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

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 () and Hiroshi Tsugawa ()
Additional contact information
Hiroaki Takeda: 2-24-16 Naka-cho
Yuki Matsuzawa: 2-24-16 Naka-cho
Manami Takeuchi: 2-24-16 Naka-cho
Mikiko Takahashi: Tsurumi-ku
Kozo Nishida: 2-24-16 Naka-cho
Takeshi Harayama: 660 Route des Lucioles
Yoshimasa Todoroki: 2-24-16 Naka-cho
Kuniyoshi Shimizu: 2-24-16 Naka-cho
Nami Sakamoto: 2-24-16 Naka-cho
Takaki Oka: 2-24-16 Naka-cho
Masashi Maekawa: Keio University
Mi Hwa Chung: 2-24-16 Naka-cho
Yuto Kurizaki: 2-24-16 Naka-cho
Saki Kiuchi: 2-24-16 Naka-cho
Kanako Tokiyoshi: 2-24-16 Naka-cho
Bujinlkham Buyantogtokh: 2-24-16 Naka-cho
Misaki Kurata: 2-24-16 Naka-cho
Aleš Kvasnička: Hněvotínská 3
Ushio Takeda: K.K. ABSciex Japan
Haruki Uchino: Keio University
Mayu Hasegawa: 3-5-8 Saiwai-cho
Junki Miyamoto: 3-5-8 Saiwai-cho
Kana Tanabe: 1-1 Suehiro-cho
Shigenori Takeda: 1-1 Suehiro-cho
Tetsuya Mori: Tsurumi-ku
Ryota Kumakubo: 2-24-16 Naka-cho
Tsuyoshi Tanaka: 2-24-16 Naka-cho
Tomoko Yoshino: 2-24-16 Naka-cho
Mami Okamoto: 1 Nishinokyo Kuwabara-cho
Hidenori Takahashi: 1 Nishinokyo Kuwabara-cho
Makoto Arita: Keio University
Hiroshi Tsugawa: 2-24-16 Naka-cho

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-54137-w

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