Mass Spectrometry-Based Omics Approaches in the Study of the Chemical Profile of Coffee
Name: MARCOS VALÉRIO VIEIRA LYRIO
Publication date: 13/08/2026
Examining board:
Name |
Role |
|---|---|
| ADRIANA FARAH DE MIRANDA PEREIRA | Examinador Externo |
| ALVARO CUNHA NETO | Examinador Interno |
| EUSTAQUIO VINICIUS RIBEIRO DE CASTRO | Presidente |
| FABIO LUIZ PARTELLI | Examinador Interno |
| LUCAS MATTOS DUARTE | Examinador Externo |
Pages
Summary: This thesis addresses the comprehensive molecular characterization of the coffee bean through mass spectrometry-based metabolomic and lipidomic strategies. The objective of this work was to apply high- and low-resolution tools associated with chemometrics and computational methods to determine the chemical profile of exotic species (Coffea racemosa and Coffea zanguebariae) and monitor the longitudinal metabolic and lipid dynamics during the maturation of Coffea canephora var. Conilon clones. The research sought to address thematic gaps in the literature regarding Conilon coffee development, the study of alternative species, the chemical evaluation of maturation, and the expansion of omics sciences in coffee production. Regarding the instrumental aspect, the study of fragmentation patterns by collision-induced dissociation (CID) in low-resolution systems (LC-LTQ-MS) enabled the annotation of 60 polar compounds and demonstrated the potential of the ion trap analyzer in characterizing coffee compounds. These results serve as a reference base for future annotation studies using low-resolution mass spectrometry, given that this study gathered, discussed, and organized the profiles and fragmentation pathways of a wide variety of molecules in a single text. In the characterization of exotic species, this work provides the first metabolomic profile of C. racemosa and C. zanguebariae and establishes statistical comparisons against species already consolidated in production, C. arabica and C. canephora. The work also confirmed that direct infusion works for rapid screening, but chromatographic separation is indispensable for resolving isomer mixtures of chlorogenic acids. This study highlights the potential of wild and exotic species as sources of genetic diversification and climate change resilience. Furthermore, crossing the chemical profiles with sensory attributes described in the literature allowed for a discussion on the probable sensory behavior of these non commercial species. In the study of Conilon coffee maturation, the research presents the first lipidomic profile of this variety and constitutes the first longitudinal metabolomic and lipidomic study on its ripening. High-resolution lipidomics (LC-Orbitrap-MS) evaluated the dynamics of 220 lipophilic compounds throughout bean development. This stage relied on molecular networks and in silico tools to annotate the chemical markers of bean cellular growth and identify indicators for the optimal harvest time. In parallel, the use of low-resolution mass spectrometry with direct infusion analysis aligned with statistical treatment via ASCA-PCA evaluated the effect of maturation across different Conilon clones. This approach measured the weight of time and genetic factors on changes in the chemical profiles of the samples. The study established sucrose accumulation and caffeine reduction as the main chemical indicators of physiological maturity, which show a strong correlation with the visual aspect of the fruits. On the other hand, the variations found in chlorogenic acids showed a greater association with the genetic profile of each clone. This thesis contributes to the expansion of mass spectrometry-based omics approaches for the chemical characterization of coffee. The structured models and proposed biomarkers provide support for future studies in breeding programs, plant taxonomy, agronomic management in coffee farming, and quality-determining factors.
