Distinguishing Artifactual Fatty Acid Dimers from Fatty Acid Esters of Hydroxy Fatty Acids in Untargeted LC-MS Pipelines

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 2855; p. 67
• Main Authors: Nelson, Alisa B, Queathem, Eric D, Puchalska, Patrycja
• Format: Journal Article
• Language: English
• Published: United States 2025
• Subjects: Chromatography, Liquid - methods; Dimerization; Esters - analysis; Esters - chemistry; Esters - metabolism; Fatty Acids - analysis; Fatty Acids - chemistry; Fatty Acids - metabolism; Humans; Hydrophobic and Hydrophilic Interactions; Hydroxy Acids - analysis; Hydroxy Acids - chemistry; Hydroxy Acids - metabolism; Liquid Chromatography-Mass Spectrometry; Mass Spectrometry - methods; Metabolomics - methods; Tandem Mass Spectrometry - methods; Lipidomics; LC-MS; Fatty acid dimers; Fatty acid esters of hydroxy fatty acids; Untargeted metabolomics
• ISSN: 1940-6029
• DOI: 10.1007/978-1-0716-4116-3_4

Untargeted metabolomics is a powerful profiling tool for the discovery of possible biomarkers of disease onset and progression. Analytical pipelines applying liquid chromatography (LC) and mass spectrometry (MS)-based methods are widely used to survey a broad range of metabolites within various metabolic pathways, including organic acids, amino acids, nucleosides, and lipids. Accurate and complete identification of putative metabolites is an ongoing challenge in untargeted metabolomics studies. Highly sensitive instrumentation can result in the detection of adduct and fragment ions that form reproducibly and contain identifiable ions that are difficult to distinguish from metabolic pathway intermediates, which may result in false-positive identification. At concentrations as low as 10 μM, free fatty acids have been found to form homo- and heterodimers in untargeted metabolomics pipelines that resemble the lipid class fatty acid esters of hydroxy fatty acids (FAHFAs), resulting in misidentification. This chapter details a protocol for LC-MS-based untargeted metabolomics using hydrophilic interaction chromatography (HILIC) that specifically aids in distinguishing artifactual fatty acid dimers from endogenous FAHFAs.