lobster-metabolomics 1.1.419

Metabolomics agent for Lobster AI (LC-MS, GC-MS, NMR untargeted metabolomics)

lobster-metabolomics

Metabolomics analysis for LC-MS, GC-MS, and NMR untargeted metabolomics workflows.

Installation

pip install lobster-metabolomics

Agents

Agent	Description
metabolomics_expert	Full metabolomics workflow orchestration with auto-detection of platform type (LC-MS, GC-MS, NMR) and appropriate preprocessing.

Services

Service	Purpose
MetabolomicsQualityService	QC assessment: RSD, TIC CV, QC sample evaluation, missing value analysis
MetabolomicsPreprocessingService	Feature filtering, imputation (KNN, min, LOD/2, median, MICE), normalization (PQN, TIC, IS, median, quantile), batch correction (ComBat, median centering, QC-RLSC)
MetabolomicsAnalysisService	Univariate statistics (t-test, Wilcoxon, ANOVA, Kruskal-Wallis with FDR), PCA, PLS-DA with VIP scores, OPLS-DA, fold change analysis
MetabolomicsAnnotationService	m/z-based metabolite annotation against bundled reference database (HMDB/KEGG), MSI confidence levels, lipid class classification

Features

• Auto-detection of platform type from data characteristics (LC-MS, GC-MS, NMR)
• Platform-specific defaults for QC thresholds, normalization, and imputation
• Multiple normalization methods including PQN (gold standard for metabolomics)
• Supervised multivariate analysis (PLS-DA, OPLS-DA) with permutation testing
• VIP score calculation for biomarker discovery
• Metabolite annotation with MSI confidence levels (1-4)
• Lipid class classification from m/z ranges

Platform Support

Platform	Missing Values	Normalization	Notes
LC-MS	20-60%	PQN + log2	Most common untargeted platform
GC-MS	10-40%	TIC + log2	Lower missing rates, derivatization
NMR	0-10%	PQN (no log)	Near-complete feature detection

Requirements

• Python 3.12+
• lobster-ai >= 1.0.0

Tier Requirement

This is a free agent. Available to all Lobster AI users.

Documentation

Full documentation: docs.omics-os.com/docs/agents/metabolomics

License

AGPL-3.0-or-later