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Open AccessArticle

Choosing an Optimal Sample Preparation in Caulobacter crescentus for Untargeted Metabolomics Approaches

1
Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University Medical Centre, 1206 Geneva, Switzerland
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Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, University Medical Centre, 1206 Geneva, Switzerland
3
Swiss Centre for Applied Human Toxicology, 4055 Basel, Switzerland
*
Author to whom correspondence should be addressed.
Metabolites 2019, 9(10), 193; https://doi.org/10.3390/metabo9100193
Received: 27 August 2019 / Revised: 13 September 2019 / Accepted: 17 September 2019 / Published: 20 September 2019
(This article belongs to the Special Issue Sample Preparation in Metabolomics)
Untargeted metabolomics aims to provide a global picture of the metabolites present in the system under study. To this end, making a careful choice of sample preparation is mandatory to obtain reliable and reproducible biological information. In this study, eight different sample preparation techniques were evaluated using Caulobacter crescentus as a model for Gram-negative bacteria. Two cell retrieval systems, two quenching and extraction solvents, and two cell disruption procedures were combined in a full factorial experimental design. To fully exploit the multivariate structure of the generated data, the ANOVA multiblock orthogonal partial least squares (AMOPLS) algorithm was employed to decompose the contribution of each factor studied and their potential interactions for a set of annotated metabolites. All main effects of the factors studied were found to have a significant contribution on the total observed variability. Cell retrieval, quenching and extraction solvent, and cell disrupting mechanism accounted respectively for 27.6%, 8.4%, and 7.0% of the total variability. The reproducibility and metabolome coverage of the sample preparation procedures were then compared and evaluated in terms of relative standard deviation (RSD) on the area for the detected metabolites. The protocol showing the best performance in terms of recovery, versatility, and variability was centrifugation for cell retrieval, using MeOH:H2O (8:2) as quenching and extraction solvent, and freeze-thaw cycles as the cell disrupting mechanism. View Full-Text
Keywords: metabolomics; sample preparation; hydrophilic interaction liquid chromatography; ion mobility spectrometry; high resolution mass spectrometry; design of experiments; AMOPLS metabolomics; sample preparation; hydrophilic interaction liquid chromatography; ion mobility spectrometry; high resolution mass spectrometry; design of experiments; AMOPLS
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Pezzatti, J.; Bergé, M.; Boccard, J.; Codesido, S.; Gagnebin, Y.; H. Viollier, P.; González-Ruiz, V.; Rudaz, S. Choosing an Optimal Sample Preparation in Caulobacter crescentus for Untargeted Metabolomics Approaches. Metabolites 2019, 9, 193.

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