In silico optimization of mass spectrometry fragmentation strategies in metabolomics

Joe Wandy, Vinny Davies, Justin J.J. Van Der Hooft, Stefan Weidt, R. Daly, Simon Rogers*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Abstract

Liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) is widely used in identifying small molecules in untargeted metabolomics. Various strategies exist to acquire MS/MS fragmentation spectra; however, the development of new acquisition strategies is hampered by the lack of simulators that let researchers prototype, compare, and optimize strategies before validations on real machines. We introduce Virtual Metabolomics Mass Spectrometer (ViMMS), a metabolomics LC-MS/MS simulator framework that allows for scan-level control of the MS2 acquisition process in silico. ViMMS can generate new LC-MS/MS data based on empirical data or virtually re-run a previous LC-MS/MS analysis using pre-existing data to allow the testing of different fragmentation strategies. To demonstrate its utility, we show how ViMMS can be used to optimize N for Top-N data-dependent acquisition (DDA) acquisition, giving results comparable to modifying N on the mass spectrometer. We expect that ViMMS will save method development time by allowing for offline evaluation of novel fragmentation strategies and optimization of the fragmentation strategy for a particular experiment.

Original languageEnglish
Article number219
JournalMetabolites
Volume9
Issue number10
DOIs
Publication statusPublished - 1 Oct 2019

Keywords

  • Data-dependent acquisition (DDA)
  • Fragmentation (MS/MS)
  • In silico
  • Liquid chromatography–mass spectrometry (LC/MS)
  • Simulator

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