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Updated: May 27, 2025

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
Published on: January 20, 2022
SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry
Tornike Onoprishvili1, Jui-Hung Yuan2, Kamen Petrov2
1Independent Consultant.
Motivation:
Untargeted metabolomics involves a large-scale comparison of the fragmentation pattern of a mass spectrum against a database containing known spectra. Given the number of comparisons involved, this step can be time-consuming.
Results:
In this work, we present a GPU-accelerated cosine similarity implementation for Tandem Mass Spectrometry (MS), with an approximately 1000-fold speedup compared to the MatchMS reference implementation, without any loss of accuracy. This improvement enables repository-scale spectral library matching for compound identification without the need for large compute clusters. This impact extends to any spectral comparison-based methods such as molecular networking approaches and analogue search.
Availability And Implementation:
All code, results, and notebooks supporting are freely available under the MIT license at https://github.com/pangeAI/simms/.
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