Workflow4Metabolomics (W4M): A User-Friendly Metabolomics
Platform for Analysis of Mass Spectrometry and Nuclear Magnetic
Resonance Data

J 2025

Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data

DELPORTE, Cedric; Marie TREMBLAY-FRANCO; Yann GUITTON; Cecile CANLET; Ralf J. M. WEBER et al.

Základní údaje

Originální název

Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data

Autoři

Vydání

Current Protocols, HOBOKEN, Wiley, 2025, 2691-1299

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.200 v roce 2024

Označené pro přenos do RIV

Ano

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

annotation; chemometrics; GC-MS; LC-MS; NMR; statistics; untargeted metabolomics

Štítky

143180, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 6. 2025 15:18, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Various spectrometric methods can be used to conduct metabolomics studies. Nuclear magnetic resonance (NMR) or mass spectrometry (MS) coupled with separation methods, such as liquid or gas chromatography (LC and GC, respectively), are the most commonly used techniques. Once the raw data have been obtained, the real challenge lies in the bioinformatics required to conduct: (i) data processing (including preprocessing, normalization, and quality control); (ii) statistical analysis for comparative studies (such as univariate and multivariate analyses, including PCA or PLS-DA/OPLS-DA); (iii) annotation of the metabolites of interest; and (iv) interpretation of the relationships between key metabolites and the relevant phenotypes or scientific questions to be addressed. Here, we will introduce and detail a stepwise protocol for use of the Workflow4Metabolomics platform (W4M), which provides user-friendly access to workflows for processing of LC-MS, GC-MS, and NMR data. Those modular and extensible workflows are composed of existing standalone components (e.g., XCMS and CAMERA packages) as well as a suite of complementary W4M-implemented modules. This tool suite is accessible worldwide through a web interface and is hosted on UseGalaxy France. The extensible Virtual Research Environment (VRE) provided offers pre-configured workflows for metabolomics communities (platforms, end users, etc.), as well as possibilities for sharing among users. By providing a consistent ecosystem of tools and workflows through Galaxy, W4M makes it possible to process MS and NMR data from hundreds of samples using an ordinary personal computer, after step-by-step workflow optimization. (c) 2025 Wiley Periodicals LLC.Basic Protocol 1: W4M account creation, working history preparation, and data uploadSupport Protocol 1: How to prepare an NMR zip fileSupport Protocol 2: How to convert MS data from proprietary format to open formatSupport Protocol 3: How to get help with W4M (IFB forum) and how to report a problem on the GitHub repositoryBasic Protocol 2: LC-MS data processingAlternate Protocol 1: GC-MS data processingAlternate Protocol 2: NMR data processingBasic Protocol 3: Statistical analysisBasic Protocol 4: Annotation of metabolites from LC-MS dataAlternate Protocol 3: Annotation of metabolites from NMR data

Návaznosti

LM2023069, projekt VaV

Název: Výzkumná infrastruktura RECETOX

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Výzkumná infrastruktura RECETOX

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

Název: CETOCOEN Excellence (Akronym: CETOCOEN Excellence)

Investor: Evropská unie, CETOCOEN Excellence, Spreading excellence and widening participation

Citovat

DELPORTE, Cedric; Marie TREMBLAY-FRANCO; Yann GUITTON; Cecile CANLET; Ralf J. M. WEBER; Helge HECHT; Elliott James PRICE; Jana KLÁNOVÁ; Charlotte JOLY; Celine DALLE; Julien ST-VANNE; Etienne THEVENOT; Isabelle SCHMITZ; Sylvain CHEREAU; Sylvain DECHAUMET; Binta DIEME; Franck GIACOMONI; Gildas LE CORGUILLE; Melanie PETERA a Florence SOUARD. Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data. Current Protocols. HOBOKEN: Wiley, 2025, roč. 5, č. 2, s. 1-72. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70095.

@article{2483607,
   author = {Delporte, Cedric and TremblayandFranco, Marie and Guitton, Yann and Canlet, Cecile and Weber, Ralf J. M. and Hecht, Helge and Price, Elliott James and Klánová, Jana and Joly, Charlotte and Dalle, Celine and StandVanne, Julien and Thevenot, Etienne and Schmitz, Isabelle and Chereau, Sylvain and Dechaumet, Sylvain and Dieme, Binta and Giacomoni, Franck and Le Corguille, Gildas and Petera, Melanie and Souard, Florence},
   article_location = {HOBOKEN},
   article_number = {2},
   doi = {https://doi.org/10.1002/cpz1.70095},
   keywords = {annotation; chemometrics; GC-MS; LC-MS; NMR; statistics; untargeted metabolomics},
   language = {eng},
   issn = {2691-1299},
   journal = {Current Protocols},
   note = {Nedoplňovat EF17_043/0009632.},
   title = {Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data},
   url = {https://currentprotocols.onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70095},
   volume = {5},
   year = {2025}
}

TY  - JOUR
ID  - 2483607
AU  - Delporte, Cedric - Tremblay-Franco, Marie - Guitton, Yann - Canlet, Cecile - Weber, Ralf J. M. - Hecht, Helge - Price, Elliott James - Klánová, Jana - Joly, Charlotte - Dalle, Celine - St-Vanne, Julien - Thevenot, Etienne - Schmitz, Isabelle - Chereau, Sylvain - Dechaumet, Sylvain - Dieme, Binta - Giacomoni, Franck - Le Corguille, Gildas - Petera, Melanie - Souard, Florence
PY  - 2025
TI  - Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data
JF  - Current Protocols
VL  - 5
IS  - 2
SP  - 1-72
EP  - 1-72
PB  - Wiley
SN  - 26911299
N1  - Nedoplňovat EF17_043/0009632.
KW  - annotation
KW  - chemometrics
KW  - GC-MS
KW  - LC-MS
KW  - NMR
KW  - statistics
KW  - untargeted metabolomics
UR  - https://currentprotocols.onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70095
N2  - Various spectrometric methods can be used to conduct metabolomics studies. Nuclear magnetic resonance (NMR) or mass spectrometry (MS) coupled with separation methods, such as liquid or gas chromatography (LC and GC, respectively), are the most commonly used techniques. Once the raw data have been obtained, the real challenge lies in the bioinformatics required to conduct: (i) data processing (including preprocessing, normalization, and quality control); (ii) statistical analysis for comparative studies (such as univariate and multivariate analyses, including PCA or PLS-DA/OPLS-DA); (iii) annotation of the metabolites of interest; and (iv) interpretation of the relationships between key metabolites and the relevant phenotypes or scientific questions to be addressed. Here, we will introduce and detail a stepwise protocol for use of the Workflow4Metabolomics platform (W4M), which provides user-friendly access to workflows for processing of LC-MS, GC-MS, and NMR data. Those modular and extensible workflows are composed of existing standalone components (e.g., XCMS and CAMERA packages) as well as a suite of complementary W4M-implemented modules. This tool suite is accessible worldwide through a web interface and is hosted on UseGalaxy France. The extensible Virtual Research Environment (VRE) provided offers pre-configured workflows for metabolomics communities (platforms, end users, etc.), as well as possibilities for sharing among users. By providing a consistent ecosystem of tools and workflows through Galaxy, W4M makes it possible to process MS and NMR data from hundreds of samples using an ordinary personal computer, after step-by-step workflow optimization. (c) 2025 Wiley Periodicals LLC.Basic Protocol 1: W4M account creation, working history preparation, and data uploadSupport Protocol 1: How to prepare an NMR zip fileSupport Protocol 2: How to convert MS data from proprietary format to open formatSupport Protocol 3: How to get help with W4M (IFB forum) and how to report a problem on the GitHub repositoryBasic Protocol 2: LC-MS data processingAlternate Protocol 1: GC-MS data processingAlternate Protocol 2: NMR data processingBasic Protocol 3: Statistical analysisBasic Protocol 4: Annotation of metabolites from LC-MS dataAlternate Protocol 3: Annotation of metabolites from NMR data
ER  -

DELPORTE, Cedric; Marie TREMBLAY-FRANCO; Yann GUITTON; Cecile CANLET; Ralf J. M. WEBER; Helge HECHT; Elliott James PRICE; Jana KLÁNOVÁ; Charlotte JOLY; Celine DALLE; Julien ST-VANNE; Etienne THEVENOT; Isabelle SCHMITZ; Sylvain CHEREAU; Sylvain DECHAUMET; Binta DIEME; Franck GIACOMONI; Gildas LE CORGUILLE; Melanie PETERA a Florence SOUARD. Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data. \textit{Current Protocols}. HOBOKEN: Wiley, 2025, roč.~5, č.~2, s.~1-72. ISSN~2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70095.

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