TY - JOUR A1 - Schorn, Michelle A. A1 - Verhoeven, Stefan A1 - Ridder, Lars A1 - Huber, Florian A1 - Acharya, Deepa D. A1 - Aksenov, Alexander A. A1 - Aleti, Gajender A1 - Moghaddam, Jamshid Amiri A1 - Aron, Allegra T. A1 - Aziz, Saefuddin A1 - Bauermeister, Anelize A1 - Bauman, Katherine D. A1 - Baunach, Martin A1 - Beemelmanns, Christine A1 - Beman, J. Michael A1 - Berlanga-Clavero, María Victoria A1 - Blacutt, Alex A. A1 - Bode, Helge B. A1 - Boullie, Anne A1 - Brejnrod, Asker A1 - Bugni, Tim S. A1 - Calteau, Alexandra A1 - Cao, Liu A1 - Carrión, Víctor J. A1 - Castelo-Branco, Raquel A1 - Chanana, Shaurya A1 - Chase, Alexander B. A1 - Chevrette, Marc G. A1 - Costa-Lotufo, Leticia V. A1 - Crawford, Jason M. A1 - Currie, Cameron R. A1 - Cuypers, Bart A1 - Dang, Tam A1 - de Rond, Tristan A1 - Demko, Alyssa M. A1 - Dittmann, Elke A1 - Du, Chao A1 - Drozd, Christopher A1 - Dujardin, Jean-Claude A1 - Dutton, Rachel J. A1 - Edlund, Anna A1 - Fewer, David P. A1 - Garg, Neha A1 - Gauglitz, Julia M. A1 - Gentry, Emily C. A1 - Gerwick, Lena A1 - Glukhov, Evgenia A1 - Gross, Harald A1 - Gugger, Muriel A1 - Guillén Matus, Dulce G. A1 - Helfrich, Eric J. N. A1 - Hempel, Benjamin-Florian A1 - Hur, Jae-Seoun A1 - Iorio, Marianna A1 - Jensen, Paul R. A1 - Kang, Kyo Bin A1 - Kaysser, Leonard A1 - Kelleher, Neil L. A1 - Kim, Chung Sub A1 - Kim, Ki Hyun A1 - Koester, Irina A1 - König, Gabriele M. A1 - Leao, Tiago A1 - Lee, Seoung Rak A1 - Lee, Yi-Yuan A1 - Li, Xuanji A1 - Little, Jessica C. A1 - Maloney, Katherine N. A1 - Männle, Daniel A1 - Martin H, Christian A1 - McAvoy, Andrew C. A1 - Metcalf, Willam W. A1 - Mohimani, Hosein A1 - Molina-Santiago, Carlos A1 - Moore, Bradley S. A1 - Mullowney, Michael W. A1 - Muskat, Mitchell A1 - Nothias, Louis-Félix A1 - O'Neill, Ellis C. A1 - Parkinson, Elizabeth I. A1 - Petras, Daniel A1 - Piel, Jörn A1 - Pierce, Emily C. A1 - Pires, Karine A1 - Reher, Raphael A1 - Romero, Diego A1 - Roper, M. Caroline A1 - Rust, Michael A1 - Saad, Hamada A1 - Saenz, Carmen A1 - Sanchez, Laura M. A1 - Sørensen, Søren Johannes A1 - Sosio, Margherita A1 - Süssmuth, Roderich D. A1 - Sweeney, Douglas A1 - Tahlan, Kapil A1 - Thomson, Regan J. A1 - Tobias, Nicholas J. A1 - Trindade-Silva, Amaro E. A1 - van Wezel, Gilles P. A1 - Wang, Mingxun A1 - Weldon, Kelly C. A1 - Zhang, Fan A1 - Ziemert, Nadine A1 - Duncan, Katherine R. A1 - Crüsemann, Max A1 - Rogers, Simon A1 - Dorrestein, Pieter C. A1 - Medema, Marnix H. A1 - van der Hooft, Justin J. J. T1 - A community resource for paired genomic and metabolomic data mining JF - Nature Chemical Biology Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34708 UR - http://www.ncbi.nlm.nih.gov/pubmed/33589842 SN - 1552-4469 N1 - Additional information: Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41589-020-00724-z. VL - 17 IS - 4 SP - 363 EP - 368 PB - Nature 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 - 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 -