Model selection for within-batch effect correction in UPLC-MS metabolomics using quality control - Support vector regression

Analytica Chimica Acta
Ángel Sánchez-IllanaJulia Kuligowski

Abstract

Ultra performance liquid chromatography - mass spectrometry (UPLC-MS) is increasingly being used for untargeted metabolomics in biomedical research. Complex matrices and a large number of samples per analytical batch lead to gradual changes in the instrumental response (i.e. within-batch effects) that reduce the repeatability and reproducibility and limit the power to detect biological responses. A strategy for within-batch effect correction based on the use of quality control (QC) samples and Support Vector Regression (QC-SVRC) with a radial basis function kernel was recently proposed. QC-SVRC requires the optimization of three hyperparameters that determine the accuracy of the within-batch effects elimination: the tolerance threshold (ε), the penalty term (C) and the kernel width (γ). This work compares three widely used strategies for QC-SVRC hyperparameter optimization (grid search, random search and particle swarm optimization) using a UPLC-MS data set containing 193 urine injections as model example. Results show that QC-SVRC is robust to hyperparameter selection and that a pre-selection of C and ε, followed by optimization of γ is competitive in terms of accuracy, precision and number of function evaluations with full gr...Continue Reading

Citations

Jul 10, 2019·Scientific Reports·Teresa Martínez-SenaJulia Kuligowski
Mar 31, 2020·Metabolomics : Official Journal of the Metabolomic Society·Guillermo QuintasGil Rodas
Apr 15, 2020·Analytical and Bioanalytical Chemistry·Paula Cuevas-DelgadoCoral Barbas
Sep 25, 2019·Metabolites·Ana K Rosen VollmarCaroline H Johnson
Nov 26, 2020·Mass Spectrometry Reviews·Wei Han, Liang Li
Aug 31, 2020·Clinical Nutrition : Official Journal of the European Society of Parenteral and Enteral Nutrition·José David Piñeiro-RamosMáximo Vento
May 7, 2021·Pediatric Research·José David Piñeiro-RamosUNKNOWN Hypotop Study Group
Jul 19, 2021·Archives of Toxicology·Guillermo QuintásJosé V Castell

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