Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F25%3A00140814" target="_blank" >RIV/00216224:14310/25:00140814 - isvavai.cz</a>
Result on the web
<a href="https://currentprotocols.onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70095" target="_blank" >https://currentprotocols.onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70095</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/cpz1.70095" target="_blank" >10.1002/cpz1.70095</a>
Alternative languages
Result language
angličtina
Original language name
Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data
Original language description
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
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10609 - Biochemical research methods
Result continuities
Project
<a href="/en/project/LM2023069" target="_blank" >LM2023069: RECETOX Research Infrastructure</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Current Protocols
ISSN
2691-1299
e-ISSN
2691-1299
Volume of the periodical
5
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
72
Pages from-to
1-72
UT code for WoS article
001420849400001
EID of the result in the Scopus database
2-s2.0-85218831503