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 journalArticle

12 Citations (Scopus)

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/ ).

Original languageEnglish
Article number19
JournalJournal of Cheminformatics
Volume9
Issue number1
DOIs
Publication statusPublished - 2017 Mar 15

Fingerprint

Sphingolipids
Ceramides
Tissue
computer programs
mice
differential absorption lidar
Electrospray ionization
Liquid chromatography
Fatty acids
Liver
Lipids
Mass spectrometry
Websites
Negative ions
Cells
annotations
websites
Molecules
liquid chromatography
Ions

Keywords

  • 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

Cite this

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. / Tsugawa, Hiroshi; Ikeda, Kazutaka; Tanaka, Wataru; Senoo, Yuya; Arita, Makoto; Arita, Masanori.

In: Journal of Cheminformatics, Vol. 9, No. 1, 19, 15.03.2017.

Research output: Contribution to journalArticle

Tsugawa, Hiroshi ; Ikeda, Kazutaka ; Tanaka, Wataru ; Senoo, Yuya ; Arita, Makoto ; Arita, Masanori. / Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. In: Journal of Cheminformatics. 2017 ; Vol. 9, No. 1.
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