Cited by 82Metabolomics and Mass Spectrometry StudiesSphingolipid Metabolism and SignalingMass Spectrometry Techniques and Applications

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

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Tsugawa, Hiroshi, Ikeda, Kazutaka, Tanaka, Wataru, Senoo, Yuya, Arita, Makoto, Arita, Masanori·2017·Journal of Cheminformatics

Abstract

BACKGROUND: , 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/).

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Crossref · 10.1186/s13321-017-0205-3

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  • The peak detected at 12.86 min in mouse epidermis was C26:0 BS.

    “The fragmentation pattern of this peak is consistent with that of C26:0 BS in previous reports (12,42), demonstrating that the peak detected at 12.86 min was C26:0 BS.”

    From Comparative profiling and comprehensive quantification of stratum corneum ceramides in humans and mice by LC/MS/MS (2020) · cites this paper as [12]

    The Results and discussion section, under “Annotation of β-hydroxy ceramide,” identifies an experimental MS/MS spectrum as Ceramide [BS] (d18:1/26:0) and reports Ceramide [BS] in murine ear tissue. It does not identify a peak at 12.86 min or report that measurement in mouse epidermis, so those specifics are not supported by this source. (LLM, conf=0.85)

    Experimental — accuracy not yet measured
  • The fragmentation pattern of the peak at 12.86 min is consistent with that of C26:0 BS in previous reports.

    “The fragmentation pattern of this peak is consistent with that of C26:0 BS in previous reports (12,42), demonstrating that the peak detected at 12.86 min was C26:0 BS.”

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Research works printed but not linked: 1

  1. [24]Yokomizo T Murakami M Bioactive lipid mediators: current reviews and protocols 2015 Berlin Springer

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Authors
Tsugawa, H., Ikeda, K., Tanaka, W., Senoo, Y., Arita, M., & Arita, M.
Affiliations
  • RIKEN Center for Sustainable Resource Science (JP)
  • Japan Agency for Medical Research and Development (JP)
  • The Graduate University for Advanced Studies, SOKENDAI (JP)
  • RIKEN Center for Integrative Medical Sciences (JP)
  • National Institute of Genetics (JP)
Corresponding author
  • Arita, Makoto
  • Arita, Masanori
Venue
Journal of Cheminformatics
Published
2017-03-15
Volume
9
Issue
1
Pages
19-19
ISSN
1758-2946 (ISSN-L)
OpenAlex
W2597634187
Cited by
82
References
25
Citations by year
2026: 9 · 2025: 9 · 2024: 6 · 2023: 8 · 2022: 11 · 2021: 8 · 2020: 9 · 2019: 13 · 2018: 6 · 2017: 3
FWCI
3.46
Type
journal article
Language
en
Open access
Locations
  • Journal of Cheminformatics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Bioscience Database Center
  • Grant-in-Aid for Scientific Research on Innovative Areas (15H05897, 15H05898)
  • JST-CREST
  • Grant-in-aid for scientific research (15K01812, 15H04648)
  • Japan Agency for Medical Research and Development (PRIME)
  • Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Sphingolipid Metabolism and Signaling
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
sphingolipids, glycerolipids, MS-DIAL, untargeted metabolomics, lipid identification, human and mouse tissues

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