 compounds, including polar compounds and their isomers such as chlorogenic acids, carbohydrates, amino acids, alkaloids, glycosylated diterpenes, and flavonoids. Fragmentation mechanisms were proposed and discussed. The results demonstrate the effectiveness of LC-ESI(±)LTQ MSⁿ in a detailed metabolomic analysis, providing a robust platform for future research in coffee metabolomics.