Optimization of LC-MS2 Data Acquisition Parameters for Molecular Networking Applied to Marine Natural Products

Since the introduction of the online open-source GNPS, molecular networking has quickly become a widely applied tool in the field of natural products chemistry, with applications from dereplication, genome mining, metabolomics, and visualization of chemical space. Studies have shown that data depend...

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Bibliographic Details
Published in:Metabolites 2022-03, Vol.12 (3), p.245
Main Authors: Afoullouss, Sam, Balsam, Agata, Allcock, A. Louise, Thomas, Olivier P.
Format: Article
Language:English
Subjects:
Data acquisition
data-dependent acquisition
Energy
feature-based molecular networking
Genomes
GNPS
Metabolites
Metabolomics
MZmine2
Natural products
Network topologies
optimization
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Summary:Since the introduction of the online open-source GNPS, molecular networking has quickly become a widely applied tool in the field of natural products chemistry, with applications from dereplication, genome mining, metabolomics, and visualization of chemical space. Studies have shown that data dependent acquisition (DDA) parameters affect molecular network topology but are limited in the number of parameters studied. With an aim to optimize LC-MS2 parameters for integrating GNPS-based molecular networking into our marine natural products workflow, a design of experiment (DOE) was used to screen the significance of the effect that eleven parameters have on both Classical Molecular Networking workflow (CLMN) and the new Feature-Based Molecular Networking workflow (FBMN). Our results indicate that four parameters (concentration, run duration, collision energy and number of precursors per cycle) are the most significant data acquisition parameters affecting the network topology. While concentration and the LC duration were found to be the two most important factors to optimize for CLMN, the number of precursors per cycle and collision energy were also very important factors to optimize for FBMN.
ISSN:2218-1989
2218-1989
DOI:10.3390/metabo12030245