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

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.

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Publication Details

Journal
Nature Communications
Published
2024-11-28
DOI
https://doi.org/10.1038/s41467-024-54137-w
Citations
81
Primary Topic
Metabolomics and Mass Spectrometry Studies
Type
article
Field-Weighted Citation Impact
18.71

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article

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

Junki Miyamoto, Hiroaki Takeda, Mami Okamoto, Nami Sakamoto et al.
81 citations
Nature Communications
Metabolomics and Mass Spectrometry Studies
18.71
article

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

Junki Miyamoto, Hiroaki Takeda, Mami Okamoto, Nami Sakamoto, T. HARAYAMA, Tsuyoshi Tanaka, Kozo Nishida, Ushio Takeda, Hiroshi Tsugawa, Masashi Maekawa, Aleš Kvasnička, Tomoko Yoshino, Haruki Uchino, Makoto Arita, Mayu Hasegawa, Manami Takeuchi, Tetsuya Mori, Ryota Kumakubo, Kanako Tokiyoshi, Saki Kiuchi, Yuto Kurizaki, Bujinlkham Buyantogtokh, Yoshimasa Todoroki, Mi Hwa Chung, Mikiko Takahashi, Hidenori Takahashi, Misaki Kurata, Kana Tanabe, Kuniyoshi Shimizu, Takaki Oka, Yuki Matsuzawa, Shigenori Takeda
article en
81 citations

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.

Nature CommunicationsVol. 15(1)
Oslo University Hospital (NO), Centre National de la Recherche Scientifique (FR), Inserm (FR), Université Côte d'Azur (FR), Keio University (JP), RIKEN Center for Brain Science (JP), Yokohama City University Medical Center (JP), RIKEN Center for Sustainable Resource Science (JP), University Hospital Olomouc (CZ), RIKEN Center for Integrative Medical Sciences (JP), Institut de Pharmacologie Moléculaire et Cellulaire (FR), Palacký University Olomouc (CZ), Shimadzu (Japan) (JP), Yokohama City University (JP), Tokyo University of Agriculture and Technology (JP)
Japan Agency for Medical Research and Development, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Tokyo University of Agriculture, Tokyo University of Agriculture and Technology, Japan Society for the Promotion of Science, National Bioscience Database Center, Exploratory Research for Advanced Technology
Openalex Percentile: Top 0%
Metabolomics and Mass Spectrometry Studies
18.71
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