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.

Cellular and Molecular Epigenetics Laboratory Graduate School of Medical Life Science Yokohama City University Tsurumi Yokohama 230 0045 Japan

Department of Metabolomics Institute of Physiology of the Czech Academy of Sciences Videnska 1083 14220 Prague Czech Republic

Department of Translational Metabolism Institute of Physiology of the Czech Academy of Sciences Videnska 1083 14220 Prague Czech Republic

Division of Physiological Chemistry and Metabolism Graduate School of Pharmaceutical Sciences Keio University Minato ku Tokyo 105 8512 Japan

Laboratory for metabolomics RIKEN Center for Integrative Medical Sciences Yokohama 230 0045 Japan

Metabolome informatics research team RIKEN Center for Sustainable Resource Science Yokohama 230 0045 Japan

National Institute of Genetics Mishima 411 8540 Japan

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Guiding the choice of informatics software and tools for lipidomics research applications