Development and dissemination of theoretical mass-spectral libraries

• Project/Area Number: 17H03621
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: System genome science
• Research Institution: National Institute of Genetics
• Principal Investigator: ARITA Masanori 国立遺伝学研究所, 情報研究系, 教授 (10356389)
• Co-Investigator(Kenkyū-buntansha): 田中 謙 立命館大学, 薬学部, 教授 (60418689)
• Project Period (FY): 2017-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000); Fiscal Year 2021: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2019: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2018: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2017: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
• Keywords: マススペクトル / データベース / ライブラリ / メタボロミクス / リピドミクス / リポジトリ / スペクトル / 理論ライブラリ / フラグメンテーション / ソフトウエア / セラミド / 二次代謝物

Outline of Final Research Achievements

For various lipid structures, theoretical libraries were constructed by observing fragmentation patterns for each subclass. Their abbreviated names were consolidated with the international LipidMaps project and typical product ions were identified. As examples, acylated sphingomyelins and beta-hydroxylated ceramides became identifiable.
A method to create a spectral library by choosing highly correlated MS/MS peaks was developed. The method was applied to complex MS/MS spectra of all-ions fragmentation, resulting in clean spectra for small molecules.

Academic Significance and Societal Importance of the Research Achievements

これまでのメタボロミクス、リピドミクスは実測のスペクトルをライブラリとして代謝物の同定を実施してきたが、実測のスペクトルは測定条件等により大きく変化することが知られている。そのためスペクトルから普遍的なプロダクトイオン情報を抜き出してライブラリ化する作業が重要になる。本研究では低分子代謝物と複合脂質についてフラグメンテーションの動向を解析し、理論スペクトルを構築した。フラグメンテーションを知識として表現することでライブラリの多重化を防ぎ、代謝物を同定する作業の標準化に貢献する。

Research Products

• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Int'l Joint Research] University of California, Davis(米国)
• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Journal Article] α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae (2021)
  • Author(s): Nishidono Yuto、Niwa Kotaro、Kitajima Aoi、Watanabe Shiro、Tezuka Yasuhiro、Arita Masanori、Takabayashi Junji、Tanaka Ken
  • Journal Title: Phytochemistry Volume: 188 Pages: 112796-112796
  • DOI: 10.1016/j.phytochem.2021.112796
  • Peer Reviewed
• [Journal Article] A lipidome atlas in MS-DIAL 4 (2020)
  • Author(s): Tsugawa Hiroshi、Ikeda Kazutaka、Takahashi Mikiko、Satoh Aya、Mori Yoshifumi、Uchino Haruki、Okahashi Nobuyuki、Yamada Yutaka、Tada Ipputa、Bonini Paolo、Higashi Yasuhiro、Okazaki Yozo、Zhou Zhiwei、Zhu Zheng-Jiang、Koelmel Jeremy、Cajka Tomas、Fiehn Oliver、Saito Kazuki、Arita Masanori、Arita Makoto
  • Journal Title: Nature Biotechnology Volume: 38 Issue: 10 Pages: 1159-1163
  • DOI: 10.1038/s41587-020-0531-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies (2020)
  • Author(s): Tada Ipputa、Chaleckis Romanas、Tsugawa Hiroshi、Meister Isabel、Zhang Pei、Lazarinis Nikolaos、Dahl?n Barbro、Wheelock Craig E.、Arita Masanori
  • Journal Title: Analytical Chemistry Volume: 92 Issue: 16 Pages: 11310-11317
  • DOI: 10.1021/acs.analchem.0c01980
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Lipidomics needs more standardization (2019)
  • Author(s): Lipidomics Standards Initiative Consortium
  • Journal Title: Nature Metabolism Volume: 1 Issue: 8 Pages: 745-747
  • DOI: 10.1038/s42255-019-0094-z
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics (2019)
  • Author(s): Tada Ipputa、Tsugawa Hiroshi、Meister Isabel、Zhang Pei、Shu Rie、Katsumi Riho、Wheelock Craig E.、Arita Masanori、Chaleckis Romanas
  • Journal Title: Metabolites Volume: 9 Issue: 11 Pages: 251-251
  • DOI: 10.3390/metabo9110251
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics (2019)
  • Author(s): Tsugawa Hiroshi、Satoh Aya、Uchino Haruki、Cajka Tomas、Arita Makoto、Arita Masanori
  • Journal Title: Metabolites Volume: 9 Issue: 6 Pages: 119-119
  • DOI: 10.3390/metabo9060119
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms (2019)
  • Author(s): Tsugawa Hiroshi、Nakabayashi Ryo、Mori Tetsuya、Yamada Yutaka、Takahashi Mikiko、Rai Amit、Sugiyama Ryosuke、Yamamoto Hiroyuki、Nakaya Taiki、Yamazaki Mami、Kooke Rik、Bac-Molenaar Johanna A.、Oztolan-Erol Nihal、Keurentjes Joost J. B.、Arita Masanori、Saito Kazuki
  • Journal Title: Nature Methods Volume: 16 Issue: 4 Pages: 295-298
  • DOI: 10.1038/s41592-019-0358-2
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines (2018)
  • Author(s): Burla Bo、Arita Makoto、Arita Masanori et al.
  • Journal Title: Journal of Lipid Research Volume: 59 Issue: 10 Pages: 2001-2017
  • DOI: 10.1194/jlr.s087163
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. (2017)
  • Author(s): Tsugawa H, Ikeda K, Tanaka W, Senoo Y, Arita M, Arita M.
  • Journal Title: J Cheminform Volume: 9 Issue: 1 Pages: 19-19
  • DOI: 10.1186/s13321-017-0205-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics (2017)
  • Author(s): Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O
  • Journal Title: Nature Methods Volume: 15 Issue: 1 Pages: 53-56
  • DOI: 10.1038/nmeth.4512
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Computational Mass Spectrometry (2017)
  • Author(s): Arita M
  • Organizer: SLING workshop `Mass spectrometry-based lipidomics of human blood plasma'
  • Int'l Joint Research / Invited
• [Presentation] Prediction of Molecular Structures from their Spectra (2017)
  • Author(s): Arita M
  • Organizer: The 4th International Conference on Plant Metabolism (ICPM 2017)
  • Int'l Joint Research / Invited
• [Presentation] Identifying Metabolites with Theoretical References (2017)
  • Author(s): Arita M
  • Organizer: The 26th International KOGO Annual Conference
  • Int'l Joint Research / Invited
• [Remarks]
• [Remarks]