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Importance of the Topic

Multi-omics integration combines genomic, transcriptomic, proteomic and metabolomic data to provide comprehensive insights into biological systems. This holistic approach is crucial for advancing research in drug development, diagnostics and systems biology.

Study Objectives and Overview

This article presents a consolidated set of advanced workflows, instrumentation and software developed by Agilent to accelerate multi-omics research. It encompasses sample preparation strategies, analytical platforms, data acquisition methods and informatics solutions to support metabolomics, flux analysis, proteomics and real-time cellular assays.

Methodology

• Sample Preparation: Phospholipid and protein removal using Captiva EMR-Lipid cleanup workflows.
• Chromatography: HILIC-Z columns for polar metabolites and amino acids; UHPLC, SFC and CE separation modes.
• Flux Analysis: Stable isotope labeling (13C, 15N, 2H) with VistaFlux software for qualitative tracer studies.
• Cellular Bioenergetics: Real-time measurement of oxygen consumption and proton flux using Seahorse XF assays for ATP production rate.
• Proteomics: Ion mobility All Ions MS/MS and low-energy electron ionization for enhanced peptide fragmentation and identification.

Used Instrumentation

• LC/MS platforms: 1290 Infinity II UHPLC, 6500 Q-TOF, 6400/7000 QQQ systems, Jet Stream ion source.
• GC/MS platforms: 7250 GC/Q-TOF, 7200B GC/Q-TOF, 5977B GC/MS, 7000D GC/QQQ.
• Capillary Electrophoresis: 7100 CE system.
• Seahorse XF analyzers for live cell metabolic assays.

Key Findings and Discussion

• Captiva EMR-Lipid achieves >99% phospholipid removal across diverse biological fluids, improving LC/MS stability and sensitivity.
• HILIC-Z methods enable robust separation of underivatized amino acids and central carbon metabolites in both positive and negative ion modes.
• Culture media metabolomics and isotope tracing reveal dynamic metabolic fluxes, supported by automated VistaFlux workflows.
• GC/Q-TOF with low-energy electron ionization and iterative exclusion enhances untargeted compound identification and spectral quality.
• Seahorse XF assays deliver kinetic, label-free multiparameter readouts of mitochondrial and glycolytic activity with minimal cell numbers.
• Proteomic workflows using IM All Ions MS/MS and Jet Stream source increase sensitivity, reproducibility and throughput for discovery and targeted analyses.
• Integrated software tools streamline batch feature extraction, statistical analysis, compound identification and pathway-centric visualization.

Benefits and Practical Applications

• Automated cleanup and preprocessing reduce sample handling time and matrix effects.
• High-throughput, robust LC/MS and GC/MS methods support routine monitoring of key metabolites and biomarkers.
• Flux and real-time bioenergetic assays provide functional insights into cellular physiology and drug responses.
• Advanced proteomic techniques facilitate comprehensive protein profiling and biomarker discovery.
• Multi-omics integration accelerates hypothesis testing and systems-level modeling for translational research.

Future Trends and Applications

Advancements in high-resolution MS, automation and AI-driven informatics will enable deeper, scalable multi-omics analyses. Emerging directions include real-time single-cell omics, cloud-based data integration, expanded stable isotope tracing, and targeted databases for personalized medicine and environmental omics.

Conclusion

Agilent’s end-to-end multi-omics ecosystem—spanning sample preparation, diverse analytical platforms and comprehensive software—empowers researchers to unravel complex biological processes with enhanced sensitivity, throughput and interpretability. This integrated approach accelerates discovery and translation in metabolomics, proteomics and systems biology.