Baptiste Féraud1,2, Estelle Martineau3,4, Justine Leenders5, Bernadette Govaerts6, Pascal de Tullio5, Patrick Giraudeau3. 1. Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA), Université Catholique de Louvain (UCL), Voie du Roman Pays 20, bte L1.04.01, 1348, Louvain-la-Neuve, Belgium. baptiste.feraud@uclouvain.be. 2. Machine Learning Group, Université Catholique de Louvain (UCL), 1348, Louvain-la-Neuve, Belgium. baptiste.feraud@uclouvain.be. 3. Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France. 4. Spectromaîtrise, CAPACITES SAS, 26 Bd Vincent Gâche, 44200, Nantes, France. 5. Metabolomics Group, Center for Interdisciplinary Research on Medicines (CIRM), Université de Liège (ULG), Liège, Belgium. 6. Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA), Université Catholique de Louvain (UCL), Voie du Roman Pays 20, bte L1.04.01, 1348, Louvain-la-Neuve, Belgium.
Abstract
INTRODUCTION: The use of 2D NMR data sources (COSY in this paper) allows to reach general metabolomics results which are at least as good as the results obtained with 1D NMR data, and this with a less advanced and less complex level of pre-processing. But a major issue still exists and can largely slow down a generalized use of 2D data sources in metabolomics: the experiment duration. OBJECTIVE: The goal of this paper is to overcome the experiment duration issue in our recently published MIC strategy by considering faster 2D COSY acquisition techniques: a conventional COSY with a reduced number of transients and the use of the Non-Uniform Sampling (NUS) method. These faster alternatives are all submitted to novel 2D pre-processing workflows and to Metabolomic Informative Content analyses. Eventually, results are compared to those obtained with conventional COSY spectra. METHODS: To pre-process the 2D data sources, the Global Peak List (GPL) workflow and the Vectorization workflow are used. To compare this data sources and to detect the more informative one(s), MIC (Metabolomic Informative Content) indexes are used, based on clustering and inertia measures of quality. RESULTS: Results are discussed according to a multi-factor experimental design (which is unsupervised and based on human urine samples). Descriptive PCA results and MIC indexes are shown, leading to the direct and objective comparison of the different data sets. CONCLUSION: In conclusion, it is demonstrated that conventional COSY spectra recorded with only one transient per increment and COSY spectra recorded with 50% of non-uniform sampling provide very similar MIC results as the initial COSY recorded with four transients, but in a much shorter time. Consequently, using techniques like the reduction of the number of transients or NUS can really open the door to a potential high-throughput use of 2D COSY spectra in metabolomics.
INTRODUCTION: The use of 2D NMR data sources (COSY in this paper) allows to reach general metabolomics results which are at least as good as the results obtained with 1D NMR data, and this with a less advanced and less complex level of pre-processing. But a major issue still exists and can largely slow down a generalized use of 2D data sources in metabolomics: the experiment duration. OBJECTIVE: The goal of this paper is to overcome the experiment duration issue in our recently published MIC strategy by considering faster 2D COSY acquisition techniques: a conventional COSY with a reduced number of transients and the use of the Non-Uniform Sampling (NUS) method. These faster alternatives are all submitted to novel 2D pre-processing workflows and to Metabolomic Informative Content analyses. Eventually, results are compared to those obtained with conventional COSY spectra. METHODS: To pre-process the 2D data sources, the Global Peak List (GPL) workflow and the Vectorization workflow are used. To compare this data sources and to detect the more informative one(s), MIC (Metabolomic Informative Content) indexes are used, based on clustering and inertia measures of quality. RESULTS: Results are discussed according to a multi-factor experimental design (which is unsupervised and based on human urine samples). Descriptive PCA results and MIC indexes are shown, leading to the direct and objective comparison of the different data sets. CONCLUSION: In conclusion, it is demonstrated that conventional COSY spectra recorded with only one transient per increment and COSY spectra recorded with 50% of non-uniform sampling provide very similar MIC results as the initial COSY recorded with four transients, but in a much shorter time. Consequently, using techniques like the reduction of the number of transients or NUS can really open the door to a potential high-throughput use of 2D COSY spectra in metabolomics.