MetaboAnalyst supports MS/MS pattern matching-based compound identification since version 6.0, introducing two key scores for result evaluation: the matching score and the similarity score. The following provides an explanation of these two scores:
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Similarity Score: MetaboAnalyst employs the dot-product or spectral entropy method for its calculation. This score exclusively reflects the pattern similarity between the query spectrum and the reference spectrum.
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Matching Score: This score offers a comprehensive evaluation, taking into account MS/MS pattern similarity, m/z deviation (calculated by assessing differences between experimental and reference values based on the Gaussian distribution of m/z error), and the ratio of matched fragments.
In summary, while the similarity score concentrates solely on MS/MS pattern comparison, the matching score provides a more thorough evaluation of results by considering additional factors such as m/z deviation and the ratio of matched fragments.