Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminants

Alygizakis, Nikiforos; Lestremau, Francois; Gago-Ferrero, Pablo; Gil-Solsona, Rubén; Arturi, Katarzyna; Hollender, Juliane; Schymanski, Emma; Dulio, Valeria; Slobodnik, Jaroslav; Thomaidis, Nikolaos S.

doi:10.1016/j.trac.2023.116944

Article (Scientific journals)

Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminants

Alygizakis, Nikiforos; Lestremau, Francois; Gago-Ferrero, Pablo et al.

2023 • In TrAC: Trends in Analytical Chemistry, 159, p. 116944

Peer reviewed

Permalink
https://hdl.handle.net/10993/54240

DOI
10.1016/j.trac.2023.116944

Files (2)Send to Details Statistics Bibliography Similar publications

Files

Full Text

Manuscript IP system_AuthorSubmission.pdf

Embargo Until 27/Jan/2025 - Author postprint (1.35 MB)

Request a copy

Annexes

Alygizakis_etal_2023_1-s2.0-S0165993623000316-main.pdf

(2.76 MB)

Download

All documents in ORBilu are protected by a user license.

Send to

RIS BibTex APA Chicago Permalink X Linkedin

Details

Abstract :

[en] Non-target screening (NTS) methods are rapidly gaining in popularity, empowering researchers to search for an ever-increasing number of chemicals. Given this possibility, communicating the confidence of identification in an automated, concise and unambiguous manner is becoming increasingly important. In this study, we compiled several pieces of evidence necessary for communicating NTS identification confidence and developed a machine learning approach for classification of the identifications as reliable and unreliable. The machine learning approach was trained using data generated by four laboratories equipped with different instrumentation. The model discarded substances with insufficient identification evidence efficiently, while revealing the relevance of different parameters for identification. Based on these results, a harmonized IP-based system is proposed. This new NTS-oriented system is compatible with the currently widely used five level system. It increases the precision in reporting and the reproducibility of current approaches via the inclusion of evidence scores, while being suitable for automation.

Disciplines :

Environmental sciences & ecology

Author, co-author :

Alygizakis, Nikiforos

Lestremau, Francois

Gago-Ferrero, Pablo

Gil-Solsona, Rubén

Arturi, Katarzyna

Hollender, Juliane

Schymanski, Emma ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)

Dulio, Valeria

Slobodnik, Jaroslav

Thomaidis, Nikolaos S.

External co-authors :

yes

Language :

English

Title :

Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminants

Publication date :

2023

Journal title :

TrAC: Trends in Analytical Chemistry

ISSN :

0165-9936

Volume :

159

Pages :

116944

Peer reviewed :

Peer reviewed

Focus Area :

Computational Sciences

Additional URL :

https://linkinghub.elsevier.com/retrieve/pii/S0165993623000316

FnR Project :

FNR12341006 - Environmental Cheminformatics To Identify Unknown Chemicals And Their Effects, 2018 (01/10/2018-30/09/2023) - Emma Schymanski

Available on ORBilu :

since 27 January 2023

Statistics

Number of views

94 (2 by Unilu)

Number of downloads

1 (0 by Unilu)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

WoS citations^™

Bibliography

Hollender, J., van Bavel, B., Dulio, V., Farmen, E., Furtmann, K., Koschorreck, J., Kunkel, U., Krauss, M., Munthe, J., Schlabach, M., Slobodnik, J., Stroomberg, G., Ternes, T., Thomaidis, N.S., Togola, A., Tornero, V., Environ. Sci. Eur., 31, 2019, 10.1021/acs.est.7b02184.
Wang, Z., Walker, G.W., Muir, D.C.G., Nagatani-Yoshida, K., Environ. Sci. Technol., 54, 2020, 2575, 10.1021/acs.est.9b06379.
Finckh, S., Beckers, L.-M., Busch, W., Carmona, E., Dulio, V., Kramer, L., Krauss, M., Posthuma, L., Schulze, T., Slootweg, J., Von der Ohe, P.C., Brack, W., Environ. Int., 164, 2022, 107234, 10.1016/j.envint.2022.107234.
Petromelidou, S., Margaritis, D., Nannou, C., Keramydas, C., Lambropoulou, D.A., Sci. Total Environ., 848, 2022, 157696, 10.1016/j.scitotenv.2022.157696.
Yang, W., Tang, Y., Jiang, L., Luo, P., Wu, Y., Cao, Y., Wu, X., Xiong, J., Sci. Total Environ., 809, 2022, 151117, 10.1016/j.scitotenv.2021.151117.
Han, Y., Hu, L.-X., Liu, T., Liu, J., Wang, Y.-Q., Zhao, J.-H., Liu, Y.-S., Zhao, J.-L., Ying, G.-G., Sci. Total Environ., 837, 2022, 155705, 10.1016/j.scitotenv.2022.155705.
Menger, F., Gago-Ferrero, P., Wiberg, K., Ahrens, L., Trends Environ. Anal. Chem., 28, 2020, e00102, 10.1016/j.teac.2020.e00102.
Chen, W.-L., Lin, S.-C., Huang, C.-H., Peng, S.-Y., Ling, Y.S., Sci. Total Environ., 750, 2021, 141519, 10.1016/j.scitotenv.2020.141519.
Freeling, F., Alygizakis, N.A., von der Ohe, P.C., Slobodnik, J., Oswald, P., Aalizadeh, R., Cirka, L., Thomaidis, N.S., Scheurer, M., Sci. Total Environ., 681, 2019, 475, 10.1016/j.scitotenv.2019.04.445.
Schymanski, E.L., Jeon, J., Gulde, R., Fenner, K., Ruff, M., Singer, H.P., Hollender, J., Environ. Sci. Technol., 48, 2014, 2097, 10.1021/es5002105.
Charbonnet, J.A., McDonough, C.A., Xiao, F., Schwichtenberg, T., Cao, D., Kaserzon, S., Thomas, K.V., Dewapriya, P., Place, B.J., Schymanski, E.L., Field, J.A., Helbling, D.E., Higgins, C.P., Environ. Sci. Technol. Lett., 9, 2022, 473, 10.1021/acs.estlett.2c00206.
Pourchet, M., Debrauwer, L., Klanova, J., Price, E.J., Covaci, A., Caballero-Casero, N., Oberacher, H., Lamoree, M., Damont, A., Fenaille, F., Vlaanderen, J., Meijer, J., Krauss, M., Sarigiannis, D., Barouki, R., Le Bizec, B., Antignac, J.P., Environ. Int., 139, 2020, 105545, 10.1016/j.envint.2020.105545.
González-Gaya, B., Lopez-Herguedas, N., Santamaria, A., Mijangos, F., Etxebarria, N., Olivares, M., Prieto, A., Zuloaga, O., Chemosphere, 274, 2021, 129964, 10.1016/j.chemosphere.2021.129964.
Gago-Ferrero, P., Krettek, A., Fischer, S., Wiberg, K., Ahrens, L., Environ. Sci. Technol., 52, 2018, 6881, 10.1021/acs.est.7b06598.
Samanipour, S., Baz-Lomba, J.A., Alygizakis, N.A., Reid, M.J., Thomaidis, N.S., Thomas, K.V., J. Chromatogr. A, 1501, 2017, 68, 10.1016/j.chroma.2017.04.040.
Schymanski, E.L., Singer, H.P., Slobodnik, J., Ipolyi, I.M., Oswald, P., Krauss, M., Schulze, T., Haglund, P., Letzel, T., Grosse, S., Thomaidis, N.S., Bletsou, A., Zwiener, C., Ibanez, M., Portoles, T., de Boer, R., Reid, M.J., Onghena, M., Kunkel, U., Schulz, W., Guillon, A., Noyon, N., Leroy, G., Bados, P., Bogialli, S., Stipanicev, D., Rostkowski, P., Hollender, J., Anal. Bioanal. Chem., 407, 2015, 6237, 10.1007/s00216-015-8681-7.
Gago-Ferrero, P., Bletsou, A.A., Damalas, D.E., Aalizadeh, R., Alygizakis, N.A., Singer, H.P., Hollender, J., Thomaidis, N.S., J. Hazard Mater., 387, 2020, 121712, 10.1016/j.jhazmat.2019.121712.
ISO Standard 21253. Water Quality - Multi-Compound Class Methods Criteria for the Identification of Target Compounds by Gas and Liquid Chromatography and Mass Spectrometry. 2019.
Helmus, R., ter Laak, T.L., van Wezel, A.P., de Voogt, P., Schymanski, E.L., J. Cheminf., 13, 2021, 1, 10.1186/s13321-020-00477-w.
Alygizakis, N.A., Oswald, P., Thomaidis, N.S., Schymanski, E.L., Aalizadeh, R., Schulze, T., Oswaldova, M., Slobodnik, J., TrAC, Trends Anal. Chem., 115, 2019, 129, 10.1016/j.trac.2019.04.008.
Caballero-Casero, N., Belova, L., Vervliet, P., Antignac, J.-P., Castaño, A., Debrauwer, L., López, M.E., Huber, C., Klanova, J., Krauss, M., Lommen, A., Mol, H.G.J., Oberacher, H., Pardo, O., Price, E.J., Reinstadler, V., Vitale, C.M., van Nuijs, A.L.N., Covaci, A., TrAC, Trends Anal. Chem., 136, 2021, 116201, 10.1016/j.trac.2021.116201.
Rostkowski, P., Haglund, P., Aalizadeh, R., Alygizakis, N., Thomaidis, N., Arandes, J.B., Nizzetto, P.B., Booij, P., Budzinski, H., Brunswick, P., Covaci, A., Gallampois, C., Grosse, S., Hindle, R., Ipolyi, I., Jobst, K., Kaserzon, S.L., Leonards, P., Lestremau, F., Letzel, T., Magnér, J., Matsukami, H., Moschet, C., Oswald, P., Plassmann, M., Slobodnik, J., Yang, C., Anal. Bioanal. Chem., 411, 2019, 1957, 10.1007/s00216-019-01615-6.
Bade, R., Bijlsma, L., Miller, T.H., Barron, L.P., Sancho, J.V., Hernández, F., Sci. Total Environ., 538, 2015, 934, 10.1016/j.scitotenv.2015.08.078.
Feng, C., Xu, Q., Qiu, X., Jin, Y.e., Ji, J., Lin, Y., Le, S., She, J., Lu, D., Wang, G., Chemosphere, 271, 2021, 129447, 10.1016/j.chemosphere.2020.129447.
Pasin, D., Mollerup, C.B., Rasmussen, B.S., Linnet, K., Dalsgaard, P.W., Anal. Chim. Acta, 1184, 2021, 339035, 10.1016/j.aca.2021.339035.
Kováts, E., Helv. Chim. Acta, 41, 1958, 1915, 10.1002/hlca.19580410703.
Aalizadeh, R., Alygizakis, N., Schymanski, E.L., Krauss, M., Schulze, T., Ibáñez, M., McEachran, A.D., Chao, A., Williams, A.J., Gago-Ferrero, P., Covaci, A., Moschet, C., Young, T., Hollender, J., Slobodnik, J., Thomaidis, N., Anal. Chem., 93, 2021, 11601, 10.1021/acs.analchem.1c02348.
MassBank. 2022 https://massbank.eu/MassBank/. (Accessed 21 September 2022)
MoNA. 2022 https://mona.fiehnlab.ucdavis.edu/. (Accessed 21 September 2022)
mzCloud. 2022 https://www.mzcloud.org/. (Accessed 21 September 2022)
Dührkop, K., Fleischauer, M., Ludwig, M., Aksenov, A.A., Melnik, A.V., Meusel, M., Dorrestein, P.C., Rousu, J., Böcker, S., Nat. Methods, 16, 2019, 299, 10.1038/s41592-019-0344-8.
Wang, F., Liigand, J., Tian, S., Arndt, D., Greiner, R., Wishart, D.S., Anal. Chem., 93, 2021, 11692, 10.1021/acs.analchem.1c01465.
Ruttkies, C., Schymanski, E.L., Wolf, S., Hollender, J., Neumann, S., J. Cheminf., 8, 2016, 3, 10.1186/s13321-016-0115-9.
Ridder, L., van der Hooft, J.J.J., Verhoeven, S., Mass Spectrom., 3, 2014, S0033, 10.5702/massspectrometry.S0033.
Loos, M., Nontarget: detecting isotope, adduct and homologue relations in LC–MS data. https://CRAN.R-project.org/package=nontarget. 2016.
Broeckling, C.D., Afsar, F.A., Neumann, S., Ben-Hur, A., Prenni, J.E., Anal. Chem., 86, 2014, 6812, 10.1021/ac501530d.
Celma, A., Ahrens, L., Gago-Ferrero, P., Hernández, F., López, F., Lundqvist, J., Pitarch, E., Sancho, J.V., Wiberg, K., Bijlsma, L., Chemosphere, 280, 2021, 130799, 10.1016/j.chemosphere.2021.130799.
Ross, D.H., Cho, J.H., Xu, L., Anal. Chem., 92, 2020, 4548, 10.1021/acs.analchem.9b05772.
Meringer, M., Schymanski, E.L., Metabolites, 3, 2013, 440, 10.3390/metabo3020440.
Meringer, M., Reinker, S., Zhang, J., Muller, A., Commun. Math. Comput. Chem., 65, 2011 0340-6253.
Dodder, N., Mullen, K., OrgMassSpecR: organic mass spectrometry. 2017 https://cran.r-project.org/web/packages/OrgMassSpecR/index.html. (Accessed 21 January 2022)
A. Togola, C. Guillemain, F. Lestremau, C. Coureau, C. Margoum, C. Soulier, Applicabilite de la Technique de « Screening non Cible » Pour la Surveillance Prospective. Réseau de Surveillance prospective-AQUAREF; Rapport BRGM/RP-70108-FR (Accessible at https://professionnels.ofb.fr/sites/default/files/pdf/documentation/Pollution/LotC_4.pdf, Last accessed 21 January 2022). 2020.
Gil-Solsona, R., Nika, M.-C., Bustamante, M., Villanueva, C.M., Foraster, M., Cosin-Tomás, M., Alygizakis, N., Gómez-Roig, M.D., Llurba-Olive, E., Sunyer, J., Thomaidis, N.S., Dadvand, P., Gago-Ferrero, P., Environ. Sci. Technol. Lett., 8, 2021, 1077, 10.1021/acs.estlett.1c00848.
Gil-Solsona, R., Rodriguez-Mozaz, S., Diaz-Cruz, M.S., Sunyer-Caldu, A., Luarte, T., Hofer, J., Galban-Malagon, C., Gago-Ferrero, P., MethodsX, 8, 2021, 101193, 10.1016/j.mex.2020.101193.
Kiefer, K., Muller, A., Singer, H., Hollender, J., Water Res., 165, 2019, 114972, 10.1016/j.watres.2019.114972.
Tautenhahn, R., Böttcher, C., Neumann, S., BMC Bioinf., 9, 2008, 504, 10.1186/1471-2105-9-504.
Libiseller, G., Dvorzak, M., Kleb, U., Gander, E., Eisenberg, T., Madeo, F., Neumann, S., Trausinger, G., Sinner, F., Pieber, T., Magnes, C., BMC Bioinf., 16, 2015, 118, 10.1186/s12859-015-0562-8.
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M., Duchesnay, E., J. Mach. Learn. Res., 12, 2011, 2825.
European Commission. Commission decision of 12 August 2002 implementing Council Directive 96/23/EC concerning the performance of analytical methods and the interpretation of results. Off. J. Eur. Comm., 221, 2002, 8.
Assoumani, A., Lestremau, F., Salomon, M., Ferret, C., Lepot, B., Campagne Emergents Nationaux 2018 (EMNAT 2018) - Résultats de la recherche de contaminants émergents dans les eaux de surface et les rejets de STEU. 2020.