SimMS: A GPU-Accelerated Cosine Similarity implementation for Tandem Mass Spectrometry

Onoprishvili, T.; Yuan, J.-H.; Petrov, K.; Ingalalli, V.; Khederlarian, L.; Leuchtenmuller, N.; Chandra, S.; Duarte, A.; Bender, A.; Gloaguen, Y.

doi:10.1101/2024.07.24.605006

bioRxiv · 10.1101/2024.07.24.605006

SimMS: A GPU-Accelerated Cosine Similarity implementation for Tandem Mass Spectrometry

Onoprishvili, T.·Yuan, J.-H.·Petrov, K.·Ingalalli, V.·Khederlarian, L.·Leuchtenmuller, N.·Chandra, S.·Duarte, A.·Bender, A.·Gloaguen, Y.

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Abstract

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. In this work, we present a GPU-accelerated cosine similarity implementation for Tandem Mass Spectrometry (MS) with approximately 1000-fold speedup compared to the MatchMS reference at a rate of 0.005% incorrect matches and a rate of 0.002% incorrect scores. We describe the underlying reasons for these errors and provide means to avoid them.

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Onoprishvili, T., Yuan, J.-H., Petrov, K., Ingalalli, V., Khederlarian, L., Leuchtenmuller, N., Chandra, S., Duarte, A., Bender, A., Gloaguen, Y.. 2024-07-25. SimMS: A GPU-Accelerated Cosine Similarity implementation for Tandem Mass Spectrometry. https://doi.org/10.1101/2024.07.24.605006

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