TY - JOUR A1 - Huber, Florian A1 - Ridder, Lars A1 - Verhoeven, Stefan A1 - Spaaks, Jurriaan H. A1 - Diblen, Faruk A1 - Rogers, Simon A1 - van der Hooft, Justin J. J. T1 - Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships JF - PLOS Computational Biology N2 - 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. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34687 UR - http://www.ncbi.nlm.nih.gov/pubmed/33591968 SN - 1553-7358 N1 - Data Availability Statement: The pre-processed, cleaned dataset with all positive ionization mode spectra can be downloaded from https://doi.org/10.5281/zenodo.3978118, the original raw data can be accessed from https://doi.org/10.5281/zenodo.3979010. Funding: J.J.J.v.d.H. acknowledges funding from an ASDI eScience grant, ASDI.2017.030, from the Netherlands eScience Center—NLeSC, www.esciencecenter.nl, The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. VL - 17 IS - 2 PB - Cold Spring Harbor Laboratory ER - TY - JOUR A1 - Huber, Florian A1 - Verhoeven, Stefan A1 - Meijer, Christiaan A1 - Spreeuw, Hanno A1 - Castilla, Efraín A1 - Geng, Cunliang A1 - van der Hooft, Justin J. J. A1 - Rogers, Simon A1 - Belloum, Adam A1 - Diblen, Faruk A1 - Spaaks, Jurriaan H. T1 - matchms - processing and similarity evaluation of mass spectrometry data JF - Journal of Open Source Software KW - DOAJ Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34856 SN - 2475-9066 VL - 5 IS - 52 PB - Cold Spring Harbor Laboratory ER -