Your Path to Success - Agilent Solutions for Metabolomics

Importance of the Topic

Metabolomics examines small endogenous compounds to reveal the functional state of biological systems and bridge genotype to phenotype. This approach complements genomics and proteomics by providing direct insights into cellular pathways and dynamic metabolism. Broad applications range from disease biomarker discovery to agricultural optimization and environmental monitoring.

Objectives and Study Overview

This whitepaper presents an end-to-end Agilent workflow for metabolomics, covering sample preparation, instrument platforms, data acquisition methods, informatics solutions, and emerging functional assays. The goal is to deliver robust, reproducible, and comprehensive analysis strategies for both discovery and targeted studies.

Methodology and Instrumentation

Sample Preparation

• Quenching and protein precipitation to arrest metabolism
• Lipid removal via Captiva EMR–Lipid for reduced ion suppression
• Automated extraction using Bravo Metabolomics Sample Prep Platform for plasma

Analytical Platforms

• GC/MS systems: 5977B single quadrupole, 7000/7010 triple quadrupole, 7200B Q-TOF
• LC/MS systems: 6200 TOF, 6500 Q-TOF, 6400 triple quadrupole
• Stable HILIC-Z columns for polar metabolite separation
• METLIN Personal Compound Database with curated MS/MS spectra
• Seahorse XF Analyzers for live-cell bioenergetic profiling

Informatics Tools

• MassHunter Profinder for feature extraction and isotopologue mining
• Mass Profiler Professional for statistical analysis, clustering, and pathway mapping
• Pathway Architect for interactive visualization on KEGG, BioCyc, and WikiPathways
• VistaFlux and Omix Premium for qualitative flux analysis using stable isotopes

Main Results and Discussion

Automated sample preparation enhances throughput and reproducibility, while lipid removal improves chromatographic performance and sensitivity. Discovery workflows using GC/MS, LC/MS, CE/MS, and SFC/MS enable global profiling and identification of differential features. Targeted dMRM methods quantify central carbon metabolites with high sensitivity and dynamic range. Advanced software streamlines data processing from feature finding to pathway-centric interpretation, supporting integration across omics modalities. Qualitative flux analysis reveals dynamic pathway activity through isotope tracing, and live-cell Seahorse assays provide complementary functional metabolism data.

Benefits and Practical Applications

These solutions offer reliable, operator-independent workflows, extensive metabolite coverage, and deep biological context. They support diverse research areas including clinical biomarker discovery, crop improvement, food quality assessment, drug development, environmental toxicology, biofuel production, and systems toxicology.

Future Trends and Opportunities

Integration of multi-omics datasets and machine learning will enhance interpretation of complex metabolic networks. Expansion of spectral libraries and real-time flux monitoring promise greater coverage and dynamic insight. Advances in single-cell metabolomics and high-throughput live-cell assays will further refine understanding of metabolic heterogeneity and disease mechanisms.

Conclusion

Agilent provides a comprehensive suite of instrumentation and informatics tailored for metabolomics research. From sample processing to pathway analysis and live-cell functional assays, these solutions accelerate discovery and deliver actionable biological insights.