Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library
Open accessAbstract
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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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 measuredThe 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.”
From Comparative profiling and comprehensive quantification of stratum corneum ceramides in humans and mice by LC/MS/MS (2020) · cites this paper as [12]
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Self-citation
- 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)
- PMC
- PMC5352698
- 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
- gold
- doi.org
- 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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