Selection Guide Metabolite Analysis - Metabolomics Product Portfolio

Significance of the Topic

Metabolomics delivers a comprehensive view of biochemical dynamics by profiling small molecules produced during biological processes. It supports diagnosis, biomarker discovery, drug research, food quality control, fermentation optimization, and functional food development. Integrating mass spectrometry, dedicated databases, and advanced software, modern metabolomics workflows accelerate discovery and ensure robust, high-throughput analyses.

Goals and Overview of the Article

This whitepaper introduces Shimadzu’s end-to-end metabolomics solutions. It covers quantitative profiling of primary metabolites, non-target workflows using Q-TOF instruments, spatial imaging of metabolites, lipid mediator and phospholipid analyses, cell culture profiling methods, chiral amino acid separation, short-chain fatty acid and bile acid quantitation, as well as the associated databases and data-analysis software.

Used Methodology and Instrumentation

Shimadzu’s portfolio spans multiple LC-MS/MS and GC-MS/MS platforms, including LCMS-8060, GCMS-TQ8050 NX, LCMS-9030 (Q-TOF), and the iMScope TRIO imaging system. Key databases and libraries provide ready-to-use MRM methods covering hundreds of compounds. Software tools traverse MS data (Traverse MS), manage batch quantitation and flagging (LabSolutions Insight), and perform multi-omics integration and pathway visualization (Multi-omics Analysis Package, Signpost MS).

Main Results and Discussion

• Wide-target quantitative LC-MS/MS and GC-MS/MS methods achieve simultaneous analysis of 475 GC-amenable metabolites and over 150 primary metabolites in 15–20 min runs.
• Q-TOF workflows support high-accuracy non-target screening, enabling discovery of unknowns such as N’-formylkynurenine in cell culture profiling.
• MS imaging visualizes distribution of bioactive compounds in tissue, e.g. strictinin in mouse kidney and imidacloprid in tomato stems.
• Lipid mediator packages quantify 196 eicosanoids plus 18 internal standards in 20 min and correct retention times for isomer discrimination.
• Phospholipid libraries detect up to 867 PC/PE species and resolve fatty acyl compositions via polarity-switched MRM.
• Applications include cell supernatant profiling of 95 culture medium metabolites, chiral D/L amino acid quantitation without derivatization, and SCFA analysis using 3-NPH derivatization.

Benefits and Practical Applications of the Method

• Streamlined workflows reduce method development time by providing “ready-to-use” databases and method packages.
• High throughput and sensitivity cater to diverse fields: medical research, food science, biotechnology, QA/QC.
• Integrated software accelerates data processing, multivariate analysis, and pathway mapping, supporting multi-omics studies.

Future Trends and Potential Applications

• AI-driven, parameter-free peak picking to handle growing data volumes.
• Real-time metabolome monitoring via probe electrospray ionization (DPiMS-8060).
• Advanced imaging combined with AI for spatial metabolomics and biomarker localization.
• Expansion of multi-omics platforms to integrate transcriptomics, proteomics, fluxomics, and metabolomics seamlessly.

Conclusion

Shimadzu’s integrated solutions—from instrumentation and curated databases to specialized software—address the full spectrum of metabolomics applications. They deliver robust, high-throughput, and flexible workflows that facilitate comprehensive biochemical profiling and discovery across life-science and industrial research.

Reference

Shimadzu Metabolomics Product Portfolio Selection Guide (C146-E280D)