Proteome dynamics of chilli pepper fruits during development and ripening from two Mexican cultivars of Capsicum annuum L

Chilli pepper (Capsicum annuum L., Solanaceae family), a horticultural crop native to the Americas, is esteemed for its flavour and bioactive compounds. To enhance our understanding of the molecular basis of chilli pepper fruit development and ripening, we characterised proteome dynamics from early fruit set to ripening in two Mexican cultivars. Protein profiles were analysed using label-free quantitative (LFQ) LC-MS proteomics with data-independent acquisition (DIA), resulting in the quantification of 421 proteins, predominantly involved in primary and secondary metabolism. The developmental stage was the primary factor driving proteome variation, with limited influence from cultivar differences. Clustering and relative quantification revealed intricate patterns of protein abundance across fruit maturation. Proteins associated with carotenoid and capsaicinoid biosynthesis exhibited temporal regulation consistent with their roles in determining fruit colour and pungency. This study provides insights into the molecular changes underlying chilli pepper fruit growth, development, and ripening and offers a proteomic overview for understanding some biochemical traits that define chilli pepper fruit characteristics. SIGNIFICANCE: Understanding the molecular basis of fruit growth, development, and ripening is crucial for enhancing crop quality and nutritional value. In chilli pepper, traits such as the production of valuable secondary metabolites, pigmentation, and pungency arise from finely regulated metabolic processes during fruit maturation. Here, we investigated these processes from a proteomics perspective, complemented with clustering and functional enrichment analyses. The findings reveal that developmental stage, rather than genotype, is the dominant factor shaping the fruit proteome, underscoring a conserved maturation program. Proteins involved in primary metabolism and specialised biosynthetic pathways, including those for carotenoids and capsaicinoids, show dynamic regulation consistent with their roles in fruit quality traits. These results contribute to the understanding of the molecular processes involved in fruit growth, development, and ripening and provide a proteomic framework for studying trait formation in Capsicum annuum and related Solanaceae crops.