MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis

Area of Science:

• Plant science
• Metabolomics
• Bioinformatics

Background:

• Plant adaptation to dynamic environments relies on complex metabolic mechanisms.
• Analyzing large-scale plant metabolomics data is challenging due to complex datasets and required programming skills.
• Existing tools often lack user-friendliness and efficiency for extensive metabolomics datasets.

Purpose of the Study:

• To develop an efficient, user-friendly pipeline for plant metabolomics data analysis.
• To address limitations of current protocols in handling large datasets and accessibility for non-programmers.
• To enhance metabolite annotation and biological meaning extraction from plant metabolomics data.

Main Methods:

• Development of MetMiner, a full-functionality R shiny pipeline for plant metabolomics.
• Integration of a plant-specific mass spectrometry database for improved metabolite annotation.
• Incorporation of MDAtoolkits for statistical analysis, classification, and enrichment analysis.
• Application of an iterative weighted gene co-expression network analysis strategy for biomarker screening.

Main Results:

• MetMiner provides a user-friendly interface for deep data interaction and graphical analysis.
• The pipeline ensures transparency, traceability, and reproducibility in metabolomics data analysis.
• Optimized metabolite annotation through a plant-specific mass spectrometry database.
• Efficient biomarker metabolite screening using a novel network analysis strategy.
• Case studies validated MetMiner's efficiency and robustness in data mining and annotation.

Conclusions:

• MetMiner offers a powerful, accessible solution for plant metabolomics data analysis.
• The pipeline empowers researchers without programming skills to analyze complex datasets.
• MetMiner facilitates deeper understanding of plant metabolic mechanisms and adaptation.
• This tool enhances the scientific community's capacity for plant metabolomics research.