## 1 Introduction  
The recent global health crisis necessitates the improvement of diets by consuming healthier and more nutritious foods. Chile peppers (_Capsicum_ spp.) are good sources of vitamins and minerals that can mitigate nutritional deficiencies. These include phenols; ascorbic acid; carotenoids; chlorophylls; vitamins A, C, and E; capsaicinids; and flavonoids [1, 2]. Capsaicinoids, which give chile peppers their unique 'heat' sensation, possess anti-cancer properties [3] and have been shown to have the potential of alleviating cough, rheumat, sore throat, and toothache [4]. Phenolic compounds show great potential as strong antioxidants that can aid the human body against free radicals resulting from reactive oxygen species (ROS) to help prevent cancer, cardiovascular disorders, and neurodegenerative diseases [5, 6, 7]. These metabolites have also demonstrated anti-aging and depigmentation properties, anti-inflammatory potential, and antimicrobial activity [8]. A survey on the variation of vitamin contents in a _Capsicum_ germplasm identified eight cultivars that have higher vitamin A concentration than sweet potato (_Iponea battas_), and 16 pepper types that have vitamin C content higher than kiwi (_Actinidia delicosa_), indicating a great potential for improving nutrition through genetic improvement [9]. A deeper understanding of the different metabolites present in chile peppers will provide avenues to understand the complex array of genes resulting in quantitative phenotypes such as the nutritional quality traits. Metabolomics studies link the phenotype and genotype, acting as a bridge between the phenome and the genome [10]. Previous estimates revealed at least 200,000 metabolites in the plant kingdom, significantly higher than those found in animals; a potential consequence of a wide variety of metabolic pathways developed by plants to thrive in diverse environmental conditions [11]. In chile peppers, metabolomics approaches have profiled metabolites involved in growth, development, and adaptation to different environments [12; 13]. Numerous changes in the biochemical and physiological processes involving enzyme activity, gene expression, and metabolite synthesis result in developmental changes in the fruit in response to the environment [14]. For example, during fruit development in _C. chinense_ Jacq, a metabolomics approach revealed distinct patterns of metabolite distribution at 16 days post-anthesis across the orange and red ripening periods [15]. In another study, fruit discoloration was attributed to the reduction in carotenoid content in discolored red peppers compared to normal peppers, where lipid and flavonoid synthesis were significantly associated with discoloration [16]. Increased lipid metabolism and decrease in capsaicinoid, flavones, flavanol compounds, and terpenids were further observed in domesticed chile peppers compared to their wild ancestors [17], indicating that genetic improvement for increased nutritional quality through breeding and selection have been implemented for the cultivated chile peppers. Widely targeted metabolomics is the next generation of metabolomics, combining the benefits of the targeted and untargeted approaches, and has several advantages, including being high-throughput, highly sensitive, and having a broad coverage [18], in contrast to targeted approaches where some metabolites may be left unidentified [19]. The detection and identification of broadly targeted metabolites are made possible by Q-TRAP mass spectrometry based on multiple reaction monitoring mode, which allows for the simultaneous quantification of hundreds of known metabolites over a thousand of unknown metabolites [20; 21]. The objectives of this study were to: (1) survey the metabolite diversity in jalapeno and serrano peppers using a nontargeted metabolomics approach; (2) identify differentially expressed metabolites; and (3) perform the functional annotation of genes involved in different metabolic pathways.