Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H Spaaks, Faruk Diblen, Simon Rogers, Justin J J van der Hooft
2021 PLoS Computational Biology  
Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing
more » ... Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.
doi:10.1371/journal.pcbi.1008724 pmid:33591968 pmcid:PMC7909622 fatcat:4iugdivf3vgi3o6vcjpz5tatca