matchms
MA
Python library for fuzzy comparison of mass spectrum data and other Python objects
Updated 6 months ago
60 14
Get started
1287 commits | Last commit ≈ 8 months ago
Ctrl K
spec2vec
spec2vec is a novel similarity measure for comparing mass spectrometry data, which learns peak representations using Word2Vec.
114
mentions
10
contributors
Cite this software
What spec2vec can do for you
- Allows to learn abstract mass spectra representations from large mass spectral data sets (unsupervised learning).
- Computes mass spectra similarities that show a high correlation with actual molecular similarity.
Spec2vec is a novel spectral similarity score inspired by a natural language processing
algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences,
spec2vec does so for mass fragments and neutral losses in MS/MS spectra.
The spectral similarity score is based on spectral embeddings learnt
from the fragmental relationships within a large set of spectral data.
Keywords
Programming languages
License
- Apache-2.0
</>Source code
Participating organisations
Reference papers
Mentions
Build a mass spectrometry analysis pipeline in Python using matchms — part II: Spec2Vec
Author(s): Florian Huber
Published in 2021
Build a mass spectrometry analysis pipeline in Python using matchms — part III: molecular…
Author(s): Florian Huber
Published in 2021
Book section
3- 1.Deep Learning Models for LC-MS Untargeted Metabolomics Data AnalysisAuthor(s): Francesco Russo, Filip Ottosson, Justin J. J. van der Hooft, Madeleine ErnstPublished in Lecture Notes in Computer Science, From Computational Logic to Computational Biology by Springer Nature Switzerland in 2024, page: 128-14410.1007/978-3-031-55248-9_7
- 2.Microbial Metabolites Annotation by Mass Spectrometry-Based MetabolomicsAuthor(s): Paulo Wender P. Gomes, Talita Carla de Tralia Medeiros, Naydja Moralles Maimone, Tiago F. Leão, Luiz Alberto Beraldo de Moraes, Anelize BauermeisterPublished in Advances in Experimental Medicine and Biology, Microbial Natural Products Chemistry by Springer International Publishing in 2023, page: 225-24810.1007/978-3-031-41741-2_9
- 3.Molecular networking in infectious disease modelsAuthor(s): Morgan B. Harris, Mahbobeh Lesani, Zongyuan Liu, Laura-Isobel McCallPublished in Methods in Enzymology, Antimicrobial Peptides by Elsevier in 2022, page: 341-37510.1016/bs.mie.2021.09.018
Computer programs
1Journal articles
75- 1.Tailored Mass Spectral Data Exploration Using the SpecXplore Interactive DashboardAuthor(s): Kevin Mildau, Henry Ehlers, Ian Oesterle, Manuel Pristner, Benedikt Warth, Maria Doppler, Christoph Bueschl, Jürgen Zanghellini, Justin J. J. van der HooftPublished in Analytical Chemistry by American Chemical Society (ACS) in 2024, page: 5798-580610.1021/acs.analchem.3c04444
- 2.The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applicationsAuthor(s): Jefferson Brendon Almeida dos Reis, Adriana Sturion Lorenzi, Danilo Batista Pinho, Patrícia Cardoso Cortelo, Helson Mario Martins do ValePublished in Archives of Microbiology by Springer Science and Business Media LLC in 202410.1007/s00203-024-03911-x
- 3.Chemical Profile of Ocotea delicata (Lauraceae) Using Ultra High-Performance Liquid Chromatography–High-Resolution Mass Spectrometry–Global Natural Products Social Molecular Networking WorkflowAuthor(s): Ananda da Silva Antonio, Gustavo Ramalho Cardoso dos Santos, Henrique Marcelo Gualberto Pereira, Valdir Florêncio da Veiga-Junior, Larissa Silveira Moreira WiedemannPublished in Plants by MDPI AG in 2024, page: 85910.3390/plants13060859
- 4.Generating Molecular Fragmentation Graphs with Autoregressive Neural NetworksAuthor(s): Samuel Goldman, Janet Li, Connor W. ColeyPublished in Analytical Chemistry by American Chemical Society (ACS) in 2024, page: 3419-342810.1021/acs.analchem.3c04654
- 5.IMN4NPD: An Integrated Molecular Networking Workflow for Natural Product DereplicationAuthor(s): Yanghao Sheng, Jue Wang, Shao Liu, Yueping JiangPublished in Analytical Chemistry by American Chemical Society (ACS) in 202410.1021/acs.analchem.3c04746
- 6.IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectraAuthor(s): Sadjad Fakouri Baygi, Dinesh Kumar BarupalPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 202410.1186/s13321-024-00804-5
- 7.A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug DiscoveryAuthor(s): Arnaud Gaudry, Marco Pagni, Florence Mehl, Sébastien Moretti, Luis-Manuel Quiros-Guerrero, Luca Cappelletti, Adriano Rutz, Marcel Kaiser, Laurence Marcourt, Emerson Ferreira Queiroz, Jean-Robert Ioset, Antonio Grondin, Bruno David, Jean-Luc Wolfender, Pierre-Marie AllardPublished in ACS Central Science by American Chemical Society (ACS) in 2024, page: 494-51010.1021/acscentsci.3c00800
- 8.Nontargeted screening method for detection of illicit adulterants in dietary supplements and herbal medicines using UHPLC-QTOF-MS with fine-tuned Spec2Vec-based spectral similarity and chemical classification filterAuthor(s): Yanghao Sheng, Ying Xue, Jue Wang, Shao Liu, Yueping JiangPublished in Journal of Pharmaceutical and Biomedical Analysis by Elsevier BV in 2024, page: 11587710.1016/j.jpba.2023.115877
- 9.Integration of Wnt-inhibitory activity and structural novelty scoring results to uncover novel bioactive natural products: new Bicyclo[3.3.1]non-3-ene-2,9-diones from the leaves of Hymenocardia punctataAuthor(s): Luis-Manuel Quiros-Guerrero, Laurence Marcourt, Nathareen Chaiwangrach, Alexey Koval, Emerson Ferreira Queiroz, Bruno David, Antonio Grondin, Vladimir L. Katanaev, Jean-Luc WolfenderPublished in Frontiers in Chemistry by Frontiers Media SA in 202410.3389/fchem.2024.1371982
- 10.Real-Time Spectral Library Matching for Sample Multiplexed Quantitative ProteomicsAuthor(s): Chris D. McGann, William D. Barshop, Jesse D. Canterbury, Chuwei Lin, Wassim Gabriel, Jingjing Huang, David Bergen, Vlad Zabrouskov, Rafael D. Melani, Mathias Wilhelm, Graeme C. McAlister, Devin K. SchweppePublished in Journal of Proteome Research by American Chemical Society (ACS) in 2023, page: 2836-284610.1021/acs.jproteome.3c00085
- 11.BLINK enables ultrafast tandem mass spectrometry cosine similarity scoringAuthor(s): Thomas V. Harwood, Daniel G. C. Treen, Mingxun Wang, Wibe de Jong, Trent R. Northen, Benjamin P. BowenPublished in Scientific Reports by Springer Science and Business Media LLC in 202310.1038/s41598-023-40496-9
- 12.Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomicsAuthor(s): Yuping Cai, Zhiwei Zhou, Zheng-Jiang ZhuPublished in TrAC Trends in Analytical Chemistry by Elsevier BV in 2023, page: 11690310.1016/j.trac.2022.116903
- 13.Advances in the integration of metabolomics and metagenomics for human gut microbiome and their clinical applicationsAuthor(s): Francesc Puig-Castellví, Romina Pacheco-Tapia, Maxime Deslande, Manyi Jia, Petros Andrikopoulos, Kanta Chechi, Amélie Bonnefond, Philippe Froguel, Marc-Emmanuel DumasPublished in 202310.1016/j.trac.2023.117248
- 14.Segregation of the genus Parahypoxylon (Hypoxylaceae, Xylariales) from Hypoxylon by a polyphasic taxonomic approachAuthor(s): Marjorie Cedeño-Sanchez, Esteban Charria-Girón, Christopher Lambert, J. Jennifer Luangsa-ard, Cony Decock, Raimo Franke, Mark Brönstrup, Marc StadlerPublished in MycoKeys by Pensoft Publishers in 2023, page: 131-16210.3897/mycokeys.95.98125
- 15.Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matchingAuthor(s): Joris J. R. Louwen, Marnix H. Medema, Justin J. J. van der HooftPublished in Microbiome by Springer Science and Business Media LLC in 202310.1186/s40168-022-01444-3
- 16.Ultra-fast and accurate electron ionization mass spectrum matching for compound identification with million-scale in-silico libraryAuthor(s): Qiong Yang, Hongchao Ji, Zhenbo Xu, Yiming Li, Pingshan Wang, Jinyu Sun, Xiaqiong Fan, Hailiang Zhang, Hongmei Lu, Zhimin ZhangPublished in Nature Communications by Springer Science and Business Media LLC in 202310.1038/s41467-023-39279-7
- 17.Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomicsAuthor(s): Wout Bittremieux, Nicole E. Avalon, Sydney P. Thomas, Sarvar A. Kakhkhorov, Alexander A. Aksenov, Paulo Wender P. Gomes, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M. Gauglitz, William H. Gerwick, Tao Huan, Alan K. Jarmusch, Rima F. Kaddurah-Daouk, Kyo Bin Kang, Hyun Woo Kim, Todor Kondić, Helena Mannochio-Russo, Michael J. Meehan, Alexey V. Melnik, Louis-Felix Nothias, Claire O’Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L. Schymanski, Justin J. J. van der Hooft, Kelly C. Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C. DorresteinPublished in Nature Communications by Springer Science and Business Media LLC in 202310.1038/s41467-023-44035-y
- 18.BUDDY: molecular formula discovery via bottom-up MS/MS interrogationAuthor(s): Shipei Xing, Sam Shen, Banghua Xu, Xiaoxiao Li, Tao HuanPublished in Nature Methods by Springer Science and Business Media LLC in 2023, page: 881-89010.1038/s41592-023-01850-x
- 19.The Role of Mass Spectrometry in the Discovery of Antibiotics and Bacterial Resistance Mechanisms: Proteomics and Metabolomics ApproachesAuthor(s): Miguel Cuevas-Cruz, Ulises Hernández-Guzmán, Poulette Carolina Álvarez-Rosales, Meike Schnabel, Saúl Gómez-Manzo, Roberto Arreguín-EspinosaPublished in Current Medicinal Chemistry by Bentham Science Publishers Ltd. in 2023, page: 30-5810.2174/0929867329666220329090822
- 20.Recent advances in mass spectrometry-based computational metabolomicsAuthor(s): Timothy M.D. Ebbels, Justin J.J. van der Hooft, Haley Chatelaine, Corey Broeckling, Nicola Zamboni, Soha Hassoun, Ewy A. MathéPublished in 202310.1016/j.cbpa.2023.102288
- 21.Annotation of natural product compound families using molecular networking topology and structural similarity fingerprintingAuthor(s): Nicholas J. Morehouse, Trevor N. Clark, Emily J. McMann, Jeffrey A. van Santen, F. P. Jake Haeckl, Christopher A. Gray, Roger G. LiningtonPublished in Nature Communications by Springer Science and Business Media LLC in 202310.1038/s41467-022-35734-z
- 22.MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometryAuthor(s): Mahnoor Zulfiqar, Luiz Gadelha, Christoph Steinbeck, Maria Sorokina, Kristian PetersPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 202310.1186/s13321-023-00695-y
- 23.Simulated-to-real benchmarking of acquisition methods in untargeted metabolomicsAuthor(s): Joe Wandy, Ross McBride, Simon Rogers, Nikolaos Terzis, Stefan Weidt, Justin J. J. van der Hooft, Kevin Bryson, Rónán Daly, Vinny DaviesPublished in Frontiers in Molecular Biosciences by Frontiers Media SA in 202310.3389/fmolb.2023.1130781
- 24.A Structure-Guided Molecular Network Strategy for Global Untargeted Metabolomics Data AnnotationAuthor(s): Xinxin Wang, Chao Li, Zaifang Li, Yanpeng Qi, Xiuqiong Zhang, Xinjie Zhao, Chunxia Zhao, Xiaohui Lin, Xin Lu, Guowang XuPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 11603-1161210.1021/acs.analchem.3c00849
- 25.Fast screening and identification of illegal adulteration in dietary supplements and herbal medicines using molecular networking with deep-learning-based similarity algorithmsAuthor(s): Yanghao Sheng, Ying Xue, Jue Wang, Shao Liu, Yueping JiangPublished in Analytical and Bioanalytical Chemistry by Springer Science and Business Media LLC in 2023, page: 3285-329310.1007/s00216-023-04708-5
- 26.Exploring applications of electron ionization mass spectrometry in dense embedding spaceAuthor(s): Zenghui Wang, Qing Xia, Jun ZhangPublished in Chemometrics and Intelligent Laboratory Systems by Elsevier BV in 2023, page: 10484310.1016/j.chemolab.2023.104843
- 27.Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research softwareAuthor(s): Xinsong Du, Farhad Dastmalchi, Hao Ye, Timothy J. Garrett, Matthew A. Diller, Mei Liu, William R. Hogan, Mathias Brochhausen, Dominick J. LemasPublished in Metabolomics by Springer Science and Business Media LLC in 202310.1007/s11306-023-01974-3
- 28.An end-to-end deep learning framework for translating mass spectra to de-novo moleculesAuthor(s): Eleni E. Litsa, Vijil Chenthamarakshan, Payel Das, Lydia E. KavrakiPublished in Communications Chemistry by Springer Science and Business Media LLC in 202310.1038/s42004-023-00932-3
- 29.MS2Query: reliable and scalable MS2 mass spectra-based analogue searchAuthor(s): Niek F. de Jonge, Joris J. R. Louwen, Elena Chekmeneva, Stephane Camuzeaux, Femke J. Vermeir, Robert S. Jansen, Florian Huber, Justin J. J. van der HooftPublished in Nature Communications by Springer Science and Business Media LLC in 202310.1038/s41467-023-37446-4
- 30.Spectral Library Searching Algorithms in MetabolomicsAuthor(s): Hiroshi TsugawaPublished in Journal of the Mass Spectrometry Society of Japan by The Mass Spectrometry Society of Japan in 2023, page: 87-8910.5702/massspec.s23-26
- 31.Contrastive Learning-Based Embedder for the Representation of Tandem Mass SpectraAuthor(s): Hao Guo, Kebing Xue, Haiming Sun, Weihao Jiang, Shiliang PuPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 7888-789610.1021/acs.analchem.3c00260
- 32.Machine learning-assisted structure annotation of natural products based on MS and NMR dataAuthor(s): Guilin Hu, Minghua QiuPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2023, page: 1735-175310.1039/d3np00025g
- 33.Evolutionary metabolomics of specialized metabolism diversification in the genus <i>Nicotiana</i> highlights <i>N-</i> acylnornicotine innovationsAuthor(s): David Elser, David Pflieger, Claire Villette, Baptiste Moegle, Laurence Miesch, Emmanuel GaquerelPublished in Science Advances by American Association for the Advancement of Science (AAAS) in 202310.1126/sciadv.ade8984
- 34.In Search of Disentanglement in Tandem Mass Spectrometry DatasetsAuthor(s): Krzysztof Jan Abram, Douglas McCloskeyPublished in Biomolecules by MDPI AG in 2023, page: 134310.3390/biom13091343
- 35.From structural determination of natural products in complex mixtures to single cell resolution: Perspectives on advances and challenges for mass spectrometryAuthor(s): Norberto Peporine Lopes, Ricardo Roberto da SilvaPublished in Frontiers in Natural Products by Frontiers Media SA in 202310.3389/fntpr.2023.1109557
- 36.Annotating metabolite mass spectra with domain-inspired chemical formula transformersAuthor(s): Samuel Goldman, Jeremy Wohlwend, Martin Stražar, Guy Haroush, Ramnik J. Xavier, Connor W. ColeyPublished in Nature Machine Intelligence by Springer Science and Business Media LLC in 2023, page: 965-97910.1038/s42256-023-00708-3
- 37.Artificial intelligence for natural product drug discoveryAuthor(s): Michael W. Mullowney, Katherine R. Duncan, Somayah S. Elsayed, Neha Garg, Justin J. J. van der Hooft, Nathaniel I. Martin, David Meijer, Barbara R. Terlouw, Friederike Biermann, Kai Blin, Janani Durairaj, Marina Gorostiola González, Eric J. N. Helfrich, Florian Huber, Stefan Leopold-Messer, Kohulan Rajan, Tristan de Rond, Jeffrey A. van Santen, Maria Sorokina, Marcy J. Balunas, Mehdi A. Beniddir, Doris A. van Bergeijk, Laura M. Carroll, Chase M. Clark, Djork-Arné Clevert, Chris A. Dejong, Chao Du, Scarlet Ferrinho, Francesca Grisoni, Albert Hofstetter, Willem Jespers, Olga V. Kalinina, Satria A. Kautsar, Hyunwoo Kim, Tiago F. Leao, Joleen Masschelein, Evan R. Rees, Raphael Reher, Daniel Reker, Philippe Schwaller, Marwin Segler, Michael A. Skinnider, Allison S. Walker, Egon L. Willighagen, Barbara Zdrazil, Nadine Ziemert, Rebecca J. M. Goss, Pierre Guyomard, Andrea Volkamer, William H. Gerwick, Hyun Uk Kim, Rolf Müller, Gilles P. van Wezel, Gerard J. P. van Westen, Anna K. H. Hirsch, Roger G. Linington, Serina L. Robinson, Marnix H. MedemaPublished in Nature Reviews Drug Discovery by Springer Science and Business Media LLC in 2023, page: 895-91610.1038/s41573-023-00774-7
- 38.An <i>In Silico</i> Infrared Spectral Library of Molecular Ions for Metabolite IdentificationAuthor(s): Kas J. Houthuijs, Giel Berden, Udo F. H. Engelke, Vasuk Gautam, David S. Wishart, Ron A. Wevers, Jonathan Martens, Jos OomensPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 8998-900510.1021/acs.analchem.3c01078
- 39.Mining Small Molecules from Teredinibacter turnerae Strains Isolated from Philippine TeredinidaeAuthor(s): Jamaine B. Villacorta, Camille V. Rodriguez, Jacquelyn E. Peran, Jeremiah D. Batucan, Gisela P. Concepcion, Lilibeth A. Salvador-Reyes, Hiyas A. JunioPublished in Metabolites by MDPI AG in 2022, page: 115210.3390/metabo12111152
- 40.MS/MS-Based Molecular Networking: An Efficient Approach for Natural Products DereplicationAuthor(s): Guo-Fei Qin, Xiao Zhang, Feng Zhu, Zong-Qing Huo, Qing-Qiang Yao, Qun Feng, Zhong Liu, Gui-Min Zhang, Jing-Chun Yao, Hong-Bao LiangPublished in Molecules by MDPI AG in 2022, page: 15710.3390/molecules28010157
- 41.NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clustersAuthor(s): Tiago F Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli F Fiore, Justin J J van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C DorresteinPublished in PNAS Nexus by Oxford University Press (OUP) in 202210.1093/pnasnexus/pgac257
- 42.Addressing big data challenges in mass spectrometry-based metabolomicsAuthor(s): Jian Guo, Huaxu Yu, Shipei Xing, Tao HuanPublished in Chemical Communications by Royal Society of Chemistry (RSC) in 2022, page: 9979-999010.1039/d2cc03598g
- 43.Tandem Mass Spectrometry Molecular Networking as a Powerful and Efficient Tool for Drug Metabolism StudiesAuthor(s): Jun Sang Yu, Louis-Félix Nothias, Mingxun Wang, Dong Hyun Kim, Pieter C. Dorrestein, Kyo Bin Kang, Hye Hyun YooPublished in Analytical Chemistry by American Chemical Society (ACS) in 2022, page: 1456-146410.1021/acs.analchem.1c04925
- 44.Raman spectrum matching with contrastive representation learningAuthor(s): Bo Li, Mikkel N. Schmidt, Tommy S. AlstrømPublished in The Analyst by Royal Society of Chemistry (RSC) in 2022, page: 2238-224610.1039/d2an00403h
- 45.Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samplesAuthor(s): Zhitao Tian, Fangzhou Liu, Dongqin Li, Alisdair R. Fernie, Wei ChenPublished in Computational and Structural Biotechnology Journal by Elsevier BV in 2022, page: 5085-509710.1016/j.csbj.2022.09.004
- 46.Alignstein: Optimal transport for improved LC-MS retention time alignmentAuthor(s): Grzegorz Skoraczyński, Anna Gambin, Błażej MiasojedowPublished in GigaScience by Oxford University Press (OUP) in 202210.1093/gigascience/giac101
- 47.Integrative omics approaches for biosynthetic pathway discovery in plantsAuthor(s): Kumar Saurabh Singh, Justin J. J. van der Hooft, Saskia C. M. van Wees, Marnix H. MedemaPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2022, page: 1876-189610.1039/d2np00032f
- 48.Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networkingAuthor(s): Zhiwei Zhou, Mingdu Luo, Haosong Zhang, Yandong Yin, Yuping Cai, Zheng-Jiang ZhuPublished in Nature Communications by Springer Science and Business Media LLC in 202210.1038/s41467-022-34537-6
- 49.Networks and Graphs Discovery in Metabolomics Data Analysis and InterpretationAuthor(s): Adam Amara, Clément Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva María Novoa-del-Toro, Reza M Salek, Liesa Salzer, Sarah Scharfenberg, Michael WittingPublished in Frontiers in Molecular Biosciences by Frontiers Media SA in 202210.3389/fmolb.2022.841373
- 50.What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imagingAuthor(s): Gerard Baquer, Lluc Sementé, Toufik Mahamdi, Xavier Correig, Pere Ràfols, María García‐AltaresPublished in Mass Spectrometry Reviews by Wiley in 2022, page: 1927-196410.1002/mas.21794
Presentations
2Video recordings
2Webpages
2Other
25- 1.Reliable cross-ion mode chemical similarity prediction between MS<sup>2</sup>spectraAuthor(s): Niek de Jonge, David Joas, Lem-Joe Truong, Justin J.J. van der Hooft, Florian HuberPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.03.25.586580
- 2.Mass2SMILES: deep learning based fast prediction of structures and functional groups directly from high-resolution MS/MS spectraAuthor(s): David Elser, Florian Huber, Emmanuel GaquerelPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.07.06.547963
- 3.Deciphering Complex Natural Mixtures through Metabolome Mining of Mass Spectrometry DataAuthor(s): Justin J.J. van der Hooft, Madeleine Ernst, Daniel Papenberg, Kyo Bin Kang, Iris F. Kappers, Marnix H. Medema, Pieter C. Dorrestein, Simon RogersPublished in Recent Advances in Polyphenol Research by Wiley in 2023, page: 139-16810.1002/9781119844792.ch5
- 4.BLINK: Ultrafast tandem mass spectrometry cosine similarity scoringAuthor(s): Thomas Harwood, Daniel G.C. Treen, Mingxun Wang, Wibe de Jong, Trent R. Northen, Benjamin P. BowenPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.02.14.528550
- 5.Mining structural information in gas chromatography-mass spectrometry data for analytical-descriptor-based quantitative structure–activity relationshipAuthor(s): Yasuyuki ZushiPublished by Research Square Platform LLC in 202310.21203/rs.3.rs-2983844/v1
- 6.Anticipating the chemical compositions of organisms across the tree of lifeAuthor(s): Marco VisaniPublished by Pensoft Publishers in 202310.3897/arphapreprints.e116230
- 7.Evolutionary metabolomics of specialized metabolism diversification in the genus<i>Nicotiana</i>highlights allopolyploidy-mediated innovations in<i>N</i>-acylnornicotine metabolismAuthor(s): David Elser, David Pflieger, Claire Villette, Baptiste Moegle, Laurence Miesch, Emmanuel GaquerelPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.09.12.507566
- 8.Molecular formula discovery via bottom-up MS/MS interrogationAuthor(s): Shipei Xing, Sam Shen, Banghua Xu, Tao HuanPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.08.03.502704
- 9.MAW - The Reproducible Metabolome Annotation Workflow for Untargeted Tandem Mass SpectrometryAuthor(s): Mahnoor Zulfiqar, Luiz Gadelha, Christoph Steinbeck, Maria Sorokina, Kristian PetersPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.10.17.512224
- 10.Good Practices and Recommendations for Using and Benchmarking Computational Metabolomics Metabolite Annotation ToolsAuthor(s): Niek F. de Jonge, Kevin Mildau, David Meijer, Joris R. Louwen, Christoph Bueschl, Florian Huber, Justin J.J. van der HooftPublished by Research Square Platform LLC in 202210.21203/rs.3.rs-1662223/v1
- 11.Molecular formula discovery via bottom-up MS/MS interrogationAuthor(s): Tao Huan, Shipei Xing, Sam Shen, Banghua XuPublished by Research Square Platform LLC in 202210.21203/rs.3.rs-1927294/v1
- 12.MS2Query: Reliable and Scalable MS<sup>2</sup> Mass Spectral-based Analogue SearchAuthor(s): Niek F. de Jonge, Joris R. Louwen, Elena Chekmeneva, Stephane Camuzeaux, Femke J. Vermeir, Robert S. Jansen, Florian Huber, Justin J.J. van der HooftPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.07.22.501125
- 13.MS2Prop: A machine learning model that directly predicts chemical properties from mass spectrometry data for novel compoundsAuthor(s): Gennady Voronov, Abe Frandsen, Brian Bargh, David Healey, Rose Lightheart, Tobias Kind, Pieter Dorrestein, Viswa Colluru, Thomas ButlerPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.10.09.511482
- 14.Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related MoleculesAuthor(s): Wout Bittremieux, Robin Schmid, Florian Huber, Justin JJ van der Hooft, Mingxun Wang, Pieter C DorresteinPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.06.01.494370
- 15.Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted MetabolomicsAuthor(s): Wout Bittremieux, Nicole E. Avalon, Sydney P. Thomas, Sarvar A. Kakhkhorov, Alexander A. Aksenov, Paulo Wender P. Gomes, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M. Gauglitz, William H. Gerwick, Tao Huan, Alan K. Jarmusch, Rima F. Kaddurah-Daouk, Kyo Bin Kang, Hyun Woo Kim, Todor Kondić, Helena Mannochio-Russo, Michael J. Meehan, Alexey V. Melnik, Louis-Felix Nothias, Claire O’Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L. Schymanski, Justin J. J. van der Hooft, Kelly C. Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C. DorresteinPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.05.15.490691
- 16.Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networkAuthor(s): Zhiwei Zhou, Mingdu Luo, Haosong Zhang, Yandong Yin, Yuping Cai, Zheng-Jiang ZhuPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.06.02.494523
- 17.MEMO: Mass Spectrometry-based Sample Vectorization to Explore Chemodiverse DatasetsAuthor(s): Arnaud Gaudry, Florian Huber, Louis-Félix Nothias, Sylvian Cretton, Marcel Kaiser, Jean-Luc Wolfender, Pierre-Marie AllardPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.12.24.474089
- 18.Large-scale tandem mass spectrum clustering using fast nearest neighbor searchingAuthor(s): Wout Bittremieux, Kris Laukens, William Stafford Noble, Pieter C. DorresteinPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.02.05.429957
- 19.Bi-modal Variational Autoencoders for Metabolite Identification Using Tandem Mass SpectrometryAuthor(s): Svetlana Kutuzova, Christian Igel, Mads Nielsen, Douglas McCloskeyPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.08.03.454944
- 20.MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisonsAuthor(s): Florian Huber, Sven van der Burg, Justin J.J. van der Hooft, Lars RidderPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.04.18.440324
- 21.NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clustersAuthor(s): Tiago F. Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P. Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T. Aron, Joris J. R. Louwen, Hyun Woo Kim, Raphael Reher, Marli F. Fiore, Justin J.J. van der Hooft, Lena Gerwick, William H. Gerwick, Nuno Bandeira, Pieter C. DorresteinPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.10.05.463235
- 22.Peer Review #2 of "Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize (v0.1)"Published by PeerJ in 202110.7287/peerj.11359v0.1/reviews/2
- 23.SIMILE enables alignment of fragmentation mass spectra with statistical significanceAuthor(s): Daniel G.C. Treen, Trent R. Northen, Benjamin P. BowenPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.02.24.432767
- 24.Peer Review #1 of "Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize (v0.1)"Published by PeerJ in 202110.7287/peerj.11359v0.1/reviews/1
- 25.Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationshipsAuthor(s): Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J.J. van der HooftPublished by Cold Spring Harbor Laboratory in 202010.1101/2020.08.11.245928
Contributors
Contact person
AB
Adam Belloum
Netherlands eScience Center
Christiaan Meijer
Netherlands eScience Center
Cunliang Geng
Netherlands eScience Center
Faruk Diblen
Netherlands eScience Center
Florian Huber
Netherlands eScience Center
HS
Hanno Spreeuw
Netherlands eScience Center
Jurriaan H. Spaaks
Netherlands eScience Center
JvdH
Justin J. J. van der Hooft
Wageningen University & Research
SR
Simon Rogers
University of Glasgow
Stefan Verhoeven
Netherlands eScience Center
Related projects
Integrated omics analysis for small molecule-mediated host-microbiome interactions
Advancing our understanding of molecular mechanisms of health and disease
Updated 17 months ago
Finished