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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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 algorithm—Word2Vec. Spec2Vec learns frag-mental 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.

Original languageEnglish
Article numbere1008724
JournalPLoS Computational Biology
Issue number2
Publication statusPublished - 16 Feb 2021

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