Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics
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 previou...
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doaj-bf58ec54f51d4650b44ab1099333533d2020-11-24T23:55:37ZengMDPI AGMetabolites2218-19892019-06-019611910.3390/metabo9060119metabo9060119Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational MetabolomicsHiroshi Tsugawa0Aya Satoh1Haruki Uchino2Tomas Cajka3Makoto Arita4Masanori Arita5Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, JapanMetabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, JapanLaboratory for metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, JapanDepartment of Metabolomics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech RepublicLaboratory for metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, JapanMetabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, JapanMass 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 <i>Pavlova lutheri</i> and <i>Pleurochrysis carterae</i>, glucuronosyldiacylglycerol (GlcADG) in <i>Euglena gracilis,</i> and <i>P. carterae</i>, phosphatidylmethanol (PMeOH) in <i>E. gracilis</i>, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in <i>Chlorella variabilis</i> 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 MS<sup>1</sup>-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.https://www.mdpi.com/2218-1989/9/6/119data repositorycomputational metabolomicsreanalysislipidomicsdata processing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hiroshi Tsugawa Aya Satoh Haruki Uchino Tomas Cajka Makoto Arita Masanori Arita |
spellingShingle |
Hiroshi Tsugawa Aya Satoh Haruki Uchino Tomas Cajka Makoto Arita Masanori Arita Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics Metabolites data repository computational metabolomics reanalysis lipidomics data processing |
author_facet |
Hiroshi Tsugawa Aya Satoh Haruki Uchino Tomas Cajka Makoto Arita Masanori Arita |
author_sort |
Hiroshi Tsugawa |
title |
Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics |
title_short |
Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics |
title_full |
Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics |
title_fullStr |
Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics |
title_full_unstemmed |
Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics |
title_sort |
mass spectrometry data repository enhances novel metabolite discoveries with advances in computational metabolomics |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2019-06-01 |
description |
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 <i>Pavlova lutheri</i> and <i>Pleurochrysis carterae</i>, glucuronosyldiacylglycerol (GlcADG) in <i>Euglena gracilis,</i> and <i>P. carterae</i>, phosphatidylmethanol (PMeOH) in <i>E. gracilis</i>, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in <i>Chlorella variabilis</i> 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 MS<sup>1</sup>-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. |
topic |
data repository computational metabolomics reanalysis lipidomics data processing |
url |
https://www.mdpi.com/2218-1989/9/6/119 |
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