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

J 2024

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

LENNON, Sarah, Jade CHAKER, Elliott James PRICE, Juliane HOLLENDER, Carolin HUBER et. al.

Basic information

Original name

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

Authors

LENNON, Sarah, Jade CHAKER, Elliott James PRICE (826 United Kingdom of Great Britain and Northern Ireland, guarantor, belonging to the institution), Juliane HOLLENDER, Carolin HUBER, Tobias SCHULZE, Lutz AHRENS, Frederic BEEN, Nicolas CREUSOT, Laurent DEBRAUWER, Gaud DERVILLY, Catherine GABRIEL, Thierry GUERIN, Baninia HABCHI, Emilien L. JAMIN, Jana KLÁNOVÁ (203 Czech Republic, belonging to the institution), Tina KOSJEK, Bruno LE BIZEC, Jeroen MEIJER, Hans MOL, Rosalie NIJSSEN, Herbert OBERACHER, Nafsika PAPAIOANNOU, Julien PARINET, Dimosthenis SARIGIANNIS, Michael A. STRAVS, Žiga TKALEC (705 Slovenia, belonging to the institution), Emma L. SCHYMANSKI, Marja LAMOREE, Jean-Philippe ANTIGNAC and Arthur DAVID

Edition

TrAC Trends in Analytical Chemistry, Oxford, Elsevier, 2024, 0165-9936

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10406 Analytical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 13.100 in 2022

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1016/j.trac.2024.117674

UT WoS

001223574100001

Keywords in English

High-resolution mass spectrometry; Exposomics; Metabolomics; Non-targeted analysis; Suspect screening analysis; Data preprocessing; Contaminants of emerging concern; Chemical exposome; Harmonized QA/QC

Abstract

V originále

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.

Links

EF17_043/0009632, research and development project

Name: CETOCOEN Excellence

LM2023069, research and development project

Name: Výzkumná infrastruktura RECETOX

Investor: Ministry of Education, Youth and Sports of the CR, RECETOX research infrastructure

101057014, interní kód MU

Name: Partnership for the Assessment of Risks from Chemicals (Acronym: PARC)

Investor: European Union, Cluster 1 - Health

857560, interní kód MU
(CEP code: EF17_043/0009632)

Name: CETOCOEN Excellence (Acronym: CETOCOEN Excellence)

Investor: European Union, Spreading excellence and widening participation

Citovat

LENNON, Sarah, Jade CHAKER, Elliott James PRICE, Juliane HOLLENDER, Carolin HUBER, Tobias SCHULZE, Lutz AHRENS, Frederic BEEN, Nicolas CREUSOT, Laurent DEBRAUWER, Gaud DERVILLY, Catherine GABRIEL, Thierry GUERIN, Baninia HABCHI, Emilien L. JAMIN, Jana KLÁNOVÁ, Tina KOSJEK, Bruno LE BIZEC, Jeroen MEIJER, Hans MOL, Rosalie NIJSSEN, Herbert OBERACHER, Nafsika PAPAIOANNOU, Julien PARINET, Dimosthenis SARIGIANNIS, Michael A. STRAVS, Žiga TKALEC, Emma L. SCHYMANSKI, Marja LAMOREE, Jean-Philippe ANTIGNAC and Arthur DAVID. 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. TrAC Trends in Analytical Chemistry. Oxford: Elsevier, 2024, vol. 174, May 2024, p. 1-13. ISSN 0165-9936. Available from: https://dx.doi.org/10.1016/j.trac.2024.117674.

@article{2407861,
   author = {Lennon, Sarah and Chaker, Jade and Price, Elliott James and Hollender, Juliane and Huber, Carolin and Schulze, Tobias and Ahrens, Lutz and Been, Frederic and Creusot, Nicolas and Debrauwer, Laurent and Dervilly, Gaud and Gabriel, Catherine and Guerin, Thierry and Habchi, Baninia and Jamin, Emilien L. and Klánová, Jana and Kosjek, Tina and Le Bizec, Bruno and Meijer, Jeroen and Mol, Hans and Nijssen, Rosalie and Oberacher, Herbert and Papaioannou, Nafsika and Parinet, Julien and Sarigiannis, Dimosthenis and Stravs, Michael A. and Tkalec, Žiga and Schymanski, Emma L. and Lamoree, Marja and Antignac, JeanandPhilippe and David, Arthur},
   article_location = {Oxford},
   article_number = {May 2024},
   doi = {http://dx.doi.org/10.1016/j.trac.2024.117674},
   keywords = {High-resolution mass spectrometry; Exposomics; Metabolomics; Non-targeted analysis; Suspect screening analysis; Data preprocessing; Contaminants of emerging concern; Chemical exposome; Harmonized QA/QC},
   language = {eng},
   issn = {0165-9936},
   journal = {TrAC Trends in Analytical Chemistry},
   title = {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},
   url = {https://www.sciencedirect.com/science/article/pii/S0165993624001560?via%3Dihub},
   volume = {174},
   year = {2024}
}

TY  - JOUR
ID  - 2407861
AU  - Lennon, Sarah - Chaker, Jade - Price, Elliott James - Hollender, Juliane - Huber, Carolin - Schulze, Tobias - Ahrens, Lutz - Been, Frederic - Creusot, Nicolas - Debrauwer, Laurent - Dervilly, Gaud - Gabriel, Catherine - Guerin, Thierry - Habchi, Baninia - Jamin, Emilien L. - Klánová, Jana - Kosjek, Tina - Le Bizec, Bruno - Meijer, Jeroen - Mol, Hans - Nijssen, Rosalie - Oberacher, Herbert - Papaioannou, Nafsika - Parinet, Julien - Sarigiannis, Dimosthenis - Stravs, Michael A. - Tkalec, Žiga - Schymanski, Emma L. - Lamoree, Marja - Antignac, Jean-Philippe - David, Arthur
PY  - 2024
TI  - 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
JF  - TrAC Trends in Analytical Chemistry
VL  - 174
IS  - May 2024
SP  - 1-13
EP  - 1-13
PB  - Elsevier
SN  - 01659936
KW  - High-resolution mass spectrometry
KW  - Exposomics
KW  - Metabolomics
KW  - Non-targeted analysis
KW  - Suspect screening analysis
KW  - Data preprocessing
KW  - Contaminants of emerging concern
KW  - Chemical exposome
KW  - Harmonized QA/QC
UR  - https://www.sciencedirect.com/science/article/pii/S0165993624001560?via%3Dihub
N2  - 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.
ER  -

LENNON, Sarah, Jade CHAKER, Elliott James PRICE, Juliane HOLLENDER, Carolin HUBER, Tobias SCHULZE, Lutz AHRENS, Frederic BEEN, Nicolas CREUSOT, Laurent DEBRAUWER, Gaud DERVILLY, Catherine GABRIEL, Thierry GUERIN, Baninia HABCHI, Emilien L. JAMIN, Jana KLÁNOVÁ, Tina KOSJEK, Bruno LE BIZEC, Jeroen MEIJER, Hans MOL, Rosalie NIJSSEN, Herbert OBERACHER, Nafsika PAPAIOANNOU, Julien PARINET, Dimosthenis SARIGIANNIS, Michael A. STRAVS, Žiga TKALEC, Emma L. SCHYMANSKI, Marja LAMOREE, Jean-Philippe ANTIGNAC and Arthur DAVID. 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. \textit{TrAC Trends in Analytical Chemistry}. Oxford: Elsevier, 2024, vol.~174, May 2024, p.~1-13. ISSN~0165-9936. Available from: https://dx.doi.org/10.1016/j.trac.2024.117674.

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