Published June 8, 2022 | Version v1
Poster Open

Comparison of spectrum similarity measures for discovery of structurally related molecules

  • 1. University of California San Diego
  • 2. University of Applied Sciences Düsseldorf
  • 3. Wageningen University


The cosine similarity is the most widely used approach to match near-identical tandem mass (MS/MS) spectra with each other. An adaptation thereof, the modified cosine similarity, can be used to discover non-identical but related spectra using analog searching and molecular networking. Recently, neutral loss-based spectrum alignment was introduced as a strategy to match MS/MS spectra of analog molecules.

We have systematically evaluated the performance of neutral loss matching, cosine similarity, and modified cosine similarity on a large collection of spectrum pairs of modified peptides and small molecules to assess how spectral alignment can be used for the discovery of structurally related molecules.


ASMS 2022 - Spectrum similarity comparison.pdf

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