fermo

fermo integrates liquid chromatography-tandem mass spectrometry (LC-MS) metabolomics data with phenotype information, sample grouping, and genomic data to prioritize and rank molecular features associated with phenotypic traits.

Key Features:

• Automated Data Processing: Streamlines handling and organization of large-scale LC-MS metabolomics datasets through automated processing steps.
• Annotation and Integration: Performs annotation of molecular features and integrates LC-MS data with phenotype, sample grouping, and genomic data.
• Feature Extraction and Ranking: Extracts molecular features and applies reproducible prioritization and ranking based on phenotypic relevance.
• Data Filtering: Enables filtering of features and samples according to specified criteria to refine analyses.
• Modular Framework: Provides a modular architecture that automates processing, annotation, and integration workflows.
• Exploratory and Targeted Analysis Support: Supports both exploratory analyses and targeted hypothesis-driven prioritization of molecules.
• Visualization of Feature–Phenotype Interactions: Generates visualizations that relate molecular features to phenotypes for interpretation.

Scientific Applications:

• Bioactive Compound Identification: Benchmarking studies to identify bioactive compounds from complex biological matrices.
• Natural Product Drug Discovery: Prioritization of candidate molecules in natural product discovery workflows.
• Microbiology: Linking metabolite features to microbial phenotypes and biological function.
• Agricultural Research: Identifying molecular underpinnings of phenotypic variation in agricultural studies.
• Phenotype Association Studies: Associating small molecules with phenotypic traits to support hypothesis generation.

Methodology:

Automated data processing, annotation, and integration of LC-MS metabolomics with phenotype, sample grouping, and genomic data, followed by feature extraction, reproducible prioritization/ranking, data filtering, and visualization of feature–phenotype interactions.