Metabolic Pathway Analysis Solutions

Importance of the Topic

Metabolic pathway analysis underpins our understanding of cellular function, homeostasis and disease. Mapping the flow of small molecules through glycolysis, the citric acid cycle, amino acid and lipid metabolism reveals enzyme activity, regulatory points and flux distributions critical for drug discovery, biotechnology, personalized medicine and quality control in industrial bioprocesses.

Objectives and Overview

This article presents a comprehensive suite of analytical solutions and workflows for targeted and untargeted metabolomics. It demonstrates applications across diverse sample types—human plasma and serum, cultured cells, microbial strains and model organisms—highlighting both quantitative profiling and flux analysis using Shimadzu LC-MS, GC-MS, ICP-MS and AA platforms together with dedicated software and databases.

Methodology

Each application follows a structured workflow: sample collection and preparation (protein precipitation, solid-phase extraction, derivatization for GC-MS, or dilution for LC-MS/ICP-MS/AA), instrumental analysis in multiple reaction monitoring (MRM) or high-resolution modes, and data processing with statistical tools (PCA, clustering, volcano plots) and metabolic map visualization.

Instrumentation

• Triple quadrupole LC-MS/MS: LCMS-8060NX, LCMS-8040 (homocysteine), LCMS-8030/8000 series (primary metabolites), LCMS-8060 for lipid mediators
• Gas chromatograph mass spectrometer: GCMS-TQ8040 NX (model organisms, microbial flux)
• Quadruple time-of-flight LC-MS: LCMS-9030 (untargeted profiling with Metabolite Precision Mass Database)
• Inductively coupled plasma MS: ICPMS-2030 (trace metals in cell culture)
• Atomic absorption spectrophotometer: AA-7000F/AAC (flame and furnace for metal monitoring)
• Software and databases: Multi-omics Analysis Package, LabSolutions Insight, Smart Metabolites Database™ Ver. 2, LC/MS/MS Method Packages, Metabolite Precision Mass Database

Main Results and Discussion

• Lipid mediator profiling in plasma/serum: 196-component assay detected 68 eicosanoids with rapid metabolic map visualization.
• Drosophila metabolomics: GC-MS and LC-MS combined revealed genetic mutation effects on central metabolism and amino acid pools.
• Homocysteine quantification: Sensitive MRM assay in plasma demonstrated reliable detection for research on methionine cycle.
• CHO cell culture analysis: Simultaneous organic/inorganic profiling uncovered interactions of trace metals and metabolites affecting antibody yield and glycosylation.
• Microbial breeding: LC-MS analysis of cysteine-producing E. coli under different sulfur sources showed dynamic shifts in sulfur metabolites and nucleosides.
• 13C metabolic flux analysis (GC-MS): Flux distributions in E. coli central carbon pathways quantified, revealing glycolytic, pentose phosphate and TCA cycle branch points.
• Untargeted to targeted workflow (Q-TOF to triple quadrupole): iPS cell medium analysis identified culture-dependent metabolite variations and enabled MRM method expansion for 470 endogenous compounds.

Benefits and Practical Applications

• Comprehensive coverage: Integration of targeted assays and untargeted discovery supports broad metabolome interrogation.
• High sensitivity and throughput: MRM workflows deliver rapid, reliable quantification of dozens to hundreds of metabolites in under 20 minutes.
• Data visualization: Metabolic maps and statistical tools accelerate interpretation of complex multi-omics datasets.
• Process optimization: Real-time monitoring of cell culture media and microbial fermentation guides quality control and strain engineering.
• Clinical research support: Accurate profiling of biomarkers (e.g., homocysteine) informs translational studies and personalized medicine.

Future Trends and Potentials

Advances in high-resolution MS, expanded isotope tracing, AI-driven data mining and cloud-based metabolic databases will enhance pathway reconstruction, flux quantification and biomarker discovery. Automated sample handling and integrated multi-omics platforms promise real-time metabolic monitoring in bioprocessing and precision diagnostics.

Conclusion

Shimadzu’s integrated solutions—combining robust MS instrumentation, specialized software, targeted method packages and comprehensive databases—enable end-to-end metabolic pathway analysis. These tools facilitate discovery, quantification and visualization of metabolic networks across research, biomanufacturing and clinical applications.