Publications

The following publications directly describe ViMMS and can be cited to reference the project:

• Wandy, Joe, et al. “In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics.” Metabolites 9.10 (2019): 219.
• Wandy, Joe, et al. “ViMMS 2.0: A Framework to Develop, Test and Optimize Fragmentation Strategies in LC-MS Metabolomics” Journal of Open Source Software 7.71 (2022): 3990.

The following publications have utilised ViMMS to develop or benchmark innovative data acquisition methods:

• Davies, Vinny, et al. “Rapid Development of Improved Data-dependent Acquisition Strategies.” Analytical Chemistry 19.43 (2021): 5676-5683.
• Wandy, Joe, et al. “Simulated-to-real Benchmarking of Acquisition Methods in Untargeted Metabolomics.” Frontiers in Molecular Biosciences 10 (2023): 1130781.
• Ross McBride, et al., TopNEXt: Automatic DDA Exclusion Framework for Multi-sample Mass Spectrometry Experiments, Bioinformatics, Volume 39, Issue 7, July 2023.