Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides
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J. Am. Soc. Mass Spectrom. (2019) DOI: 10.1007/s13361-019-02314-3
RESEARCH ARTICLE
Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides Mickaël Chevalier,1 Emma Ricart,2 Emeline Hanozin,3 Maude Pupin,4,5 Philippe Jacques,6 Nicolas Smargiasso,3 Edwin De Pauw,3 Frédérique Lisacek,2 Valérie Leclère,1 Christophe Flahaut1 1
Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d’Opale, EA 7394-Institut Charles Viollette (ICV), F-59000, Lille, France 2 Proteome informatics Group, SIB Swiss Institute of Bioinformatics (SIB), and Computer Science Department, University of Geneva, Geneva, Switzerland 3 Mass Spectrometry Laboratory, Molecular Systems - MolSys Research Unit, University of Liège, Liège, Belgium 4 Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France 5 Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d’Ascq Cedex, France 6 TERRA Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech University of Liège, B-5030, Gembloux, Belgium
Abstract. The identification of known (dereplication) or unknown nonribosomal peptides (NRPs) produced by microorganisms is a time consuming, expensive, and challenging task where mass spectrometry and nuclear magnetic resonance play a key role. The first step of the identification process always involves the establishment of a molecular formula. Unfortunately, the number of potential molecular formulae increases significantly with higher molecular masses and the lower precision of their measurements. In the present article, we demonstrate that molecular formula assignment can be achieved by a combined approach using the regular Kendrick mass defect (RKMD) and NORINE, the reference curated database of NRPs. We observed that irrespective of the molecular formula, the addition and subtraction of a given atom or atom group always leads to the same RKMD variation and nominal Kendrick mass (NKM). Graphically, these variations translated into a vector mesh can be used to connect an unknown molecule to a known NRP of the NORINE database and establish its molecular formula. We explain and illustrate this concept through the high-resolution mass spectrometry analysis of a commercially available mixture composed of four surfactins. The Kendrick approach enriched with the NORINE database content is a fast, useful, and easy-to-use tool for molecular mass assignment of known and unknown NRP structures.
Electronic supplementary material The online version of this article (https:// doi.org/10.1007/s13361-019-02314-3) contains supplementary material, which is available to authorized users. Correspondence to: Christophe Flahaut; e-mail: christophe.flahaut@univ– artois.fr
M. Chevalier et al.: KMD for Molecular Formula Assignment of NRPs
Keywords: Kendrick map, Mass defect, Molecular formula, Nonribosomal peptides, NORINE Abbreviations ESI, Electrospray ionization; FT, Fourier transform; ICR, Ion cyclo
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