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

Huber, Florian ; Ridder, Lars ; Verhoeven, Stefan ; Spaaks, Jurriaan H ; Diblen, Faruk ; Rogers, Simon ; van der Hooft, Justin J J Jensen, Lars Juhl

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008724-e1008724 [Periódico revisado por pares]

United States: Public Library of Science

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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
Autor: Huber, Florian ; Ridder, Lars ; Verhoeven, Stefan ; Spaaks, Jurriaan H ; Diblen, Faruk ; Rogers, Simon ; van der Hooft, Justin J J
Jensen, Lars Juhl
Assuntos: Algorithms ; Annotations ; Biology and Life Sciences ; Computer and Information Sciences ; Datasets ; Ionization ; Machine learning ; Mass spectra ; Mass spectrometry ; Natural language processing ; Physical Sciences ; Research and Analysis Methods ; Scientific imaging ; Similarity
É parte de: PLoS computational biology, 2021-02, Vol.17 (2), p.e1008724-e1008724
Notas: new_version
ObjectType-Article-1
SourceType-Scholarly Journals-1
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The authors have declared that no competing interests exist.
Descrição: 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 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.
Editor: United States: Public Library of Science
Idioma: Inglês

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

Huber, Florian ; Ridder, Lars ; Verhoeven, Stefan ; Spaaks, Jurriaan H ; Diblen, Faruk ; Rogers, Simon ; van der Hooft, Justin J J Jensen, Lars Juhl

United States: Public Library of Science

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