## 4 Discussion
### Differentially Expressed Metabolites Have Implications on Human Health and Nutrition  
Widely targeted metabolomics for jalapeno and serrano peppers revealed differentially expressed metabolites comprising mostly of upregulated phenolic acids and flavonoids. Phenolic acids are among the most commonly found compounds in _Capsicum_ fruits and have been observed to possess vital functions in human health, nutrition, and the prevention of diseases because of their antioxidant, antiviral, and antibacterial properties [5; 39]. Phenolics have been previously identified in different species of peppers, including _C. annuum_ cultivars from India [40]; _C. annuum_, _C. chinense_, and _C. bucactum_ cultivated in New Mexico [41]; _C. bucactum_[42]; and _C. frutscens_ and _C. chinense_ cultivars from Peru, South America [35]. The human body cannot produce phenolic compounds; hence, they must be acquired from food sources [5]. Major phenolic acid derivatives, caffe acid (CA), sinapic acid (SA), and ferulic acid (FA) [5], were observed to be differentially expressed in the present work; CA and FA were upregulated, whereas SA was downregulated. Flavonoids (e.g., quercetin and luteolin) were also detected to be differentially expressed, consistent with previous studies [43; 44; 45; 46]. A total of 23 quercetin metabolites were found to be differentially expressed, where five metabolites (namely, quercetin-3-O-sambubioside-5-O-glucoside, 3-O-methylquercetin, quercetin-3-O-(2''-O-malonyl)sophroside-7-O-arabinoside, and 6-methoxyquercetin-3-O-Hammoside) were upregulated and the remaining 18 metabolites were downregulated. A total of 10 differentially expressed metabolites belong to the luteolin class, comprising mostly upregulated compounds (luteolin-4'-O-glucose, luteolin-7-O-glucose (cyanoside), luteolin-7-O-sophroside-5-O-arabinoside, luteolin-7-O-gentiobioside, luteolin-7,3'-di-O-glucose, and luteolin-7-O-glucuronide). Capsaicin and related families of 'pungent' alkaloids (or 'pseudoalkaloids'), however, were not observed to be differentially expressed in the current study, a potential consequence of the maturity (age) of the fruit samples used for analyses. Overall, the information for the differentially expressed metabolites and their correspond ing chemical classes reveal that pepper fruits can be good sources of these nutritional compounds in the diet. The KEGG map annotations for a number of the differentially expressed metabolites were related to multiple metabolic pathways such as the biosynthesis of secondary metabolites (KO01110), including lutein (\(\beta\),\(\epsilon\)-carotene-3,3'-diol), which is the predominant metabolite in the 'NuMex LotaLutein' serrano pepper [23]. The production of lutein in plants generally takes place through the mevalonate pathway, in which isopentyl diphosphate (IPP) is converted to geranylgeranyl pyrophosphate (GPP), which is then synthesized into phytoene and lycopene, the precursor of lutein [47; 48; 49]. The most upregulated phenolic acid, chlorogenic acid (3-O-caffeoylquinic acid), had four different pathway annotations related to phenylpropanol biosynthesis (pathway ID: KO00940); flavonoid biosynthesis (KO00941); stilbenoid, diarylheptanoid, and gingerol biosynthesis (KO00945); and the biosynthesis of secondary metabolites (KO01110). 3,7-Di-O-methylquercetin (flavonoid) and phenol (phenolic acid) had two pathway annotations; namely, K00944 and KO01110 (secondary metabolite biosynthesis), and KO00350 (Tyrosine metabolism) and KO01110 (secondary metabolite biosynthesis). Adenosine 5'-triphosphate (ATP), also an upregulated metabolite, has seven different KEGG pathway annotations, including oxidative phosphorylation (KO00190), photosynthesis (KO00195), nucleotide metabolism (KO01232), and the biosynthesis of cofactors (KO01240), among others. Altogether, these functional annotations indicate the relevance of these upregulated compounds in the production of a wide array of important nutritional metabolites in _Capsicum_.