Mass spectrometry data repository enhances novel metabolite discoveries with advances in computational metabolomics

Hiroshi Tsugawa, Aya Satoh, Haruki Uchino, Tomas Cajka, Makoto Arita, Masanori Arita

Research output: Contribution to journalArticle

Abstract

Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine algal species, resulting in the annotation of 1437 lipids achieving a 40% increase in annotation compared to the previous results. Specifically, diacylglyceryl-carboxyhydroxy-methylcholine (DGCC) in Pavlova lutheri and Pleurochrysis carterae, glucuronosyldiacylglycerol (GlcADG) in Euglena gracilis, and P. carterae, phosphatidylmethanol (PMeOH) in E. gracilis, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in Chlorella variabilis were newly characterized with the enriched lipid spectral databases. Moreover, we integrated the data from untargeted and targeted analyses from data independent tandem mass spectrometry (DIA-MS/MS) acquisition, specifically the sequential window acquisition of all theoretical fragment-ion MS/MS (SWATH-MS/MS) spectra, to increase the lipidomic annotation coverage. After the creation of a global library of precursor and diagnostic ions of lipids by the MS-DIAL untargeted analysis, the co-eluted DIA-MS/MS spectra were resolved in MRMPROBS targeted analysis by tracing the specific product ions involved in acyl chain compositions. Our results indicated that the metabolite quantifications based on DIA-MS/MS chromatograms were somewhat inferior to the MS1-centric quantifications, while the annotation coverage outperformed those of the untargeted analysis of the data dependent and DIA-MS/MS data. Consequently, integrated analyses of untargeted and targeted approaches are necessary to extract the maximum amount of metabolome information, and our results showcase the value of data repositories for the discovery of novel insights in lipid biology.

Original languageEnglish
Article number119
JournalMetabolites
Volume9
Issue number6
DOIs
Publication statusPublished - 2019 Jan 1

Fingerprint

Metabolomics
Metabolites
Mass spectrometry
Mass Spectrometry
Haptophyta
Euglena gracilis
Lipids
Ions
Chlorella
Phosphatidylglycerols
Metabolome
Tandem Mass Spectrometry
Phosphatidylinositols
Phosphatidylcholines
Transparency
Libraries
Phospholipids
Databases
Chemical analysis

Keywords

  • Computational metabolomics
  • Data processing
  • Data repository
  • Lipidomics
  • Reanalysis

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Molecular Biology

Cite this

Mass spectrometry data repository enhances novel metabolite discoveries with advances in computational metabolomics. / Tsugawa, Hiroshi; Satoh, Aya; Uchino, Haruki; Cajka, Tomas; Arita, Makoto; Arita, Masanori.

In: Metabolites, Vol. 9, No. 6, 119, 01.01.2019.

Research output: Contribution to journalArticle

Tsugawa, Hiroshi ; Satoh, Aya ; Uchino, Haruki ; Cajka, Tomas ; Arita, Makoto ; Arita, Masanori. / Mass spectrometry data repository enhances novel metabolite discoveries with advances in computational metabolomics. In: Metabolites. 2019 ; Vol. 9, No. 6.
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