Virtual Mass Spectrometry
In Liquid Chromatography (LC) tandem Mass Spectrometry (MS/MS), information is collected about small molecules called metabolites with the hope of identifying them in later analyses. These experiments are carried out across the world in variety of different scientific experiments, but often the methods used to collect the data are very limited and can only collect information for about 20-30% of metabolites in a sample. The development of new more complex methods for acquiring data has been limited by the lack of simulators which would allow researchers to develop, test and prototype new methods. ViMMS is a Virtual Metabolomics Mass Spectrometer which allows realistic simulations of LC-MS/MS experiments. The ViMMS framework allows real time control of both the simulated and real mass spectrometer, allowing seamless development and use of new LC-MS/MS acquisition methods. Using ViMMS we have optimised existing experiments and designed new methods which give an almost 100% increase in performance over existing methods. More recently we have developed methods which are able to adapt to similarities and differences between related samples, using statistical methods to correct for changes resulting from machine noise.
Researchers
Publications
- TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments, Bioinformatics, 39(7), (2023).
- Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics, Frontiers in Molecular Biosciences, 10 (2023).
- ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics, Journal of Open Source Software, 7 (71), 3990, (2022).
- Rapid Development of Improved Data-Dependent Acquisition Strategies, Analytical Chemistry, 93 (14), (2021).
- In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics, Metabolites, 9 (10), (2019).