A lipidome atlas in MS-DIAL 4

Hiroshi Tsugawa^{1

2}, Kazutaka Ikeda^{3

4}, Mikiko Takahashi⁵, Aya Satoh⁵, Yoshifumi Mori⁶, Haruki Uchino^{3

7}, Nobuyuki Okahashi^{3

8}, Yutaka Yamada⁵, Ipputa Tada⁹, Paolo Bonini¹⁰, Yasuhiro Higashi⁵, Yozo Okazaki^{5

11}, Zhiwei Zhou^{12

13}, Zheng-Jiang Zhu¹², Jeremy Koelmel^{14

15}, Tomas Cajka¹⁶, Oliver Fiehn¹⁷, Kazuki Saito^{5

18}, Masanori Arita^{5

19}, Makoto Arita^{20

21

22}

Affiliations

¹ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. hiroshi.tsugawa@riken.jp.
² RIKEN Center for Sustainable Resource Science, Yokohama, Japan. hiroshi.tsugawa@riken.jp.
³ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
⁴ Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan.
⁵ RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
⁶ Bruker, Yokohama, Japan.
⁷ Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan.
⁸ Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
⁹ Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Miura, Japan.
¹⁰ NGAlab, Tarragona, Spain.
¹¹ Graduate School of Bioresources, Mie University, Tsu, Japan.
¹² Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
¹³ University of Chinese Academy of Sciences, Beijing, China.
¹⁴ Department of Pathology, University of Florida, Gainsville, FL, USA.
¹⁵ Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA.
¹⁶ Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
¹⁷ West Coast Metabolomics Center, UC Davis, Davis, CA, USA.
¹⁸ Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
¹⁹ National Institute of Genetics, Mishima, Japan.
²⁰ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. makoto.arita@riken.jp.
²¹ Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan. makoto.arita@riken.jp.
²² Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan. makoto.arita@riken.jp.

PMID: 32541957
DOI: 10.1038/s41587-020-0531-2

A lipidome atlas in MS-DIAL 4

Hiroshi Tsugawa et al. Nat Biotechnol. 2020 Oct.

. 2020 Oct;38(10):1159-1163.

doi: 10.1038/s41587-020-0531-2. Epub 2020 Jun 15.

Authors

Affiliations

¹ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. hiroshi.tsugawa@riken.jp.
² RIKEN Center for Sustainable Resource Science, Yokohama, Japan. hiroshi.tsugawa@riken.jp.
³ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
⁴ Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan.
⁵ RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
⁶ Bruker, Yokohama, Japan.
⁷ Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan.
⁸ Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
⁹ Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Miura, Japan.
¹⁰ NGAlab, Tarragona, Spain.
¹¹ Graduate School of Bioresources, Mie University, Tsu, Japan.
¹² Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
¹³ University of Chinese Academy of Sciences, Beijing, China.
¹⁴ Department of Pathology, University of Florida, Gainsville, FL, USA.
¹⁵ Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA.
¹⁶ Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
¹⁷ West Coast Metabolomics Center, UC Davis, Davis, CA, USA.
¹⁸ Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
¹⁹ National Institute of Genetics, Mishima, Japan.
²⁰ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. makoto.arita@riken.jp.
²¹ Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan. makoto.arita@riken.jp.
²² Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan. makoto.arita@riken.jp.

PMID: 32541957
DOI: 10.1038/s41587-020-0531-2

Abstract

We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.

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References

1. Harayama, T. & Riezman, H. Nat. Rev. Mol. Cell Biol. 19, 281–296 (2018). - PubMed
1. Kind, T. et al. Mass Spectrom. Rev. 37, 513–532 (2018). - PubMed
1. Tsugawa, H., Ikeda, K. & Arita, M. Biochim. Biophys. Acta Mol. Cell. Biol. Lipids 1862, 762–765 (2017). - PubMed
1. Liebisch, G. et al. Nat. Metab. 1, 745–747 (2019).
1. Hoffmann, N. et al. Anal. Chem. 91, 3302–3310 (2019). - PubMed - PMC

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A lipidome atlas in MS-DIAL 4

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A lipidome atlas in MS-DIAL 4

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