-
Je něco špatně v tomto záznamu ?
MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities
H. Takeda, Y. Matsuzawa, M. Takeuchi, M. Takahashi, K. Nishida, T. Harayama, Y. Todoroki, K. Shimizu, N. Sakamoto, T. Oka, M. Maekawa, MH. Chung, Y. Kurizaki, S. Kiuchi, K. Tokiyoshi, B. Buyantogtokh, M. Kurata, A. Kvasnička, U. Takeda, H....
Jazyk angličtina Země Anglie, Velká Británie
Typ dokumentu časopisecké články
Grantová podpora
21K18216, 24K02011, 24H00043, 24H00392, 24K21269
MEXT | Japan Society for the Promotion of Science (JSPS)
21wm0325036h0001, JP15dm0207001
Japan Agency for Medical Research and Development (AMED)
JPMJER2101
MEXT | JST | Exploratory Research for Advanced Technology (ERATO)
JPMJND2305
MEXT | JST | National Bioscience Database Center (NBDC)
NLK
Directory of Open Access Journals
od 2015
Free Medical Journals
od 2010
Nature Open Access
od 2010-12-01
PubMed Central
od 2012
Europe PubMed Central
od 2012
ProQuest Central
od 2010-01-01
Open Access Digital Library
od 2015-01-01
Open Access Digital Library
od 2015-01-01
Medline Complete (EBSCOhost)
od 2012-11-01
Health & Medicine (ProQuest)
od 2010-01-01
ROAD: Directory of Open Access Scholarly Resources
od 2010
Springer Nature OA/Free Journals
od 2010-12-01
- MeSH
- data mining * metody MeSH
- fosfatidylcholiny metabolismus chemie MeSH
- HeLa buňky MeSH
- hmotnostní spektrometrie metody MeSH
- lidé MeSH
- lipidomika * metody MeSH
- lipidy chemie analýza MeSH
- metabolomika metody MeSH
- nenasycené mastné kyseliny metabolismus chemie MeSH
- software MeSH
- tandemová hmotnostní spektrometrie metody MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
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.
Department of Medical Biochemistry Oslo University Hospital Sognsvannsveien 20 0372 Oslo Norway
Graduate School of Medical Life Science Yokohama City University Yokohama Japan
Graduate School of Pharmaceutical Sciences Keio University Minato ku Tokyo 105 8512 Japan
Innovative Technology Laboratories AGC Inc 1 1 Suehiro cho Tsurumi ku Yokohama 230 0045 Japan
K K ABSciex Japan Shinagawa Tokyo 140 0001 Japan
RIKEN Center for Brain Science 2 1 Hirosawa Wako Saitama 351 0106 Japan
Shimadzu Corporation 1 Nishinokyo Kuwabara cho Nakagyo ku Kyoto 604 8511 Japan
Citace poskytuje Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc25003369
- 003
- CZ-PrNML
- 005
- 20250206104311.0
- 007
- ta
- 008
- 250121s2024 enk f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1038/s41467-024-54137-w $2 doi
- 035 __
- $a (PubMed)39609386
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a enk
- 100 1_
- $a Takeda, Hiroaki $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $u RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0106, Japan $1 https://orcid.org/0000000292994748
- 245 10
- $a MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities / $c H. Takeda, Y. Matsuzawa, M. Takeuchi, M. Takahashi, K. Nishida, T. Harayama, Y. Todoroki, K. Shimizu, N. Sakamoto, T. Oka, M. Maekawa, MH. Chung, Y. Kurizaki, S. Kiuchi, K. Tokiyoshi, B. Buyantogtokh, M. Kurata, A. Kvasnička, U. Takeda, H. Uchino, M. Hasegawa, J. Miyamoto, K. Tanabe, S. Takeda, T. Mori, R. Kumakubo, T. Tanaka, T. Yoshino, M. Okamoto, H. Takahashi, M. Arita, H. Tsugawa
- 520 9_
- $a 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.
- 650 12
- $a lipidomika $x metody $7 D000081362
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a HeLa buňky $7 D006367
- 650 12
- $a data mining $x metody $7 D057225
- 650 _2
- $a zvířata $7 D000818
- 650 _2
- $a software $7 D012984
- 650 _2
- $a metabolomika $x metody $7 D055432
- 650 _2
- $a tandemová hmotnostní spektrometrie $x metody $7 D053719
- 650 _2
- $a lipidy $x chemie $x analýza $7 D008055
- 650 _2
- $a fosfatidylcholiny $x metabolismus $x chemie $7 D010713
- 650 _2
- $a nenasycené mastné kyseliny $x metabolismus $x chemie $7 D005231
- 650 _2
- $a hmotnostní spektrometrie $x metody $7 D013058
- 655 _2
- $a časopisecké články $7 D016428
- 700 1_
- $a Matsuzawa, Yuki $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Takeuchi, Manami $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Takahashi, Mikiko $u RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan $1 https://orcid.org/0000000245292284
- 700 1_
- $a Nishida, Kozo $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Harayama, Takeshi $u Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur - CNRS UMR7275 - Inserm U1323, 660 Route des Lucioles, 06560, Valbonne, France. harayama@ipmc.cnrs.fr $u Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan. harayama@ipmc.cnrs.fr $1 https://orcid.org/0000000322554197
- 700 1_
- $a Todoroki, Yoshimasa $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Shimizu, Kuniyoshi $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $1 https://orcid.org/0009000072157742
- 700 1_
- $a Sakamoto, Nami $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $1 https://orcid.org/0009000619986561
- 700 1_
- $a Oka, Takaki $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Maekawa, Masashi $u Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, 105-8512, Japan $1 https://orcid.org/0000000295741906
- 700 1_
- $a Chung, Mi Hwa $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Kurizaki, Yuto $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Kiuchi, Saki $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Tokiyoshi, Kanako $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $1 https://orcid.org/0009000824459402
- 700 1_
- $a Buyantogtokh, Bujinlkham $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Kurata, Misaki $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Kvasnička, Aleš $u Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 3, 779 00, Olomouc, Czech Republic $u Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Zdravotníků 248/7, 779 00, Olomouc, Czech Republic $u Department of Medical Biochemistry, Oslo University Hospital, Sognsvannsveien 20, 0372, Oslo, Norway $1 https://orcid.org/000000015973316X
- 700 1_
- $a Takeda, Ushio $u K.K. ABSciex Japan, Shinagawa, Tokyo, 140-0001, Japan
- 700 1_
- $a Uchino, Haruki $u Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, 105-8512, Japan $u RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan $1 https://orcid.org/0000000312045436
- 700 1_
- $a Hasegawa, Mayu $u Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- 700 1_
- $a Miyamoto, Junki $u Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan $1 https://orcid.org/0000000269941787
- 700 1_
- $a Tanabe, Kana $u Innovative Technology Laboratories, AGC Inc., 1-1 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- 700 1_
- $a Takeda, Shigenori $u Innovative Technology Laboratories, AGC Inc., 1-1 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan $1 https://orcid.org/0009000616759427
- 700 1_
- $a Mori, Tetsuya $u RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- 700 1_
- $a Kumakubo, Ryota $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
- 700 1_
- $a Tanaka, Tsuyoshi $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $1 https://orcid.org/0000000326012256
- 700 1_
- $a Yoshino, Tomoko $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan $1 https://orcid.org/0000000245052774
- 700 1_
- $a Okamoto, Mami $u Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
- 700 1_
- $a Takahashi, Hidenori $u Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan $1 https://orcid.org/0000000168871724
- 700 1_
- $a Arita, Makoto $u Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, 105-8512, Japan. marita@keio.jp $u RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. marita@keio.jp $u Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan. marita@keio.jp $1 https://orcid.org/0000000199020463
- 700 1_
- $a Tsugawa, Hiroshi $u Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan. htsugawa@go.tuat.ac.jp $u RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. htsugawa@go.tuat.ac.jp $u Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan. htsugawa@go.tuat.ac.jp $u RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. htsugawa@go.tuat.ac.jp $u Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan. htsugawa@go.tuat.ac.jp $1 https://orcid.org/0000000220153958
- 773 0_
- $w MED00184850 $t Nature communications $x 2041-1723 $g Roč. 15, č. 1 (2024), s. 9903
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/39609386 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y - $z 0
- 990 __
- $a 20250121 $b ABA008
- 991 __
- $a 20250206104306 $b ABA008
- 999 __
- $a ok $b bmc $g 2263257 $s 1239376
- BAS __
- $a 3
- BAS __
- $a PreBMC-MEDLINE
- BMC __
- $a 2024 $b 15 $c 1 $d 9903 $e 20241128 $i 2041-1723 $m Nature communications $n Nat Commun $x MED00184850
- GRA __
- $a 21K18216, 24K02011, 24H00043, 24H00392, 24K21269 $p MEXT | Japan Society for the Promotion of Science (JSPS)
- GRA __
- $a 21wm0325036h0001, JP15dm0207001 $p Japan Agency for Medical Research and Development (AMED)
- GRA __
- $a JPMJER2101 $p MEXT | JST | Exploratory Research for Advanced Technology (ERATO)
- GRA __
- $a JPMJND2305 $p MEXT | JST | National Bioscience Database Center (NBDC)
- LZP __
- $a Pubmed-20250121
