Metabolomic Analysis of Chilli Peppers

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The chilli pepper is typically associated with Mexican food, but it is of much more value than simply providing characteristic culinary dishes. The chilli is a valuable economic resource for Mexico, which is the sixth largest chilli exporter in the world1. With the chilli pepper being such an important commercial commodity it is desirable to be able to determine the quality of the chilli peppers being traded in terms of both flavour and nutritional value. Reliable, quick, and user-friendly analytical methods are therefore critical to chilli pepper producers


Metabolomics is the study of all metabolites in the cells of living organisms2. It provides a unique chemical fingerprint and can be used to assess responses to external conditions. It has been widely used in research across many disciplines, including toxicology and drug discovery.

The simultaneous measurement of numerous endogenous metabolites, as is needed for metabolomic analysis, has been made feasible by the development of high-frequency nuclear magnetic resonance (NMR). Although NMR does not provide the same level of sensitivity as mass spectroscopy technologies, it has numerous advantages that have resulted in it becoming the preferred tool for metabolomic analyses. NMR produces highly reproducible spectra in a few minutes without damaging or contaminating the sample and there are a range of automated NMR instruments available that can be operated by non-experts3.

NMR has been effectively used in the chemical profiling of several types of natural produce, including cabbage, grapes, coffee and green tea, from a range of different geographical areas4,5. The information provided by NMR analysis can help determine the nutritional properties of a cultivated vegetable species and explore how these differ between crops from distinct geographical origins.

The specific chemical fingerprint of chilli peppers is now being explored using NMR metabolomic analysis to assess the properties of crops grown under differing conditions.

Analysis of chilli peppers

The serrano green chilli (Capsicum annuum L) is a varietyof chilli pepper commonly cultivated and traded in Mexico. Previous analyses of its chemical composition have revealed that it includes a wide range of compounds, including protein, vitamins Band C, fatty acids, carotenoids, anthocyanins, volatile organic compounds, sulfur compounds, and capsaicinoids, which provided the characteristic pungent flavour6.

The relative proportions of the various metabolites present in the serrano chilli pepper have been shown to be linked to genetic variability as well as the ripeness of the fruit and the conditions in which it is cultivated7,8.

NMR metabolomic profiling of serrano chilli peppers

A new 1H NMR method for metabolomic profiling has recently been used to compare the chemical fingerprints of serrano chilli peppers cultivated in different regions of Mexico9. The Oaxaca area is characterised by a semi-dry, semi-warm climate whilst the Veracruz area has a warm climate with abundant rain in the summer and early autumn.

The aqueous phase of serrano peppers harvested from the Oaxaca and Veracruz regions were analysed using a Bruker 750 MHz NMR spectrometer equipped with a TXI cryoprobe.

The 1H NMR spectra of the serrano chilli peppers showed them to contain 40 different metabolites, the majority of which are compounds of nutritional relevance. For example, 13 different amino acids, including seven essential amino acids, were identified9.

The main differences in the metabolomic profiles of the chilli peppers from Oaxaca and Veracruz related to the levels of organic acids. Interestingly, the chilli peppers from Oaxaca contained lactate but not succinate, whilst the chilli peppers from Veracruz contained succinate but not lactate. In addition, levels of aspartate citrate, leucine and sucrose were found to be higher in chilli peppers cultivated in the Veracruz region compared with those grown in the Oaxaca region9. In contrast, the chilli peppers from Oaxaca contained more acetate, formate, fumarate, malonate, phosphocholine, and pyruvate than the chilli peppers from Veracruz9.

Since the synthesis of organic acids by chilli peppers varies according to the stage of development, these levels provide an indication of the maturity of the chilli peppers. This also determines the level of vitamin C in the chilli peppers, which is produced by conversion of the organic acid oxalic acid.

The latest findings highlight how differences in temperature and water availability can affect the organic acid profiles of serrano chilli peppers, which in turn can impact the nutritional value.

The authors also reported that the NMR spectrometric analysis was simple to execute and showed high degrees of robustness and reproducibility. NMR spectroscopy thus represents a reliable and user-friendly methodology for comparing the metabolomic fingerprints of serrano peppers grown under different environmental conditions.


  1. Gaytan D, Benita F. Economics of Agriculture 2014;61(2):307‑317.
  2. Nicholson JK, Lindon JC. Systems biology: metabonomics. Nature 2008;455:1054–1056.
  3. Larive CK, et al. Analytical Chemistry 2015;87(1):133‑146.
  4. Wei F, et al. Journal of Agricultural and Food Chemistry 2016;64(33):6459‑6465.
  5. Jahan K, et al. Food Chemistry2013;137(2):68‑75.
  6. González-Zamora A, et al. Molecules 2013;18(11):13471‑13486.
  7. Kim S, et al.  International Journal of Food Science and Technology 2008; 43(5):915‑920.
  8. Okunlola GO, et al. Sciences in Cold and Arid Regions 2016;8(3):205‑211.
  9. Becerra-Martínez E, et al. Food Research International 2017;102:163–170.

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Last updated: Mar 6, 2019 at 5:54 AM

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