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

Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita, Masanori Arita

Research output: Contribution to journalArticlepeer-review

45 Citations (Scopus)


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 ( ).

Original languageEnglish
Article number19
JournalJournal of Cheminformatics
Issue number1
Publication statusPublished - 2017 Mar 15


  • In silico MS/MS
  • Lipids
  • Mass fragmentation
  • Retention time prediction

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Library and Information Sciences


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