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Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library.
J Cheminform 2017; 9:19JC

Abstract

BACKGROUND

Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) is used for comprehensive metabolome and lipidome analyses. Compound identification relies on similarity matching of the retention time (RT), precursor m/z, isotopic ratio, and MS/MS spectrum with reference compounds. For sphingolipids, however, little information on the RT and MS/MS references is available.

RESULTS

Negative-ion ESI-MS/MS is a useful method for the structural characterization of sphingolipids. We created theoretical MS/MS spectra for 21 sphingolipid classes in human and mouse (109,448 molecules), with substructure-level annotation of unique fragment ions by MS-FINDER software. The existence of ceramides with β-hydroxy fatty acids was confirmed in mouse tissues based on cheminformatic- and quantum chemical evidences. The RT of sphingo- and glycerolipid species was also predicted for our LC condition. With this information, MS-DIAL software for untargeted metabolome profiling could identify 415 unique structures including 282 glycerolipids and 133 sphingolipids from human cells (HEK and HeLa) and mouse tissues (ear and liver).

CONCLUSIONS

MS-DIAL and MS-FINDER software programs can identify 42 lipid classes (21 sphingo- and 21 glycerolipids) with the in silico RT and MS/MS library. The library is freely available as Microsoft Excel files at the software section of our RIKEN PRIMe website (http://prime.psc.riken.jp/).

Authors+Show Affiliations

RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan.RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan. Japan Agency for Medical Research and Development (AMED-PRIME), 1-7-1 Yomiuri Shimbun Building, Otemachi, Chiyoda-ku, Tokyo, 100-0004 Japan. Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540 Japan.RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan.RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan. Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan. Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512 Japan.RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan. Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540 Japan. National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28316657

Citation

Tsugawa, Hiroshi, et al. "Comprehensive Identification of Sphingolipid Species By in Silico Retention Time and Tandem Mass Spectral Library." Journal of Cheminformatics, vol. 9, 2017, p. 19.
Tsugawa H, Ikeda K, Tanaka W, et al. Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. J Cheminform. 2017;9:19.
Tsugawa, H., Ikeda, K., Tanaka, W., Senoo, Y., Arita, M., & Arita, M. (2017). Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. Journal of Cheminformatics, 9, p. 19. doi:10.1186/s13321-017-0205-3.
Tsugawa H, et al. Comprehensive Identification of Sphingolipid Species By in Silico Retention Time and Tandem Mass Spectral Library. J Cheminform. 2017;9:19. PubMed PMID: 28316657.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. AU - Tsugawa,Hiroshi, AU - Ikeda,Kazutaka, AU - Tanaka,Wataru, AU - Senoo,Yuya, AU - Arita,Makoto, AU - Arita,Masanori, Y1 - 2017/03/15/ PY - 2016/09/21/received PY - 2017/03/06/accepted PY - 2017/3/21/entrez PY - 2017/3/21/pubmed PY - 2017/3/21/medline KW - In silico MS/MS KW - Lipids KW - Mass fragmentation KW - Retention time prediction SP - 19 EP - 19 JF - Journal of cheminformatics JO - J Cheminform VL - 9 N2 - BACKGROUND: Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) is used for comprehensive metabolome and lipidome analyses. Compound identification relies on similarity matching of the retention time (RT), precursor m/z, isotopic ratio, and MS/MS spectrum with reference compounds. For sphingolipids, however, little information on the RT and MS/MS references is available. RESULTS: Negative-ion ESI-MS/MS is a useful method for the structural characterization of sphingolipids. We created theoretical MS/MS spectra for 21 sphingolipid classes in human and mouse (109,448 molecules), with substructure-level annotation of unique fragment ions by MS-FINDER software. The existence of ceramides with β-hydroxy fatty acids was confirmed in mouse tissues based on cheminformatic- and quantum chemical evidences. The RT of sphingo- and glycerolipid species was also predicted for our LC condition. With this information, MS-DIAL software for untargeted metabolome profiling could identify 415 unique structures including 282 glycerolipids and 133 sphingolipids from human cells (HEK and HeLa) and mouse tissues (ear and liver). CONCLUSIONS: MS-DIAL and MS-FINDER software programs can identify 42 lipid classes (21 sphingo- and 21 glycerolipids) with the in silico RT and MS/MS library. The library is freely available as Microsoft Excel files at the software section of our RIKEN PRIMe website (http://prime.psc.riken.jp/). SN - 1758-2946 UR - https://www.unboundmedicine.com/medline/citation/28316657/Comprehensive_identification_of_sphingolipid_species_by_in_silico_retention_time_and_tandem_mass_spectral_library L2 - https://dx.doi.org/10.1186/s13321-017-0205-3 DB - PRIME DP - Unbound Medicine ER -