Guide to Metabolomics Analysis: A Bioinformatics Workflow
Abstract
:1. Introduction
2. The Analysis Workflow of Metabolomics
3. Statistical Analysis in Metabolomics
3.1. Univariate Analysis
3.2. Multivariate Analysis
4. Software Tools for Metabolomics Data Analysis and Integration
4.1. MS-DIAL
4.2. MZmine 3
4.3. El-MAVEN
4.4. LipidMatch
4.5. LipiDex
4.6. MetFlow
4.7. MetaboAnalyst 5.0
4.8. LipidSig
4.9. LION
4.10. METLIN
4.11. PaintOmics 3
4.12. 3Omics
4.13. IMPaLa
4.14. MetPA
4.15. MassTRIX
4.16. MetaCore™
4.17. OmicsNet
5. The Integration Algorithm of Multi-Omics Data
6. Conclusions and Prospects
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Name | Year | Description | Functions | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Data Pre-Processing | Data Processing | Statistical Analyses | Pathway Enrichment Analysis | Omics Data Integration | ||||||
Normalization | Compound Name Identification | Transcriptomics | Proteomics | Microbiome | ||||||
Mzmine3 | 2022 | MZmine3 builds on the success of MZmine 2 with many features focused on improving the user-friendly graphical | Y | Y | Y | Y | - | - | - | - |
MetaboAnalyst 5.0 | 2021 | Comprehensive web-based tool for comprehensive metabolomics data analysis, interpretation, and integration with other omics data. | Y | Y | Y | Y | Y | Y | - | - |
LipidSig | 2021 | Web-based tool for lipidomic data analysis | Y | Y | Y | Y | - | - | - | - |
MS-DIAL 4.0 | 2020 | Lipidome atlas in MS-DIAL 4.0 | Y | Y | Y | Y | - | - | - | - |
El-MAVEN | 2019 | Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics | Y | Y | Y | - | - | - | - | - |
MetFlow | 2019 | Interactive and integrated web server for metabolomics data cleaning and differential metabolite discovery. | Y | Y | Y | Y | Y | - | - | - |
LION | 2019 | Web-based ontology enrichment tool for lipidomic data analysis. | - | Y | Y | Y | Y | - | - | - |
Omicsnet | 2018 | Web-based tool for creation and visual analysis of biological networks in 3D space | - | - | - | Y | Y | Y | Y | Y |
METLIN | 2018 | Technology platform for the identification of known and unknown metabolites and other chemical entities. | - | - | Y | - | - | - | - | - |
PaintOmics 3 | 2018 | Web-based resource for the integrated visualization of multiple omics data types onto KEGG pathway diagrams. | - | - | - | - | Y | Y | Y | - |
LipiDex | 2018 | Integrated Software Package for High-Confidence Lipid Identification | Y | - | Y | - | - | - | - | - |
LipidMatch | 2017 | Automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data | Y | - | Y | - | - | - | - | - |
3Omics | 2013 | One-click web tool for fast analysis and visualization of multi-omics data. | Y | Y | - | Y | Y | Y | Y | - |
IMPaLa | 2011 | Pathway analysis of transcriptomics or proteomics and metabolomics data. | - | - | - | - | Y | Y | Y | - |
MetPA | 2010 | Pathway analysis for metabolomics data. | Y | - | - | - | Y | - | - | - |
MassTRIX | 2008 | Tool for high precision MS data annotation. | Y | - | Y | - | Y | - | - | - |
MetaCoreTM | 2004 | Commercial tool for functional analysis and integrated analysis of multi-omics data. | Y | - | - | - | Y | Y | Y | - |
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Chen, Y.; Li, E.-M.; Xu, L.-Y. Guide to Metabolomics Analysis: A Bioinformatics Workflow. Metabolites 2022, 12, 357. https://doi.org/10.3390/metabo12040357
Chen Y, Li E-M, Xu L-Y. Guide to Metabolomics Analysis: A Bioinformatics Workflow. Metabolites. 2022; 12(4):357. https://doi.org/10.3390/metabo12040357
Chicago/Turabian StyleChen, Yang, En-Min Li, and Li-Yan Xu. 2022. "Guide to Metabolomics Analysis: A Bioinformatics Workflow" Metabolites 12, no. 4: 357. https://doi.org/10.3390/metabo12040357