Kendrick Mass Defect Approach Combined to ...
Document type :
Compte-rendu et recension critique d'ouvrage
PMID :
Title :
Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides
Author(s) :
Chevalier, Mickael [Auteur]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Ricart, Emma [Auteur]
Swiss Institute of Bioinformatics [Genève] [SIB]
Hanozin, Emeline [Auteur]
Mass Spectrometry Laboratory [MS LAB]
Pupin, Maude [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Bioinformatics and Sequence Analysis [BONSAI]
Jacques, Philippe [Auteur]
Gembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
Smargiasso, Nicolas [Auteur]
Mass Spectrometry Laboratory [MS LAB]
de Pauw, Edwin [Auteur]
Mass Spectrometry Laboratory [MS LAB]
Lisacek, Frédérique [Auteur]
Swiss Institute of Bioinformatics [Lausanne] [SIB]
Leclere, Valerie [Auteur]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Flahaut, Christophe [Auteur]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Ricart, Emma [Auteur]
Swiss Institute of Bioinformatics [Genève] [SIB]
Hanozin, Emeline [Auteur]
Mass Spectrometry Laboratory [MS LAB]
Pupin, Maude [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Bioinformatics and Sequence Analysis [BONSAI]
Jacques, Philippe [Auteur]
Gembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
Smargiasso, Nicolas [Auteur]
Mass Spectrometry Laboratory [MS LAB]
de Pauw, Edwin [Auteur]
Mass Spectrometry Laboratory [MS LAB]
Lisacek, Frédérique [Auteur]
Swiss Institute of Bioinformatics [Lausanne] [SIB]
Leclere, Valerie [Auteur]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Flahaut, Christophe [Auteur]
Institut Charles Viollette (ICV) - ULR 7394 [ICV]
Journal title :
Journal of The American Society for Mass Spectrometry
Pages :
2608-2616
Publisher :
American Chemical Society
Publication date :
2019-10-28
ISSN :
1044-0305
English keyword(s) :
Kendrick map
Mass defect
Molecular formula
Nonribosomal peptides
NORINE
Mass defect
Molecular formula
Nonribosomal peptides
NORINE
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
Chimie/Chemo-informatique
Chimie/Chimie organique
Chimie/Chemo-informatique
Chimie/Chimie organique
English abstract : [en]
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 ...
Show more >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.Show less >
Show more >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.Show less >
Language :
Anglais
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Non
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