A mass spectrum is like a fingerprint for a molecule. It can be used to identify toxins, explosives, drugs, and more in urine, blood, and food. Organisms are made up of a mind-boggling number of different molecules. When screening a fluid for various molecules, you often need to perform up to 10^12 parallel comparisons.

I ported the comparison algorithm (a modified cosine similarity) to run on a GPU. On one of the latest GPUs, the H100, SimMS achieves a 1700x speedup compared to MatchMS.