Computationally unmasking each fatty acyl C=C position in complex lipids by routine LC-MS/MS lipidomics

Leonida M. Lamp, Gosia M. Murawska, Joseph P. Argus, Aaron M. Armando, Radu A. Talmazan, Marlene Pühringer, Evelyn Rampler, Oswald Quehenberger, Edward A. Dennis () and Jürgen Hartler ()
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Leonida M. Lamp: University of Graz
Gosia M. Murawska: University of California San Diego
Joseph P. Argus: University of California San Diego
Aaron M. Armando: University of California San Diego
Radu A. Talmazan: Université de Lorraine
Marlene Pühringer: University of Vienna
Evelyn Rampler: University of Vienna
Oswald Quehenberger: University of California San Diego
Edward A. Dennis: University of California San Diego
Jürgen Hartler: University of Graz

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Identifying carbon-carbon double bond (C=C) positions in complex lipids is essential for elucidating physiological and pathological processes. Currently, this is impossible in high-throughput analyses of native lipids without specialized instrumentation that compromises ion yields. Here, we demonstrate automated, chain-specific identification of C=C positions in complex lipids based on the retention time derived from routine reverse-phase chromatography tandem mass spectrometry (RPLC-MS/MS). We introduce LC=CL, a computational solution that utilizes a comprehensive database capturing the elution profile of more than 2400 complex lipid species identified in RAW264.7 macrophages, including 1145 newly reported compounds. Using machine learning, LC=CL provides precise and automated C=C position assignments, adaptable to any suitable chromatographic condition. To illustrate the power of LC=CL, we re-evaluated previously published data and discovered new C=C position-dependent specificity of cytosolic phospholipase A2 (cPLA2). Accordingly, C=C position information is now readily accessible for large-scale high-throughput studies with any MS/MS instrumentation and ion activation method.

Date: 2025
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DOI: 10.1038/s41467-025-61911-x

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