MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Abstract Lipidomics and metabolomics communities comprise various informatics tools; however, software programs handling multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 for in-depth lipidome stru...

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Main Authors: Hiroaki Takeda, Yuki Matsuzawa, Manami Takeuchi, Mikiko Takahashi, Kozo Nishida, Takeshi Harayama, Yoshimasa Todoroki, Kuniyoshi Shimizu, Nami Sakamoto, Takaki Oka, Masashi Maekawa, Mi Hwa Chung, Yuto Kurizaki, Saki Kiuchi, Kanako Tokiyoshi, Bujinlkham Buyantogtokh, Misaki Kurata, Aleš Kvasnička, Ushio Takeda, Haruki Uchino, Mayu Hasegawa, Junki Miyamoto, Kana Tanabe, Shigenori Takeda, Tetsuya Mori, Ryota Kumakubo, Tsuyoshi Tanaka, Tomoko Yoshino, Mami Okamoto, Hidenori Takahashi, Makoto Arita, Hiroshi Tsugawa
Format: Article
Language:English
Published: Nature Portfolio 2024-11-01
Series:Nature Communications
Online Access:https://doi.org/10.1038/s41467-024-54137-w
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Summary:Abstract Lipidomics and metabolomics communities comprise various informatics tools; however, software programs handling multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 for in-depth lipidome structural elucidation through electron-activated dissociation (EAD)-based tandem MS and determining their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section values. With the optimized EAD settings using 14 eV kinetic energy, the program correctly delineated lipid structures for 96.4% of authentic standards, among which 78.0% had the sn-, OH-, and/or C = C positions correctly assigned at concentrations exceeding 1 μM. We showcased our workflow by annotating the sn- and double-bond positions of eye-specific phosphatidylcholines containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and n-3-VLC-PUFA-supplemented HeLa cells, we identified glycerol 3-phosphate acyltransferase as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn1 position of phospholipids in mammalian cells, which was confirmed using EAD-MS/MS and recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering insights into lipid biology.
ISSN:2041-1723

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