The processing methods of coffee cherries after harvesting can significantly affect the lipid composition of green coffee beans, thereby influencing their in-cup properties. This study utilized ultra-high performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) technology to investigate the impact of natural, washed, and honey processing methods on the lipid composition of green coffee beans, accompanied by sensory evaluations. A total of 510 lipids, covering 27 subclasses, were detected. Of these, 150 lipids showed significant differences before and after processing, and 37 lipids were identified as potential biomarkers for distinguishing the three processing methods. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed that glycerophospholipid metabolism was the key pathway for the formation of differential lipids among the various processing methods. Significant correlations were observed between lipid composition and the flavor diversity associated with different processing methods. The findings provide a crucial basis for understanding the lipid transformation of coffee during different processing methods and its impact on flavor quality characteristics.

This study aimed to investigate the effects of maturity on the changes in major lipid metabolites of coffee and their associated pathways. UPLC-ESI-MS/MS was used to compare the lipidomic profiles of coffee beans at five different maturity stages. A total of 516 lipid metabolites across 26 subclasses were identified, with 111 showing significant differences. Glycerolipids (GL) and fatty acyls (FA) were the most abundant, followed by glycerophospholipids (GP), sphingolipids (SP) and prenol lipids (PR). PCA and OPLS-DA analyses demonstrated significant changes in coffee lipids during maturation. Glycerophospholipid metabolism and glycerolipid metabolism were identified as key metabolic pathways, with phosphatidic acid (PA), lysophosphatidic acid (LPA) and diacylglycerol (DG) as key lipid metabolites in these pathways during coffee maturation. Lipids in immature and overripe beans were significantly different from those in mature coffee beans. This study provides a foundational understanding of lipid transformation and flavor profile formation during coffee maturation.

Mass spectrometry-based lipidomics has created new opportunities to investigate the role of lipids in coffee quality formation and stability across the production chain. Coffee lipids contribute to flavor precursor formation, aroma release, mouthfeel, and storage behavior, but their molecular remodeling during maturation, processing, roasting, and storage remains insufficiently integrated. This review summarizes recent progress in lipidomics methodologies relevant to coffee research, with emphasis on sample preparation, mass spectrometry platforms, data analysis, and the strengths and limitations of current lipid annotation strategies. It further examines how lipid profiles change during bean maturation, how they differ among coffee species and varieties, and how they are reshaped by postharvest processing, roasting, and storage. However, it is important to note that most of these associations are currently correlational rather than causal; direct evidence linking specific lipid species to particular sensory attributes remains limited. Existing studies suggest that lipid composition, rather than total lipid content alone, is more informative for understanding coffee quality differences and for identifying candidate markers associated with origin, processing method, roasting degree, and storage conditions. In particular, alterations in glycerolipids, glycerophospholipids, fatty acids, diterpenes, and other minor lipid constituents are increasingly associated with lipid oxidation, thermal degradation, and flavor-related transformations in coffee. However, current evidence is still limited by incomplete structural annotation, isomeric ambiguity, platform dependence, and the frequent gap between statistical discrimination and mechanistic validation. Future work integrating high-resolution mass spectrometry, ion mobility, targeted quantification, stable isotope tracing, sensory analysis, and multi-omics approaches will be essential to improve marker reliability and to clarify the functional roles of coffee lipids. Overall, lipidomics provides a promising framework for linking molecular composition with coffee quality control, traceability, and process optimization, although substantial work is still needed to establish mechanistic links to flavor formation.