Harmonized quality assurance/quality control provisions to assess completeness and robustness of MS1 data preprocessing for LC-HRMS-based suspect screening and non-targeted analysis
Chemical exposome; Contaminants of emerging concern; Data preprocessing; Exposomics; Harmonized QA/QC; High-resolution mass spectrometry; Metabolomics; Non-targeted analysis; Suspect screening analysis; Contaminants of emerging concerns; Exposomic; High resolution mass spectrometry; Non-targeted; Non-targeted analyse; Screening analysis; Suspect screening analyse; Analytical Chemistry; Spectroscopy
Abstract :
[en] Non-targeted and suspect screening analysis using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) holds great promise to comprehensively characterize complex chemical mixtures. Data preprocessing is a crucial part of the process, however, some limitations are observed: (i) peak-picking and feature extraction might be incomplete, especially for low abundant compounds, and (ii) limited reproducibility has been observed between laboratories and software for detected features and their relative quantification. We first conducted a critical review of existing solutions that could improve the reproducibility of preprocessing for LC-HRMS. Solutions include providing repositories and reporting guidelines, open and modular processing workflows, public benchmark datasets, tools to optimize the data preprocessing and to filter out false positive detections. We then propose harmonized quality assurance/quality control guidelines that would allow to assess the sensitivity of feature detection, reproducibility, integration accuracy, precision, accuracy, and consistency of data preprocessing for human biomonitoring, food and environmental communities.
Disciplines :
Environmental sciences & ecology
Author, co-author :
Lennon, Sarah; Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) – UMR_S 1085, Rennes, France
Chaker, Jade; Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) – UMR_S 1085, Rennes, France
Hollender, Juliane; Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland ; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
Huber, Carolin; Helmholtz Center for Environmental Research – UFZ, Department of Exposure Science, Leipzig, Germany
Schulze, Tobias; German Environment Agency (UBA), Berlin, Germany
Ahrens, Lutz; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
Béen, Frederic; Chemistry for Environment & Health, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands ; KWR Water Research Institute, Nieuwegein, Netherlands
Creusot, Nicolas; INRAE, French National Research Institute for Agriculture, Food & Environment. UR1454 EABX, Bordeaux Metabolome, France
Debrauwer, Laurent; Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France
Dervilly, Gaud; Oniris, INRAE, LABERCA, Nantes, France
Gabriel, Catherine; Environmental Engineering Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, Greece ; HERACLES Research Center on the Exposome and Health, Center for Interdisciplinary Research and Innovation, Greece
Guérin, Thierry; ANSES, Strategy and Programmes Department, Maisons-Alfort, France
Habchi, Baninia; INRS, Département Toxicologie et Biométrologie Laboratoire Biométrologie 1, Cedex, France
Jamin, Emilien L.; Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France
Kosjek, Tina; Jozef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
Le Bizec, Bruno; Oniris, INRAE, LABERCA, Nantes, France
Meijer, Jeroen; Chemistry for Environment & Health, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
Mol, Hans; Wageningen Food Safety Research (WFSR), Part of Wageningen University & Research, Wageningen, Netherlands
Nijssen, Rosalie; Wageningen Food Safety Research (WFSR), Part of Wageningen University & Research, Wageningen, Netherlands
Oberacher, Herbert; Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
Papaioannou, Nafsika; Environmental Engineering Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, Greece ; HERACLES Research Center on the Exposome and Health, Center for Interdisciplinary Research and Innovation, Greece
Parinet, Julien; ANSES, Laboratory for Food Safety, Maisons-Alfort, France
Sarigiannis, Dimosthenis; Environmental Engineering Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, Greece ; HERACLES Research Center on the Exposome and Health, Center for Interdisciplinary Research and Innovation, Greece
Stravs, Michael A.; Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland ; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
Tkalec, Žiga; RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic ; Jozef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
SCHYMANSKI, Emma ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Environmental Cheminformatics
Lamoree, Marja; Chemistry for Environment & Health, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
Antignac, Jean-Philippe; Oniris, INRAE, LABERCA, Nantes, France
David, Arthur ; Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) – UMR_S 1085, Rennes, France
Harmonized quality assurance/quality control provisions to assess completeness and robustness of MS1 data preprocessing for LC-HRMS-based suspect screening and non-targeted analysis
This work was supported by the project Partnership for the Assessment of Risks from Chemicals (PARC) funded by the European Union research and innovation program Horizon Europe [grant numbers 101057014]. SL, JC and AD acknowledge the research infrastructure France Exposome. EJP, JK and DT acknowledge the research infrastructure RECETOX RI (LM2023069), H2020 CETOCOEN Excellence 857560 and OP RDE CZ.02.1.01/0.0/0.0/17_043/0009632).
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