Challenge of nonribosomal peptide (NRP) identification: Kendrick mass defect for molecular formula assignment of NRPs - Archive ouverte HAL
Communication Dans Un Congrès Année : 2019

Challenge of nonribosomal peptide (NRP) identification: Kendrick mass defect for molecular formula assignment of NRPs

Résumé

The nonribosomal peptides (NRPs) are families of natural products, displaying a broad range of biological activities and pharmacological properties. They belong to the class of microbial peptidic secondary metabolites. Despite their peptidic nature, they are not produced through ribosome machinery and therefore cannot be deduced from DNA. To reference such particular structures, a manually curated database called NORINE was created (Caboche et al. 2007) and gathers now more than 1200 NRPs structures (Areski et al. Flissi 2016). Identification of known (dereplication) or unknown NRPs produced by a microorganism still remains a time consuming and challenging task due to their nature. The first step of structural clarification process consists to accurately (<1 ppm) measure, by high-resolution mass spectrometry (HRMS), the molecular mass of compounds to deduce their molecular formulas. Unfortunately, for compounds of molecular mass > to 1,000 Da, the computer-assisted deduction of the molecular formula do not lead to a single molecular formula. In 1963, Edward Kendrick has proposed an elegant mathematic method based on the determination of a mass defect (the Kendrick mass defect (KMD)) to facilitating the distinction of homologous compounds sharing different repetitions of same base unit (e.g. CH2). This mass filtering method is best illustrated using 2D-plots representing the KMD as a function of the nominal Kendrick mass (NKM); each point of the KMD/NKM 2D-plot representing a unique monoisotopic molecular formula. Here we demonstrate that the HRMS combined to KMD, NKM calculation applied to the NORINE database is a smart, easy-to-use, fast, useful tool for molecular formula assignment of experimentally measured masses of NRPs. We have constructed a KMD/NKM 2D-plot from all compounds of the NORINE database. From surfactins used as model molecules and from supernatants of distinct Pseudomonas strains, we match the accurately-measured experimental masses on this KMD/NKM 2D-plot and identify or deduce the molecular formula of the known or unknown NRP compounds present in these supernatants.
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Dates et versions

hal-04550126 , version 1 (18-04-2024)

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  • HAL Id : hal-04550126 , version 1

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Mickaël Chevalier, Emma Ricart, Emeline Hanozin, Frédérique Lisacek, Sandra Matthijs, et al.. Challenge of nonribosomal peptide (NRP) identification: Kendrick mass defect for molecular formula assignment of NRPs. IUPAC, May 2019, GHENT, Belgium. ⟨hal-04550126⟩
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