Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides
- 28 October 2019
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Society for Mass Spectrometry
- Vol. 30 (12), 2608-2616
- https://doi.org/10.1007/s13361-019-02314-3
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.Keywords
Funding Information
- Alibiotech project
- INTERREG Va FWVL BioScreen/SmartBioControl Project
- program Hubert Curien, Germaine de Staël
- SIB Swiss Institute of Bioinformatics Fellowship program
This publication has 28 references indexed in Scilit:
- BRAIN: A Universal Tool for High-Throughput Calculations of the Isotopic Distribution for Mass SpectrometryAnalytical Chemistry, 2013
- Higher-Order Mass Defect Analysis for Mass Spectra of Complex Organic MixturesAnalytical Chemistry, 2011
- Natural Product Analysis over the Last DecadesPlanta Medica, 2009
- SIRIUS: decomposing isotope patterns for metabolite identificationBioinformatics, 2008
- NORINE: a database of nonribosomal peptidesNucleic Acids Research, 2007
- Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometryBMC Bioinformatics, 2007
- Using a triple‐quadrupole mass spectrometer in accurate mass mode and an ion correlation program to identify compoundsRapid Communications in Mass Spectrometry, 2005
- Utility of three types of mass spectrometers for determining elemental compositions of ions formed from chromatographically separated compoundsRapid Communications in Mass Spectrometry, 2002
- Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic NetworksComparative and Functional Genomics, 2001
- 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic dataXenobiotica, 1999