Trivialities in metabolomics: Artifacts in extraction and analysis

Area of Science:

• Biochemistry
• Analytical Chemistry
• Systems Biology

Background:

• Metabolomics is a key tool in systems biology for understanding metabolic networks.
• Various analytical techniques like LC-MS and GC-MS are used to study the metabolome.
• Robust preanalytical protocols are crucial for accurate metabolomics analysis.

Purpose of the Study:

• To review the risks of artifact formation during metabolomics analysis.
• To highlight the impact of preanalytical steps and solvents on data quality.
• To discuss challenges in compound identification and validation.

Main Methods:

• Review of common metabolomics analytical techniques (TLC, LC-MS, GC-MS, MS-MS, NMR).
• Analysis of preanalytical procedures: collection, processing, drying, grinding, extraction, and sample preparation.
• Examination of solvent-related artifacts and chemical reactions with analytes.
• Discussion of analytical step artifacts, including LC stationary phase and mobile phase interactions.
• Consideration of issues with poorly soluble compounds and compound identification.

Main Results:

• Artifacts can arise from chemical reactions involving common solvents and functional groups (esters, N-oxides, etc.).
• Preanalytical steps like sample handling and extraction significantly influence data integrity.
• Analytical steps, particularly in Liquid Chromatography (LC), can introduce artifacts.
• Poorly soluble compounds can be masked, impacting biomarker discovery.
• Accurate compound identification and stereochemistry confirmation remain significant challenges.

Conclusions:

• Artifacts in metabolomics can originate from both preanalytical and analytical procedures.
• Chemical reactions with solvents and contaminations pose significant risks.
• Ensuring protocol validation is critical for achieving reproducible and reliable metabolomics data.
• Addressing challenges in compound identification is necessary for advancing the field.