Two birds with one stone: doing metabolomics with your proteomics kit

Area of Science:

• Biochemistry
• Analytical Chemistry
• Systems Biology

Background:

• Increasing demand for integrating multi-omics data (genomics, proteomics, metabolomics) to understand complex biological processes.
• Existing proteomic workflows share instrumentation and methodologies with metabolomics, particularly mass spectrometry (MS).
• Chemical diversity of metabolites presents challenges for direct MS-based metabolomic analysis.

Purpose of the Study:

• To introduce metabolomics workflows to proteomic researchers.
• To compare physicochemical properties of proteins/peptides with metabolites/small molecules.
• To highlight implications for sample preparation, separation, ionization, detection, and data analysis in metabolomics.

Main Methods:

• Review of existing proteomic workflows, specifically nano liquid chromatography-mass spectrometry (nLC-MS).
• Comparative analysis of protein/peptide versus metabolite physicochemical properties.
• Discussion of how proteomic techniques can be adapted for metabolomic sample analysis.

Main Results:

• A typical proteomic nLC-MS workflow can detect various aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids, and vitamins.
• This demonstrates a straightforward entry point for proteomic labs into metabolomics.
• Identified limitations and requirements for adapting proteomic workflows for metabolomics.

Conclusions:

• Proteomic nLC-MS workflows can be effectively utilized for detecting a subset of metabolites, facilitating entry into metabolomics.
• This approach offers a cost-effective strategy for multi-omics data integration without immediate investment in dedicated metabolomics instrumentation.
• Further extensions to LC-MS workflows can broaden the range of detectable molecular classes.